Buschmann T.,Carl Gustav Carus Institute |
Bystrykh L.V.,University of Groningen
BMC Bioinformatics | Year: 2013
Background: High-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag or barcode that is attached to the sequencing or amplification primer and hence appears at the beginning of the sequence in every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence.Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and Levenshtein codes.Result: Levenshtein codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this paper we demonstrate the decreased error correction capability of Levenshtein codes in a DNA context and suggest an adaptation of Levenshtein codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaption we take the DNA context into account and redefine the word length whenever an insertion or deletion is revealed. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors.Conclusion: We present an adaptation of Levenshtein codes to DNA contexts capable of correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of recovering the new length of the corrupted codeword and of correcting on average more random mutations than traditional Levenshtein or Hamming codes.As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance. © 2013 Buschmann and Bystrykh; licensee BioMed Central Ltd.
Cheng L.E.,University of California at San Francisco |
Hartmann K.,University of Cologne |
Roers A.,Carl Gustav Carus Institute |
Krummel M.F.,University of California at San Francisco |
Locksley R.M.,Howard Hughes Medical Institute
Immunity | Year: 2013
Mast cells are tissue-resident immune cells that play a central role in allergic disease. These contributions are largely dependent on the acquisition of antigen-specific immunoglobulin E (IgE). Despite this requirement, studies of mast cell and IgE interactions have overlooked the mechanism by which mast cells acquire IgE from the blood. To address this gap, we developed reporter IgE molecules and employed imaging techniques to study mast cell function in situ. Our data demonstrate that skin mast cells exhibit selective uptake of IgE based on perivascular positioning. Furthermore, perivascular mast cells acquire IgE by extending cell processes across the vessel wall to capture luminal IgE. These data demonstrate how tissue mast cells acquire IgE and reveal a strategy by which extravascular cells monitor blood contents to capture molecules central to cellular function. © 2013 Elsevier Inc.
Linn J.,Carl Gustav Carus Institute
Clinical Neuroradiology | Year: 2015
Cerebral microbleeds (CMBs) are defined as small, rounded, or ovoid, homogeneous hypointense lesions on T2*-weighted gradient-echo and other susceptibility-sensitive magnetic resonance imaging (MRI) sequences. They must be differentiated from other causes of focal hypointensities on these sequences. Although CMBs can be caused by a variety of diseases, they are most frequently associated with different forms of cerebral small vessel diseases. This review summarizes the MRI characteristics of CMBs including methodological considerations, as well as prevalence, differential diagnosis, mimics, and clinical relevance of CMBs. © 2015, Springer-Verlag Berlin Heidelberg.
Jessberger R.,Carl Gustav Carus Institute
Genes and Development | Year: 2010
Humans suffer a steep increase in aneuploidies when oocytes age, and deterioration of cohesin was suggested recently as a prominent cause. In the November 15, 2010, issue of Genes & Development, Tachibana-Konwalski and colleagues (pp. 2505-2516) answered a question central to this hypothesis: Can cohesin be reloaded onto mouse oocyte chromosomes long after birth? They found that it cannot, or at least not with an efficiency adequate to rescue cohesin deficiency. With no chance for sufficient replenishment, age-related loss of sister chromatid cohesion seems unavoidable. © 2010 by Cold Spring Harbor Laboratory Press.
Dumke R.,Carl Gustav Carus Institute |
Jacobs E.,Carl Gustav Carus Institute
Journal of Clinical Microbiology | Year: 2014
Four commercial real-time PCR assays to detect Mycoplasma pneumoniae were tested, and the results were compared with the results for an in-house approach. Despite differences of crossing threshold values of up to 4, assays were able to detect at least 20 CFU/5 μl (52 fg DNA/5 μl) of sample with the Diagenode kit showing the best clinical sensitivity. Copyright © 2014, American Society for Microbiology. All Rights Reserved.