B Sander

Aarhus University, Aarhus, Central Jutland, Denmark

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Publications (137)571.12 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Affinity isolation has been an essential technique for molecular studies of cellular assemblies, such as the switch/sucrose non-fermentable (SWI/SNF) family of ATP-dependent chromatin remodeling complexes. However, even biochemically pure isolates can contain heterogeneous mixtures of complexes and their components. In particular, purification strategies that rely on affinity tags fused to only one component of a complex may be susceptible to this phenomenon. This study demonstrates that fusing purification tags to two different proteins enables the isolation of intact complexes of remodels the structure of chromatin (RSC). A Protein A tag was fused to one of the RSC proteins and a Twin-Strep tag to another protein of the complex. By mass spectrometry, we demonstrate the enrichment of the RSC complexes. The complexes had an apparent Svedberg value of about 20S, as shown by glycerol gradient ultracentrifugation. Additionally, purified complexes were demonstrated to be functional. Electron microscopy and single-particle analyses revealed a conformational rearrangement of RSC upon interaction with acetylated histone H3 peptides. This purification method is useful to purify functionally active, structurally well-defined macromolecular assemblies. Copyright © 2014. Published by Elsevier B.V.
    Biochimica et biophysica acta. 12/2014;
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    ABSTRACT: Peptide sequences fused to a gene of interest facilitate the isolation of proteins or protein complexes from cell extracts. In the case of fluorescent protein tags, the tagged protein can be visually localized in living cells. To tag endogenous genes, PCR-based homologous recombination is a powerful approach used in the yeast Saccharomyces cerevisiae. This approach uses short, homologous DNA sequences that flank the tagging cassette to direct recombination. Here, we constructed a set of plasmids, whose sequences were optimized for codon usage in yeast, for Strep-tag II and Twin-Strep tagging in S. cerevisiae. Some plasmids also contain sequences encoding for a fluorescent protein followed by the purification tag. We demonstrate using the yeast pyruvate dehydrogenase (PDH) complex that these plasmids can be used to purify large protein complexes efficiently. We furthermore demonstrate that purification from the endogenous pool using the Strep-tag system results in functionally active complexes. Finally, using the fluorescent tags, we show that a kinase and a phosphatase involved in regulating the activity of the PDH complex localize in the cells' mitochondria. In conclusion, our cassettes can be used as tools for biochemical, functional, and structural analyses of endogenous multi-protein assemblies in yeast.
    Molecular Biotechnology 06/2014; · 2.26 Impact Factor
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    ABSTRACT: Here, synchronous (early) and metachronous (late) brain metastasis (BM) events of sporadic ccRCC (n = 148) were retrospectively analyzed using comparative genomic hybridization (CGH). Using oncogenetic tree models and cluster analyses, chromosomal imbalances related to recurrence-free survival (RFS-BM) were observed. Losses at 9p and 9q appeared to be hallmarks of metachronous BM events, whereas an absence of detectable chromosomal changes at 3p was often associated with synchronous BM events. Correspondingly, k-means clustering showed that Cluster 1 cases generally exhibited low copy number chromosomal changes that did not involve 3p. Cluster 2 cases had a high occurrence of -9p/-9q (94–98%) deletions, while Cluster 3 cases had a higher frequency of copy number changes, including loss at chromosome 14 (80%). The higher number of synchronous cases in Cluster 1 was also associated with a significantly shorter RFS-BM compared to Clusters 2 and 3 (p = 0.02). Conversely, a significantly longer RFS-BM was observed for Cluster 2 versus Clusters 1 and 3 (p = 0.02). Taken together, these data suggest that metachronous BM events of ccRCC are characterized by loss of chromosome 9, whereas synchronous BM events may form independently of detectable genetic changes at chromosomes 9 and 3p.
    Cancer Genetics. 01/2014;
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    ABSTRACT: Previous studies suggest different pathways in the molecular development of hepatocellular carcinoma (HCC). We investigated the pattern of chromosomal imbalances in HCC depending on the type of underlying liver disease as detected by comparative genomic hybridization in 67 cases of primary HCC occurring in non-cirrhotic livers (n=30), in liver cirrhosis (LC) related to alcohol intake (n=9), cryptogenic or metabolic changes (n=11), and chronic viral hepatitis B or C (n=17). HCC were treated by liver resection in 48 patients and transplantation in 19 patients. The 10-year disease-free and overall survival rates were 51% and 68%, respectively. The copy number changes occurring in more than 10% of cases were gains at 8q (55%), 1q (49%), 7q (15%), 7p (13%), 6p (12%), and 20q (12%), as well as losses at 8p (55%), 4q (33%), 6q (33%), 13q (25%), 14q (24%), 17p (22%), 16q (19%), 1p (18%), 18q (16%), 9p (13%), 10q (13%), 4p (12%), and 9q (12%). HCC arising in alcoholic LC showed a different pattern with significantly fewer net changes (p=0.008), particularly fewer chromosomal gains (p=0.008) and fewer breakpoints (p=0.003) compared to the other investigated HCC subgroups. Future clinical studies should evaluate the prognostic relevance of these findings.
    Pathology - Research and Practice 04/2013; · 1.21 Impact Factor
  • Bjoern Sander, Mariola Monika Golas
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    ABSTRACT: Understanding tissue architecture and the morphological characteristics of cells is a central prerequisite to comprehending the basis of physiological tissue function in healthy individuals and relating this to disease states. Traditionally, medical curricula include courses where students examine glass slides of cytological or tissue samples under a light microscope. However, it is challenging to implement group and peer group learning in these courses and to give students sufficient time to study specimens. An increasing number of medical schools have thus started to implement digital slide viewers, so-called virtual microscopes, in histology and histopathology. These websites are mostly based on standard commercial software and offer limited adaptation to the special needs of first-year students. An e-learning platform has therefore been developed for use in cytology and histology courses. This virtual microscopy tool is coupled to a central database in which students can label and store the positions of individual structures for later repetition. As learning in pairs and peer groups has been shown to provide a high learning outcome, identified structures can be shared and discussed with students' peers or faculty via a built-in communication module. This website has the possibility of opening an arbitrary number of frames which all can actively be moved and changed in magnification to enable the comparison of specimens and thus encourage a more global understanding of related tissues. HistoViewer is thus suggested as an e-learning tool combining several modern teaching concepts. © 2012 American Association of Anatomists.
    Anatomical Sciences Education 11/2012;
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    ABSTRACT: PURPOSE: To gain mechanistic insights into drug loading and lyophilization of polymeric micelles. METHODS: PEGylated poly-4-(vinylpyridine) micelles were loaded with dexamethasone. Three different methods were applied and compared: O/W emulsion, direct dialysis, cosolvent evaporation. Micellar dispersions with the highest drug load were lyophilized with varying lyoprotectors: sucrose, trehalose, maltose, a polyvinylpyrrolidine derivative, and β-cyclodextrin derivatives. For comparison, other PEGylated block copolymer micelles (PEGylated polylactic acid, polylactic acid-co-glycolic acid, polycaprolactone) were freeze-dried. RESULTS: Drug loading via direct dialysis from acetone was a less effective loading method which led to dexamethasone loads <2% w/w. O/W emulsion technique from dichlormethane increased drug load up to ~13% w/w; optimized cosolvent evaporation increased load up to ~19% w/w. An important step for cosolvent evaporation was solubility screen of the drug prior to preparation. Loading was maintained upon lyophilization with β-cyclodextrins which proved to be versatile stabilizers for other block copolymer micelles. CONCLUSION: Careful solvent selection prior to cosolvent evaporation was a beneficial approach to load hydrophobic drugs into polymeric micelles. Moreover, β-cyclodextrins could be used as versatile lyoprotectors for these micelles.
    Pharmaceutical Research 11/2012; · 4.74 Impact Factor
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    ABSTRACT: Single molecule microscopy techniques play an important role in the investigation of advanced DNA structures such as those created by the DNA origami method. Three single molecule microscopy techniques are particularly interesting for the investigation of complex self-assembled three-dimensional (3D) DNA nanostructures, namely single molecule fluorescence microscopy, atomic force microscopy (AFM), and cryogenic transmission electron microscopy (cryo-EM). Here we discuss the strengths of these three techniques and demonstrate how their interplay can yield very important and unique new insights into the structure and conformation of advanced biological nanostructures. The applications of the three single molecule microscopy techniques are illustrated by focusing on a self-assembled DNA origami 3D box nanostructure. Its size and structure were studied by AFM and cryo-EM, while the lid opening, which can be controlled by the addition of oligonucleotide keys, was recorded by Förster/fluorescence resonance energy transfer (FRET) spectroscopy.
    Microscopy Research and Technique 07/2011; 74(7):688-98. · 1.59 Impact Factor
  • Bjoern Sander, Monika M Golas
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    ABSTRACT: In the recent years, nanotechnology has rapidly evolved as promising toolbox for many applications, including sensing and drug delivery. Nanotechnology aims at forming man-designed two-dimensional and three-dimensional structures in the nanometer scale using e.g., the self-assembly properties of smaller building blocks such as DNA and RNA. The visualization and structural characterization of these nanostructures do not only provide evidence for the correct formation of the desired shapes, but can also contribute to a better understanding of their formation and functionality. Transmission electron microscopy offers the possibility to directly visualize the individual nanostructures. The vitrification of the sample by using the plunge-freezing method and subsequent electron cryomicroscopy (cryo-EM) provides in-solution snapshots of the nanostructures under cryogenic conditions and thus preserves the close-to-native structure of the particles. Here, we describe the plunge-freezing and other sample preparation protocols such as negative staining and cryo-negative staining as well as the various imaging and image processing methods, including electron crystallography, electron tomography, and single-particle EM. Typical example applications are provided together with a discussion of benefits and shortcomings of these approaches. We also discuss how deviations from an ideal symmetry and structural heterogeneity, in general, can limit the resolution. Finally, we suggest that nanotechnological approaches may not only offer new applications in the field of nanomaterial science and nanomedicine, but may also emerge as tools for structural biology and structure-related biomedical research.
    Microscopy Research and Technique 07/2011; 74(7):642-63. · 1.59 Impact Factor
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    ABSTRACT: Pulmonary metastases (PM) are frequent in colorectal carcinoma (CRC). However, little is known about the chromosomal imbalances in CRC that accompany metastatic pulmonary disease. We investigated tumor specimens of CRC (n=30) and their corresponding PM by comparative genomic hybridization (CGH). There were no substantial differences in the degree of chromosomal instability between CRC and PM, neither in average number of copy alterations (ANCA; 6.6 ± 0.8 and 7.7 ± 0.9) nor in gains (2.6 ± 0.5 and 2.6 ± 0.4), losses (3.6 ± 0.5 and 4.8 ± 0.6), or amplifications (0.4 ± 0.1 and 0.3 ± 0.1). Basically, similar patterns of chromosomal imbalances could be identified in both CRC and corresponding PM, most frequently including chromosomal gains at 7, 8q, 13q, and 20q, as well as losses at 4, 8p, 18q, and 20p. CRC and corresponding PM differed in frequencies for losses at chromosome arm 5q (3 vs. 26%; P=0.012). Losses at 4q and 11q in CRC were significantly associated with lower 5-year survival rates (80 vs. 24%, P=0.026 and 74 vs. 17%, P=0.007, respectively), and they may represent candidates for adverse prognostic markers in primary CRC.
    Cancer Genetics 03/2011; 204(3):122-8. · 1.92 Impact Factor
  • Journal of Urology - J UROL. 01/2011; 185(4).
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    ABSTRACT: RNA editing within the mitochondria of kinetoplastid protozoa is performed by a multicomponent -macromolecular machine known as the editosome. Editosomes are high molecular mass protein assemblies that consist of about 15-25 individual polypeptides. They bind pre-edited transcripts and convert them into translation-competent mRNAs through a biochemical reaction cycle of enzyme-catalyzed steps. At steady-state conditions, several distinct complexes can be purified from mitochondrial detergent lysates. They likely represent RNA editing complexes at different assembly stages or at different functional stages of the processing reaction. Due to their low cellular abundance, single-particle electron microscopy (EM) represents the method of choice for their structural characterization. This chapter describes a set of techniques suitable for the purification and structural characterization of RNA editing complexes by single-particle EM. The RNA editing complexes are isolated from the endogenous pool of mitochondrial complexes by tandem-affinity purification (TAP). Since the TAP procedure results in the isolation of a mixture of different RNA editing complexes, the isolates are further subjected to an isokinetic ultracentrifugation step to separate the complexes based on their sedimentation behavior. The use of the "GraFix" protocol is presented that combines mild chemical cross-linking with ultracentrifugation. Different sample preparation protocols including negative staining, cryo-negative staining, and unstained cryotechniques as well as the single-particle image processing of electron microscopical images are described.
    Methods in molecular biology (Clifton, N.J.) 01/2011; 718:3-22. · 1.29 Impact Factor
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    ABSTRACT: The spliceosome excises introns from pre-mRNA in a two-step splicing reaction. So far, the three-dimensional (3D) structure of a spliceosome with preserved catalytic activity has remained elusive. Here, we determined the 3D structure of the human, catalytically active step I spliceosome (C complex) by cryo-electron microscopy (cryo-EM) in vitrified ice. Via immunolabeling we mapped the position of the 5' exon. The C complex contains an unusually salt-stable ribonucleoprotein (RNP) core that harbors its catalytic center. We determined the 3D structure of this RNP core and also that of a post-step II particle, the 35S U5 snRNP, which contains most of the C complex core proteins. As C complex domains could be recognized in these structures, their position in the C complex could be determined, thereby allowing the region harboring the spliceosome's catalytic core to be localized.
    Molecular cell 12/2010; 40(6):927-38. · 14.61 Impact Factor
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    ABSTRACT: To better understand the compositional and structural dynamics of the human spliceosome during its activation, we set out to isolate spliceosomal complexes formed after precatalytic B but prior to catalytically active C complexes. By shortening the polypyrimidine tract of the PM5 pre-mRNA, which lacks a 3' splice site and 3' exon, we stalled spliceosome assembly at the activation stage. We subsequently affinity purified human B(act) complexes under the same conditions previously used to isolate B and C complexes, and analyzed their protein composition by mass spectrometry. A comparison of the protein composition of these complexes allowed a fine dissection of compositional changes during the B to B(act) and B(act) to C transitions, and comparisons with the Saccharomyces cerevisiae B(act) complex revealed that the compositional dynamics of the spliceosome during activation are largely conserved between lower and higher eukaryotes. Human SF3b155 and CDC5L were shown to be phosphorylated specifically during the B to B(act) and B(act) to C transition, respectively, suggesting these modifications function at these stages of splicing. The two-dimensional structure of the human B(act) complex was determined by electron microscopy, and a comparison with the B complex revealed that the morphology of the human spliceosome changes significantly during its activation. The overall architecture of the human and S. cerevisiae B(act) complex is similar, suggesting that many of the higher order interactions among spliceosomal components, as well as their dynamics, are also largely conserved.
    RNA 10/2010; 16(12):2384-403. · 5.09 Impact Factor
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    ABSTRACT: Many fundamental processes in the cell are performed by complex macromolecular assemblies that comprise a large number of proteins. Numerous macromolecular assemblies are structurally rather fragile and may suffer during purification, resulting in the partial dissociation of the complexes. These limitations can be overcome by chemical fixation of the assemblies, and recently introduced protocols such as gradient fixation during ultracentrifugation (GraFix) offer advantages for the analysis of fragile macromolecular assemblies. The irreversible fixation, however, is thought to render macromolecular samples useless for studying their protein composition. We therefore developed a novel approach that possesses the advantages of fixation for structure determination by single particle electron microscopy while still allowing a correlative compositional analysis by mass spectrometry. In this method, which we call "electron microscopy carbon film-assisted digestion", macromolecular assemblies are chemically fixed and then adsorbed onto electron microscopical carbon films. Parallel, identically prepared specimens are then subjected to structural investigation by electron microscopy and proteomics analysis by mass spectrometry of the digested sample. As identical sample preparation protocols are used for electron microscopy and mass spectrometry, the results of both methods can directly be correlated. In addition, we demonstrate improved sensitivity and reproducibility of electron microscopy carbon film-assisted digestion as compared with standard protocols. We show that sample amounts of as low as 50 fmol are sufficient to obtain a comprehensive protein composition of two model complexes. We suggest our approach to be an optimization technique for the compositional analysis of macromolecules by mass spectrometry in general.
    Molecular &amp Cellular Proteomics 08/2010; 9(8):1729-41. · 7.25 Impact Factor
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    ABSTRACT: Single-particle electron cryomicroscopy is a powerful method for three-dimensional (3D) structure determination of macromolecular assemblies. Here we address the challenge of determining a 3D structure in the absence of reference models. The 3D structures are determined by alignment and weighted averaging of densities obtained by native cryo random conical tilt (RCT) reconstructions including consideration of missing data. Our weighted averaging scheme (wRCT) offers advantages for potentially heterogeneous 3D densities of low signal-to-noise ratios. Sets of aligned RCT structures can also be analyzed by multivariate statistical analysis (MSA) to provide insights into snapshots of the assemblies. The approach is used to compute 3D structures of the Escherichia coli 70S ribosome and the human U4/U6.U5 tri-snRNP under vitrified unstained cryo conditions, and to visualize by 3D MSA the L7/L12 stalk of the 70S ribosome and states of tri-snRNP. The approach thus combines de novo 3D structure determination with an analysis of compositional and conformational heterogeneity.
    Structure 06/2010; 18(6):667-76. · 5.99 Impact Factor
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    ABSTRACT: Information on structural chromosomal changes in brain metastases (BM) of colorectal carcinoma (CRC) is very limited. Therapeutic and diagnostic strategies to reduce the risk of BM have potential impact on cancer mortality. By using comparative genomic hybridization, the primary CRC of 11 patients and their corresponding 13 BM were analyzed. BM showed significantly more mean chromosomal aberrations than the primary CRC (13.6+/-2.1 vs. 7.9+/-1.9, P=0.03), significantly more chromosomal gains (7.2+/-0.9 vs. 3.5+/-0.9, P=0.01), and tended to have also more losses (6.1+/-1.4 vs. 4.0+/-1.1, P=0.29). Changes that occurred significantly more often in BM than in primary CRC were gains of 8q, 12p, 12q, and 20p, as well as losses of 5q. BM of CRC show a significantly higher chromosomal instability in comparison to primary tumors. The prevalently altered genomic regions in the metastases of this study are likely to harbor genes that play an important role in the genesis of brain-specific metastasis.
    Cancer genetics and cytogenetics 04/2010; 198(1):47-51. · 1.54 Impact Factor
  • Molecular and Cellular Proteomics, v.9, 1729-1741 (2010). 01/2010;
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    ABSTRACT: Oligo(ethylene glycol) methyl ether methacrylates (OEGMA) of various chain lengths (i.e., 9, 23, or 45 EG units) and N,N-dimethylaminoethyl methacrylate (DMAEMA) were copolymerized by atom transfer radical polymerization (ATRP), yielding well-defined P(DMAEMA-co-OEGMA) copolymers with increasing OEGMA molar fractions (F(OEGMA)) but a comparable degree of polymerization (DP approximately 120). Increase of both F(OEGMA) and OEGMA chain lengths correlated inversely with gene vector size, morphology, and zeta potential. P(DMAEMA-co-OEGMA) copolymers prevented gene vector aggregation at high plasmid DNA (pDNA) concentrations in isotonic solution and did not induce cytotoxicity even at high concentrations. Transfection efficiency of the most efficient P(DMAEMA-co-OEGMA) copolymers was found to be >10-fold lower compared with branched polyethylenimine (PEI) 25 kDa. Although OEGMA copolymerization largely reduced gene vector binding with the cell surface, cellular internalization of the bound complexes was less affected. These observations suggest that inefficient endolysosomal escape limits transfection efficiency of P(DMAEMA-co-OEGMA) copolymer gene vectors. Despite this observation, optimized p(DMAEMA-co-OEGMA) gene vectors remained stable under conditions for in vivo application leading to 7-fold greater gene expression in the lungs compared with PEI. Tailor-made P(DMAEMA-co-OEGMA) copolymers are promising nonviral gene transfer agents that fulfill the requirements for successful in vivo gene delivery.
    Biomacromolecules 12/2009; 11(1):39-50. · 5.37 Impact Factor
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    ABSTRACT: Enhancing gene delivery and expression in alveolar epithelial cells could offer the opportunity for the treatment of acquired and inherited lung diseases. Here, we show that particle adsorption of human insulin (INS) is capable of increasing plasmid DNA (pDNA) delivery from polyethylenimine (PEI) nanoparticles specifically in alveolar epithelial cells. INS receptors were predominantly detected on alveolar but not on bronchial epithelial cells. INS was adsorbed on the surface of PEI gene vectors by spontaneous self-assembly resulting in ternary PEI-pDNA-INS nanoparticles. Surface adsorption was confirmed by particle size, surface charge, and fluorescence resonance energy transfer (FRET) measurements. INS adsorption significantly increased gene expression of PEI-pDNA nanoparticles up to 16-fold on alveolar epithelial cells but not on bronchial epithelial cells. This increased gene expression was INS receptor specific. Our results demonstrate that targeting INS receptor for gene delivery in alveolar epithelial cells represents a promising approach for enhanced gene delivery and expression.
    Biomacromolecules 10/2009; 10(10):2912-20. · 5.37 Impact Factor
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    ABSTRACT: The unique structural motifs and self-recognition properties of DNA can be exploited to generate self-assembling DNA nanostructures of specific shapes using a 'bottom-up' approach. Several assembly strategies have been developed for building complex three-dimensional (3D) DNA nanostructures. Recently, the DNA 'origami' method was used to build two-dimensional addressable DNA structures of arbitrary shape that can be used as platforms to arrange nanomaterials with high precision and specificity. A long-term goal of this field has been to construct fully addressable 3D DNA nanostructures. Here we extend the DNA origami method into three dimensions by creating an addressable DNA box 42 x 36 x 36 nm(3) in size that can be opened in the presence of externally supplied DNA 'keys'. We thoroughly characterize the structure of this DNA box using cryogenic transmission electron microscopy, small-angle X-ray scattering and atomic force microscopy, and use fluorescence resonance energy transfer to optically monitor the opening of the lid. Controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications, for example as a logic sensor for multiple-sequence signals or for the controlled release of nanocargos.
    Nature 06/2009; 459(7243):73-6. · 38.60 Impact Factor

Publication Stats

2k Citations
571.12 Total Impact Points

Institutions

  • 2010–2014
    • Aarhus University
      • • Faculty of Health Sciences
      • • Department of Clinical Medicine
      Aarhus, Central Jutland, Denmark
  • 2006–2013
    • Georg-August-Universität Göttingen
      • Center for Biochemistry and Molecular Cell Biology
      Göttingen, Lower Saxony, Germany
    • University of Bonn
      Bonn, North Rhine-Westphalia, Germany
    • HELIOS Albert-Schweitzer-Klinik Northeim
      Northeim, Lower Saxony, Germany
  • 2011
    • Technical University Darmstadt
      Darmstadt, Hesse, Germany
  • 2003–2010
    • Max Planck Institute for Biophysical Chemistry
      • • Department of Cellular Biochemistry
      • • Group of Bioanalytical Mass Spectrometry
      Göttingen, Lower Saxony, Germany
  • 2007–2009
    • Universitätsmedizin Göttingen
      • • Department of General, Visceral and Child Surgery
      • • Department of Pathology
      Göttingen, Lower Saxony, Germany
  • 2005
    • University of Hamburg
      • Department of Urology
      Hamburg, Hamburg, Germany
  • 1996–1997
    • Humboldt-Universität zu Berlin
      • Department of Biology
      Berlín, Berlin, Germany
  • 1990–1996
    • Freie Universität Berlin
      • Department of Oncology
      Berlín, Berlin, Germany