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Redwan B, Schmidt J, Müller KM, Schmitz R, Sandkötter J, Werner C, Wiebe K. Respiratorische Insuffizienz bei massivem Pleuraerguss durch einen Lungensequester – intrauterine Intervention und postnatale chirurgische Resektion. Pneumologie 2014. [DOI: 10.1055/s-0034-1367765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Bedetti B, Redwan B, Kösek V, Mohr M, Wiewrodt R, Wiebe K, Müller KM. Diagnose einer ausgeprägten Sideroelastose in einer Schweißerlunge bei unklarer interstitieller Lungenerkrankung mit Hämoptysen. Pneumologie 2014. [DOI: 10.1055/s-0034-1367966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Hagen S, Baumann T, Wagner HJ, Morath V, Kaufmann B, Fischer A, Bergmann S, Schindler P, Arndt KM, Müller KM. Modular adeno-associated virus (rAAV) vectors used for cellular virus-directed enzyme prodrug therapy. Sci Rep 2014; 4:3759. [PMID: 24457557 PMCID: PMC3901000 DOI: 10.1038/srep03759] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 12/23/2013] [Indexed: 12/26/2022] Open
Abstract
The pre-clinical and clinical development of viral vehicles for gene transfer increased in recent years, and a recombinant adeno-associated virus (rAAV) drug took center stage upon approval in the European Union. However, lack of standardization, inefficient purification methods and complicated retargeting limit general usability. We address these obstacles by fusing rAAV-2 capsids with two modular targeting molecules (DARPin or Affibody) specific for a cancer cell-surface marker (EGFR) while simultaneously including an affinity tag (His-tag) in a surface-exposed loop. Equipping these particles with genes coding for prodrug converting enzymes (thymidine kinase or cytosine deaminase) we demonstrate tumor marker specific transduction and prodrug-dependent apoptosis of cancer cells. Coding terminal and loop modifications in one gene enabled specific and scalable purification. Our genetic parts for viral production adhere to a standardized cloning strategy facilitating rapid prototyping of virus directed enzyme prodrug therapy (VDEPT).
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Baumann T, Arndt KM, Müller KM. Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V. BMC Biotechnol 2013; 13:81. [PMID: 24090222 PMCID: PMC3856533 DOI: 10.1186/1472-6750-13-81] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 09/25/2013] [Indexed: 02/04/2023] Open
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.
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Jedrusik-Bode M, Studencka M, Smolka C, Baumann T, Schmidt H, Kampf J, Paap F, Martin S, Tazi J, Müller KM, Krüger M, Braun T, Bober E. The sirtuin SIRT6 regulates stress granule formation in C. elegans and mammals. J Cell Sci 2013; 126:5166-77. [PMID: 24013546 DOI: 10.1242/jcs.130708] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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.
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Bedetti B, Redwan B, Schmidt J, Kösek V, Heitplatz B, Müller KM, Mohr M, Wiewrodt R, Wiebe K. Tumor durchwächst biologische dezelluläre Kollagenmatrixmaterialien. Pneumologie 2013. [DOI: 10.1055/s-0033-1334651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Müller KM, Kenter M. Tabak-assoziierte siderophile und conchoide Speicherphänomene in Rauchermakrophagen mit Riesenzellen. Pneumologie 2013. [DOI: 10.1055/s-0033-1334697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Kossakowski CA, Müller KM, Otterbach F. Bronchozentrische Granulomatose in Assoziation mit diffuser neuroendokriner Zellhyperplasie (DIPNECH). Pneumologie 2013. [DOI: 10.1055/s-0033-1334625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Speck J, Räuber C, Kükenshöner T, Niemöller C, Mueller KJ, Schleberger P, Dondapati P, Hecky J, Arndt KM, Müller KM. TAT hitchhiker selection expanded to folding helpers, multimeric interactions and combinations with protein fragment complementation. Protein Eng Des Sel 2012; 26:225-42. [PMID: 23223941 DOI: 10.1093/protein/gzs098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Speck J, Hecky J, Tam HK, Arndt KM, Einsle O, Müller KM. Exploring the molecular linkage of protein stability traits for enzyme optimization by iterative truncation and evolution. Biochemistry 2012; 51:4850-67. [PMID: 22545913 DOI: 10.1021/bi2018738] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The stability of proteins is paramount for their therapeutic and industrial use and, thus, is a major task for protein engineering. Several types of chemical and physical stabilities are desired, and discussion revolves around whether each stability trait needs to be addressed separately and how specific and compatible stabilizing mutations act. We demonstrate a stepwise perturbation-compensation strategy, which identifies mutations rescuing the activity of a truncated TEM β-lactamase. Analyses relating structural stress with the external stresses of heat, denaturants, and proteases reveal our second-site suppressors as general stability centers that also improve the full-length enzyme. A library of lactamase variants truncated by 15 N-terminal and three C-terminal residues (Bla-NΔ15CΔ3) was subjected to activity selection and DNA shuffling. The resulting clone with the best in vivo performance harbored eight mutations, surpassed the full-length wild-type protein by 5.3 °C in T(m), displayed significantly higher catalytic activity at elevated temperatures, and showed delayed guanidine-induced denaturation. The crystal structure of this mutant was determined and provided insights into its stability determinants. Stepwise reconstitution of the N- and C-termini increased its thermal, denaturant, and proteolytic resistance successively, leading to a full-length enzyme with a T(m) increased by 15.3 °C and a half-denaturation concentration shifted from 0.53 to 1.75 M guanidinium relative to that of the wild type. These improvements demonstrate that iterative truncation-optimization cycles can exploit stability-trait linkages in proteins and are exceptionally suited for the creation of progressively stabilized variants and/or downsized proteins without the need for detailed structural or mechanistic information.
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Klingström T, Soldatova L, Stevens R, Roos TE, Swertz MA, Müller KM, Kalaš M, Lambrix P, Taussig MJ, Litton JE, Landegren U, Bongcam-Rudloff E. Workshop on laboratory protocol standards for the Molecular Methods Database. N Biotechnol 2012; 30:109-13. [PMID: 22687389 DOI: 10.1016/j.nbt.2012.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 05/26/2012] [Accepted: 05/26/2012] [Indexed: 10/28/2022]
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.
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Kösek V, Schmidt J, Redwan B, Rukosujew A, Müller KM, Köhler G, Scheld HH, Wiebe K. Interferenz von DIPNECH (diffuse idiopathic pulmonary neuroendocrine cell hyperplasia) mit pulmonalen Metastasen eines Osteosarkoms. Pneumologie 2012. [DOI: 10.1055/s-0032-1302642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abstract
Synthetic Biology is founded on the idea that complex biological systems are built most effectively when the task is divided in abstracted layers and all required components are readily available and well-described. This requires interdisciplinary collaboration at several levels and a common understanding of the functioning of each component. Standardization of the physical composition and the description of each part is required as well as a controlled vocabulary to aid design and ensure interoperability. Here, we describe standardization initiatives from several disciplines, which can contribute to Synthetic Biology. We provide examples of the concerted standardization efforts of the BioBricks Foundation comprising the request for comments (RFC) and the Registry of Standardized Biological parts as well as the international Genetically Engineered Machine (iGEM) competition.
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Wohlschläger J, Sommerwerck U, Jonigk D, Rische J, Baba HA, Müller KM. [Lung transplantation and rejection. Basic principles, clinical aspects and histomorphology]. DER PATHOLOGE 2011; 32:104-12. [PMID: 21424408 DOI: 10.1007/s00292-010-1403-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Lung transplantation is the ultimate therapeutical approach for the treatment of both children and adults with terminal congenital or acquired lung disease. In contrast to survival rates during the first year following transplantation, the long-term survival for patients after lung transplantation has not significantly improved in the past. In addition to other complications, acute cellular rejection constitutes a major cause for diminished function of pulmonary grafts, and can, among other factors, be causative for chronic rejection (bronchiolitis obliterans syndrome, BOS). In 2006, the International Society for Heart and Lung Transplantation (ISHLT) provided a revised version of the grading system for acute and chronic rejection of pulmonary grafts.
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Speck J, Arndt KM, Müller KM. Efficient phage display of intracellularly folded proteins mediated by the TAT pathway. Protein Eng Des Sel 2011; 24:473-84. [PMID: 21289038 DOI: 10.1093/protein/gzr001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phage display with filamentous phages is widely applied and well developed, yet proteins requiring a cytoplasmic environment for correct folding still defy attempts at functional display. To extend applicability of phage display, we employed the twin-arginine translocation (TAT) pathway to incorporate proteins fused to the C-terminal domain of the geneIII protein into phage particles. We investigated functionality and display level of fluorescent proteins depending on the translocation pathway, which was the TAT, general secretory (SEC) or signal recognition particle (SRP) pathway mediated by the TorA, PelB or DsbA signal sequences, respectively. Importantly, for green fluorescent protein, yellow fluorescent protein and cyan fluorescent protein, only TAT, but not SEC or SRP, translocation led to fluorescence of purified phage particles, although all three proteins could be displayed regardless of the translocation pathway. In contrast, the monomeric red fluorescent protein mCherry was functionally displayed regardless of the translocation pathway. Hence, correct folding and fluorophor formation of mCherry is not limited to the cytosol. Furthermore, we successfully displayed firefly luciferase as well as an 83 kDa argonaute protein, both containing free cysteines. This demonstrates broad applicability of the TAT-mediated phagemid system for the display of proteins requiring cytoplasmic factors for correct folding and should prove useful for the display of proteins requiring incorporation of co-factors or oligomerization to gain function.
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Schmidt J, Redwan B, Rukosujew A, Müller KM, Köhler G, Scheld HH, Wiebe K. Development of DIPNECH (Diffuse idiopathic pulmonary neuroendocrine cell hyperplasia) complicating multiple pulmonary metastases of a pelvic osteosarcoma. Thorac Cardiovasc Surg 2011. [DOI: 10.1055/s-0030-1269246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Staab PR, Walossek J, Nellessen D, Grünberg R, Arndt KM, Müller KM. SynBioWave--a real-time communication platform for molecular and synthetic biology. ACTA ACUST UNITED AC 2010; 26:2782-3. [PMID: 20841324 DOI: 10.1093/bioinformatics/btq518] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SUMMARY Synthetic Biology is advanced by many users and relies on the assembly of genetic elements to devices, systems and finally genomes. SynBioWave is a software suite that enables multiple distributed users to analyze and construct genetic parts in real-time collaboration. It builds on Google Wave and provides an extensible robot-robot-user communication framework, a menu driven user interface, biological data handling including DAS and an internal database communication. We demonstrate its use by implementing robots for gene-data retrieval, manipulation and display. The initial development of SynBioWave demonstrates the power of the underlying Google Wave protocol for Synthetic Biology and lays the foundation for continuous and user-friendly extensions. Specialized wave-robots with a manageable set of capabilities will divide and conquer the complex task of creating a genome in silico. AVAILABILITY The robot is available at SynBioWave@appspot.com, the source code at http://synbiowave.sourceforge.net
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Morresi-Hauf A, Müller KM, Oelker J, Tannapfel A, Heidrich G, Häußinger K. Akzelerierte Silikose als Differenzialdiagnose eines Lungengerüstprozesses. Pneumologie 2010. [DOI: 10.1055/s-0030-1251193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Schäffer U, Schlosser A, Müller KM, Schäfer A, Katava N, Baumeister R, Schulze E. SnAvi--a new tandem tag for high-affinity protein-complex purification. Nucleic Acids Res 2010; 38:e91. [PMID: 20047968 PMCID: PMC2847239 DOI: 10.1093/nar/gkp1178] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Systematic tandem-affinity-purification (TAP) of protein complexes was tremendously successful in yeast and has changed the general concept of how we understand protein function in eukaryotic cells. The transfer of this method to other model organisms has been difficult and may require specific adaptations. We were especially interested to establish a cell-type-specific TAP system for Caenorhabditis elegans, a model animal well suited to high-throughput analysis, proteomics and systems biology. By combining the high-affinity interaction between in vivo biotinylated target-proteins and streptavidin with the usage of a newly identified epitope of the publicly shared SB1 monoclonal antibody we created a novel in vivo fluorescent tag, the SnAvi-Tag. We show the versatile application of the SnAvi-Tag in Escherichia coli, vertebrate cells and in C. elegans for tandem affinity purification of protein complexes, western blotting and also for the in vivo sub-cellular localization of labelled proteins.
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Gaisser S, Reiss T, Lunkes A, Müller KM, Bernauer H. Making the most of synthetic biology. Strategies for synthetic biology development in Europe. EMBO Rep 2009; 10 Suppl 1:S5-8. [PMID: 19636305 DOI: 10.1038/embor.2009.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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46
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Schmuecking M, Baum R, Prasad V, Schneider CP, Bank P, Marx C, Wendt TG, Kloetzer KH, Presselt N, Leonhardi J, Müller KM, Bonnet R. Das Will Rogers Phänomen: Beeinflussen die PET als Stagingmethode und die Etablierung eines Referenz-Zentrums Nuklearmedizin/Radiologie das Überleben von Patienten mit nicht-kleinzelligem Lungenkarzinom, die multimodal in Phase III Studien behandelt werden? Pneumologie 2009. [DOI: 10.1055/s-0029-1213936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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47
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Müller KM. [Methods in pathology: clinical relevance--CUP syndrome]. DER PATHOLOGE 2009; 30:89. [PMID: 19221756 DOI: 10.1007/s00292-009-1125-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Gaida A, Hagemann UB, Mattay D, Räuber C, Müller KM, Arndt KM. Selection of peptides interfering with protein-protein interaction. Methods Mol Biol 2009; 535:263-291. [PMID: 19377990 DOI: 10.1007/978-1-59745-557-2_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cell physiology depends on a fine-tuned network of protein-protein interactions, and misguided interactions are often associated with various diseases. Consequently, peptides, which are able to specifically interfere with such adventitious interactions, are of high interest for analytical as well as medical purposes. One of the most abundant protein interaction domains is the coiled-coil motif, and thus provides a premier target. Coiled coils, which consist of two or more alpha-helices wrapped around each other, have one of the simplest interaction interfaces, yet they are able to confer highly specific homo- and heterotypic interactions involved in virtually any cellular process. While there are several ways to generate interfering peptides, the combination of library design with a powerful selection system seems to be one of the most effective and promising approaches. This chapter guides through all steps of such a process, starting with library options and cloning, detailing suitable selection techniques and ending with purification for further down-stream characterization. Such generated peptides will function as versatile tools to interfere with the natural function of their targets thereby illuminating their down-stream signaling and, in general, promoting understanding of factors leading to specificity and stability in protein-protein interactions. Furthermore, peptides interfering with medically relevant proteins might become important diagnostics and therapeutics.
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Jouaux EM, Schmidtkunz K, Müller KM, Arndt KM. Targeting the c-Myc coiled coil with interfering peptides. J Pept Sci 2008; 14:1022-31. [PMID: 18465834 DOI: 10.1002/psc.1038] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
c-Myc is one of the most frequently deregulated oncogenes in human cancers, and recent studies showed that even brief inactivation of Myc can be sufficient to induce tumor regression or loss. Consequently, inactivation of Myc provides a novel therapeutic opportunity and challenge, as the dimerization of Myc with Max is crucial for its function. We applied two strategies to specifically target this coiled coil mediated interaction with interfering peptides: a dominant-negative human Max sequence (Max) and a peptide selected from a genetic library (Mip). Both peptides form coiled coils and were fused to an acidic extension interacting with the basic DNA-binding region of human Myc. The genetic library was obtained by semi-rational design randomizing residues important for interaction, and selection was carried out using a protein-fragment complementation assay. The peptides Max and Mip easily outcompeted the human Myc:Max interaction and successfully interfered with the DNA binding of the complex. Both interfering peptides exhibited higher T(m) (DeltaT(m) = 13 and 15 degrees C) upon interaction with Myc compared to wt Max. The inhibitory effect of the two interfering peptides on human Myc:Max activity makes them promising molecules for analytical and therapeutic Myc-directed research.
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Copeland J, Müller KM, Müller AM. Pulmonary haemangiolymphangioma--a new entity of pulmonary vascular tumours? Histopathology 2008; 52:527-9. [PMID: 18315611 DOI: 10.1111/j.1365-2559.2008.02946.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
MESH Headings
- Antibodies, Monoclonal/analysis
- Antibodies, Monoclonal, Murine-Derived
- Antigens, CD34/analysis
- Biomarkers, Tumor
- Fluorescent Antibody Technique, Direct
- Hemangioma, Capillary/chemistry
- Hemangioma, Capillary/pathology
- Hemangioma, Cavernous/chemistry
- Hemangioma, Cavernous/pathology
- Humans
- Lung/blood supply
- Lung/chemistry
- Lung/pathology
- Lung Neoplasms/chemistry
- Lung Neoplasms/pathology
- Lymphangioma/chemistry
- Lymphangioma/pathology
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