@misc{BaumannArndtMueller2013,
  author    = {Baumann, Tobias and Arndt, Katja Maren and M{\"u}ller, Kristian M.},
  title     = {Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {983},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43108},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431085},
  pages     = {13},
  year      = {2013},
  abstract  = {Background: DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning. Results: A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions. Conclusions: The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.},
  language  = {en}
}
@article{BaumannArndtMueller2013,
  author    = {Baumann, Tobias and Arndt, Katja Maren and M{\"u}ller, Kristian M.},
  title     = {Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V},
  series = {BMC biotechnology},
  volume    = {13},
  journal   = {BMC biotechnology},
  number    = {10},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1472-6750},
  doi       = {10.1186/1472-6750-13-81},
  pages     = {11},
  year      = {2013},
  abstract  = {Background: DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning. Results: A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions. Conclusions: The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.},
  language  = {en}
}
@article{SpeckRaeuberKuekenshoeneretal.2013,
  author    = {Speck, Janina and R{\"a}uber, Christina and K{\"u}kensh{\"o}ner, Tim and Niem{\"o}ller, Christoph and Mueller, Katelyn J. and Schleberger, Paula and Dondapati, Padmarupa and Hecky, Jochen and Arndt, Katja Maren and M{\"u}ller, Kristian M.},
  title     = {TAT hitchhiker selection expanded to folding helpers, multimeric interactions and combinations with protein fragment complementation},
  series = {Protein engineering design \& selection},
  volume    = {26},
  journal   = {Protein engineering design \& selection},
  number    = {3},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1741-0126},
  doi       = {10.1093/protein/gzs098},
  pages     = {225 -- 242},
  year      = {2013},
  abstract  = {The twin-arginine translocation (TAT) pathway of the bacterial cytoplasmic membrane mediates translocation only of proteins that accomplished a native-like conformation. We deploy this feature in modular selection systems for directed evolution, in which folding helpers as well as dimeric or oligomeric proteinprotein interactions enable TAT-dependent translocation of the resistance marker TEM -lactamase (L). Specifically, we demonstrate and analyze selection of (i) enhancers for folding by direct TAT translocation selection of a target protein interposed between the TorA signal sequence and L, (ii) dimeric or oligomeric proteinprotein interactions by hitchhiker translocation (HiT) selection of proteins fused to the TorA signal sequence and to the L, respectively and (iii) heterotrimeric proteinprotein interactions by combining HiT with protein fragment complementation selection of proteins fused to two split L fragments and TorA, respectively. The lactamase fragments were additionally engineered for improved activity and stability. Applicability was benchmarked with interaction partners of known affinity and multimerization whereby cellular fitness correlated well with biophysical protein properties. Ultimately, the HiT selection was employed to identify peptides, which specifically bind to leukemia- and melanoma-relevant target proteins (MITF and ETO) by coiled-coil or tetra-helix-bundle formation with high affinity. The various versions of TAT selection led to inhibiting peptides (iPEPs) of disease-promoting interactions and enabled so far difficult to achieve selections.},
  language  = {en}
}
@article{JedrusikBodeStudenckaSmolkaetal.2013,
  author    = {Jedrusik-Bode, Monika and Studencka, Maja and Smolka, Christian and Baumann, Tobias and Schmidt, Henning and Kampf, Jan and Paap, Franziska and Martin, Sophie and Tazi, Jamal and M{\"u}ller, Kristian M. and Kr{\"u}ger, Marcus and Braun, Thomas and Bober, Eva},
  title     = {The sirtuin SIRT6 regulates stress granule formation in C. elegans and mammals},
  series = {Journal of cell science},
  volume    = {126},
  journal   = {Journal of cell science},
  number    = {22},
  publisher = {Company of Biologists Limited},
  address   = {Cambridge},
  issn      = {0021-9533},
  doi       = {10.1242/jcs.130708},
  pages     = {5166 -- +},
  year      = {2013},
  abstract  = {SIRT6 is a NAD(+)-dependent deacetylase that modulates chromatin structure and safeguards genomic stability. Until now, SIRT6 has been assigned to the nucleus and only nuclear targets of SIRT6 are known. Here, we demonstrate that in response to stress, C. elegans SIR-2.4 and its mammalian orthologue SIRT6 localize to cytoplasmic stress granules, interact with various stress granule components and induce their assembly. Loss of SIRT6 or inhibition of its catalytic activity in mouse embryonic fibroblasts impairs stress granule formation and delays disassembly during recovery, whereas deficiency of SIR-2.4 diminishes maintenance of P granules and decreases survival of C. elegans under stress conditions. Our findings uncover a novel, evolutionary conserved function of SIRT6 in the maintenance of stress granules in response to stress.},
  language  = {en}
}
@article{KlingstromSoldatovaStevensetal.2013,
  author    = {Klingstrom, Tomas and Soldatova, Larissa and Stevens, Robert and Roos, T. Erik and Swertz, Morris A. and M{\"u}ller, Kristian M. and Kalas, Matus and Lambrix, Patrick and Taussig, Michael J. and Litton, Jan-Eric and Landegren, Ulf and Bongcam-Rudloff, Erik},
  title     = {Workshop on laboratory protocol standards for the molecular methods database},
  series = {New biotechnology},
  volume    = {30},
  journal   = {New biotechnology},
  number    = {2},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {1871-6784},
  doi       = {10.1016/j.nbt.2012.05.019},
  pages     = {109 -- 113},
  year      = {2013},
  abstract  = {Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.},
  language  = {en}
}