Fraunhofer Research Institution for Marine Biotechnology

Lubeck, Germany

Fraunhofer Research Institution for Marine Biotechnology

Lubeck, Germany
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Wehner S.,Friedrich - Schiller University of Jena | Dorrich A.,Justus Liebig University | Ciba P.,Fraunhofer Research Institution for Marine Biotechnology | Wilde A.,Albert Ludwigs University of Freiburg | Marz M.,Friedrich - Schiller University of Jena
RNA Biology | Year: 2014

Promoter-associated RNAs (pRNAs) are a family of ∼90-100 nt-long divergent RNAs overlapping the promoter of the rRNA (rDNA) operon. pRNA transcripts interact with TIP5, a component of the chromatin remodeling complex NoRC, which recruits enzymes for heterochromatin formation and mediates silencing of rRNA genes. Here we present a comprehensive analysis of pRNA homologs, including different versions per species, as result of in silico studies in available metazoan genome assemblies. Comparative sequence analysis and secondary structure prediction ended up in two possible secondary structures, which let us assume a possible dual function of pRNAs for regulation of rRNA operons. Furthermore, we validated parts of our computational predictions experimentally by RT-PCR and sequencing. A representative seed alignment of the pRNA family, annotated with possible secondary structures was released to the Rfam database. © 2014 Landes Bioscience.

Mehnert J.M.,Fraunhofer Research Institution for Marine Biotechnology | Brandenburger M.,Fraunhofer Research Institution for Marine Biotechnology | Grunow B.,Fraunhofer Research Institution for Marine Biotechnology | Grunow B.,University of Manchester
Cellular Physiology and Biochemistry | Year: 2013

Background/Aims: Safety pharmacology requires novel model systems for the detection of cardiac side effects. Ranging from cell-based systems to model organisms, no model available to date reflects the complexity of the human heart and evokes the great need for improved and more affordable systems. Many drugs interact with hERG potassium channels and consequently cause life threatening ventricular arrhythmias, further highlighting the importance of suitable model systems. Methods: Spontaneously Contracting Cell aggregates (SCC) as a 3D in vitro heart-syncytium obtained from rainbow trout larvae represent a novel model system for cardiac safety pharmacology. SCCs can be harvested cost-effectively and kept in culture for several weeks while retaining their functionality and displaying contraction rates similar to the human heart. Results: Extracellular field potential recordings with multielectrode arrays revealed significant prolongation of field potential duration upon administration of common hERG potassium channel blockers. Infusion of 1 μM Dofetilide and 10 μM Terfenadine prolonged field potentials 10 fold and 2 fold, respectively. In addition, SCCs enabled analysis of autonomous contraction frequencies. Conclusion: Thus, SCCs represent a novel and low-cost cardiac model system of the human heart for application in safety pharmacology. © 2013 S. Karger AG, Basel.

Rakers S.,Fraunhofer Research Institution for Marine Biotechnology | Niklasson L.,Gothenburg University | Steinhagen D.,Leibniz University of Hanover | Kruse C.,Fraunhofer Research Institution for Marine Biotechnology | And 4 more authors.
Journal of Investigative Dermatology | Year: 2013

Mammalian and fish skin share protective activities against environments that are rich in infectious agents. Fish epidermis is endowed with an extrinsic barrier consisting of a mucus layer and antimicrobial peptides (AMPs). These operate together as a protective chemical shield. As these AMPs are evolutionarily well preserved and also found in higher vertebrate skin (including human epidermis), fish skin offers a unique opportunity to study the origins of innate antimicrobial defense systems. Furthermore, the broad spectrum of fish mucus antimicrobial activities renders piscine AMPs interesting to investigative dermatology, as these may become exploitable for various indications in clinical dermatology. Therefore, this article aims at casting light on fish mucus, the evolutionary relationship between human and fish AMPs, and the latter's antibacterial, antifungal, and even antiviral activities. Moreover, we develop dermatological lessons from, and sketch potential future clinical applications of, fish mucus and piscine AMPs. © 2013 The Society for Investigative Dermatology.

Becker T.,Fraunhofer Research Institution for Marine Biotechnology | Becker T.,University of Lübeck | Rapoport D.H.,Fraunhofer Research Institution for Marine Biotechnology | Mamlouk A.M.,University of Lübeck
Proceedings - International Symposium on Biomedical Imaging | Year: 2012

The analysis of time lapse data becomes a more and more important tool in (stem) cell biology, as this method enables a marker free analysis of cell populations over time and allows for the reconstruction of genealogical trees; these information can help to understand the mechanisms behind cell proliferation and differentiation. However, the crucial steps in a cell tracking algorithm (cell segmentation, cell tracking and mitosis detection) have to be performed with a high trustworthiness to find the correct lineage of each cell. Here, we present a novel cell tracking algorithm that combines microscopical images with different contrast mechanisms: first, oblique illumination is used to segment and track cells; second, phase contrast microscopy is used to detect the most critical events, the mitosis. The combination of both detection results in a more robust cell tracking. For evaluation, the free reference data CeTReS is used. © 2012 IEEE.

Ludtke-Buzug K.,University of Lübeck | Rapoport D.H.,Fraunhofer Research Institution for Marine Biotechnology | Schneider D.,Fraunhofer Research Institution for Marine Biotechnology
AIP Conference Proceedings | Year: 2010

Recently, magnetic particle imaging (MPI) has been presented as a new method for the measurement of the spatial distribution of superparamagnetic iron oxide nanoparticles (SPIONs). MPI is based on the nonlinear magnetization response of nanoparticles that are subjected to a sinusoidal magnetic field. Spatial resolution and signal to noise ratio of MPI depend on the particle quality. This is particularly important when stem cells shall be tracked with MPI. Stem cell-based treatment is an upcoming technology in targeted cancer-therapy. In this study, we analyzed the particle quality of newly developed dextran-coated SPIONs - with respect to their response in the imaging experiment - using magnetic particle spectrometry. The uptake of dextran-coated SPIONs into rat and human adult stem cells was monitored via transmission electron microscopy. Furthermore, adult stem cells were incubated with FITC-dextran-coated SPIONs and stained for confocal laser scanning microscopy. The dextran- and FITC-dextran coated SPIONs were localized in the cytoplasm of rat and human adult stem cells. MPI promises real-time imaging with high spatial resolution at high sensitivity. Our data support iron oxide loaded adult stem cells as a powerful tool for targeted cancer therapy. © 2010 American Institute of Physics.

Rapoport D.H.,Fraunhofer Research Institution for Marine Biotechnology | Becker T.,Fraunhofer Research Institution for Marine Biotechnology | Becker T.,University of Lübeck | Mamlouk A.M.,University of Lübeck | And 2 more authors.
PLoS ONE | Year: 2011

Automated microscopy is currently the only method to non-invasively and label-free observe complex multi-cellular processes, such as cell migration, cell cycle, and cell differentiation. Extracting biological information from a time-series of micrographs requires each cell to be recognized and followed through sequential microscopic snapshots. Although recent attempts to automatize this process resulted in ever improving cell detection rates, manual identification of identical cells is still the most reliable technique. However, its tedious and subjective nature prevented tracking from becoming a standardized tool for the investigation of cell cultures. Here, we present a novel method to accomplish automated cell tracking with a reliability comparable to manual tracking. Previously, automated cell tracking could not rival the reliability of manual tracking because, in contrast to the human way of solving this task, none of the algorithms had an independent quality control mechanism; they missed validation. Thus, instead of trying to improve the cell detection or tracking rates, we proceeded from the idea to automatically inspect the tracking results and accept only those of high trustworthiness, while rejecting all other results. This validation algorithm works independently of the quality of cell detection and tracking through a systematic search for tracking errors. It is based only on very general assumptions about the spatiotemporal contiguity of cell paths. While traditional tracking often aims to yield genealogic information about single cells, the natural outcome of a validated cell tracking algorithm turns out to be a set of complete, but often unconnected cell paths, i.e. records of cells from mitosis to mitosis. This is a consequence of the fact that the validation algorithm takes complete paths as the unit of rejection/acceptance. The resulting set of complete paths can be used to automatically extract important biological parameters with high reliability and statistical significance. These include the distribution of life/cycle times and cell areas, as well as of the symmetry of cell divisions and motion analyses. The new algorithm thus allows for the quantification and parameterization of cell culture with unprecedented accuracy. To evaluate our validation algorithm, two large reference data sets were manually created. These data sets comprise more than 320,000 unstained adult pancreatic stem cells from rat, including 2592 mitotic events. The reference data sets specify every cell position and shape, and assign each cell to the correct branch of its genealogic tree. We provide these reference data sets for free use by others as a benchmark for the future improvement of automated tracking methods. © 2011 Rapoport et al.

Becker T.,University of Lübeck | Becker T.,Fraunhofer Research Institution for Marine Biotechnology | Madany A.,University of Lübeck
Methods of Information in Medicine | Year: 2012

Objectives: The cultivation of adherently growing cell populations is a major task in the field of adult stem cell production used for drug discovery and in the field of regenerative medicine. To assess the quality of a cell population, a crucial event is the mitotic cell division: the precise knowledge of these events enables the reconstruction of lineages and accurate pro - liferation curves as well as a detailed analysis of cell cycles. To serve in an autonomous cell farming framework, such a detector requires to work reliably and unsupervised. adapts to the 3 phases of cell growth (lag, log and stationary phase). As a concurrent model, we compared ML with kernel SVMs using linear, quadratic and Gaussian kernel functions. All approaches are evaluated for their ability to distinguish between mitotic and nonmitotic events. The large, publicly available benchmark data CeTReS (reference data set A with > 240,000 segmented cells, > 2,000 mitotic events) is used for this evaluation. Results: The adaptive (unsupervised) ML approach clearly outperforms previously published non-adaptive approaches and the linear SVM. Furthermore, it robustly reaches a performance comparable to quadratic and Gaussian SVM. Conclusions: The proposed simple and label free adaptive variant might be the method of choice when it comes to autonomous cell farming. Hereby, it is essential to have reliable and unsupervised mitosis detection that covers all phases of cell growth. © Schattauer 2012.

Rakers S.,Fraunhofer Research Institution for Marine Biotechnology | Imse F.,Evotec | Gebert M.,Fraunhofer Research Institution for Marine Biotechnology
Ecotoxicology | Year: 2014

In this study, we report the use of a real-time cell analysis (RTCA) test system, the xCELLigence® RTCA, as efficient tool for a fast cytotoxicity analysis and comparison of four different vertebrate cell cultures. This new dynamic real-time monitoring and impedance-based assay allows for a combined measurement of cell adhesion, spreading and proliferation. Cell cultures were obtained from mouse, rat, human and fish, all displaying a fibroblast-like phenotype. The measured impedance values could be correlated to characteristic cell culture behaviours. In parallel, relative cytotoxicity of a commonly used but due to its very good water solubility highly hazardous pesticide, copper sulfate, was evaluated under in vitro conditions through measurements of cell viability by classical end-point based assays MTT and PrestoBlue®. Cell line responses in terms of viability as measured by these three methods were variable between the fish skin cells and cells from higher vertebrates and also between the three methods. The advantage of impedance-based measurements is mainly based on the continuous monitoring of cell responses for a broad range of different cells, including fish cells. © 2014, Springer Science+Business Media New York.

Muller F.-J.,Zentrum fur Integrative Psychiatrie | Schuldt B.M.,RWTH Aachen | Williams R.,Sanford Burnham Institute for Medical Research | Mason D.,Independent Consultant | And 11 more authors.
Nature Methods | Year: 2011

Pluripotent stem cells (PSCs) are defined by their potential to generate all cell types of an organism. The standard assay for pluripotency of mouse PSCs is cell transmission through the germline, but for human PSCs researchers depend on indirect methods such as differentiation into teratomas in immunodeficient mice. Here we report PluriTest, a robust open-access bioinformatic assay of pluripotency in human cells based on their gene expression profiles. © 2011 Nature America, Inc. All rights reserved.

Mehnert J.M.,Fraunhofer Research Institution for Marine Biotechnology
Cellular Physiology and Biochemistry | Year: 2014

Background/Aims: The treatment of peripheral nerve lesions still represents a clinical challenge. Several approaches such as novel biomaterials for nerve guides, addition of growth factors or cellular supplements moved in the focus of research. Especially the application of autologous stem cells is highly promising for future applications. Human sweat gland derived stem cells (hSGSCs) represent an easy accessible source of autologous adult stem cells and did already show a beneficial effect in dermal wound healing. Methods: In this study, the effect of hSGSCs on neurite outgrowth of primary adult or prenatal Dorsal root ganglia (DRG) neurons was analysed in an indirect co-culture model. Additionally, direct co-cultures with hSGSCs as a feeder layer were performed. Results: Adult and prenatal DRG neurons showed increased neurite outgrowth after 24 h co-culture with hSGSCs. The outgrowth increased significantly by the factors 5.6 and 2.6 respectively. Direct co-cultures revealed neurite alignment along the hSGSCs orientation. Conclusion: The paracrine influence of hSGSCs on neurite outgrowth, but also their ability to operate as a feeder layer with guidance properties shows great potential for future applications in peripheral nerve regeneration. © 2014 S. Karger AG, Basel Copyright © 2014, S. Karger AG. All rights reserved.

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