TY - JOUR A1 - Schäfer, Myriam A1 - Hildenbrand, Georg A1 - Hausmann, Michael T1 - Impact of Gold Nanoparticles and Ionizing Radiation on Whole Chromatin Organization as Detected by Single-Molecule Localization Microscopy JF - International Journal of Molecular Sciences N2 - In radiation tumor therapy, irradiation, on one hand, should cause cell death to the tumor. On the other hand, the surrounding non-tumor tissue should be maintained unaffected. Therefore, methods of local dose enhancements are highly interesting. Gold nanoparticles, which are preferentially uptaken by very-fast-proliferating tumor cells, may enhance damaging. However, the results in the literature obtained from cell culture and animal tissue experiments are very contradictory, i.e., only some experiments reveal increased cell killing but others do not. Thus, a better understanding of cellular mechanisms is required. Using the breast cancer cell model SkBr3, the effects of gold nanoparticles in combination with ionizing radiation on chromatin network organization were investigated by Single-Molecule Localization Microscopy (SMLM) and applications of mathematical topology calculations (e.g., Persistent Homology, Principal Component Analysis, etc.). The data reveal a dose and nanoparticle dependent re-organization of chromatin, although colony forming assays do not show a significant reduction of cell survival after the application of gold nanoparticles to the cells. In addition, the spatial organization of γH2AX clusters was elucidated, and characteristic changes were obtained depending on dose and gold nanoparticle application. The results indicate a complex response of ALU-related chromatin and heterochromatin organization correlating to ionizing radiation and gold nanoparticle incorporation. Such complex whole chromatin re-organization is usually associated with changes in genome function and supports the hypothesis that, with the application of gold nanoparticles, not only is DNA damage increasing but also the efficiency of DNA repair may be increased. The understanding of complex chromatin responses might help to improve the gold nanoparticle efficiency in radiation treatment. KW - Krebs, Medizin KW - Strahlentherapie Y1 - 2024 U6 - https://doi.org/https://doi.org/10.3390/ijms252312843 SN - 1422-0067 VL - 25 IS - 23 PB - MDPI AG ER - TY - JOUR A1 - Failla, Antonio Virgillo A1 - Albrecht, Benno A1 - Spöri, U. A1 - Schweitzer, A. A1 - Kroll, A. A1 - Hildenbrand, Georg A1 - Bach, M. A1 - Cremer, Christoph T1 - Nanostructure Analysis Using Spatially Modulated Illumination Microscopy JF - Complexus N2 - For an improved understanding of cellular processes, it is highly desirable to develop light optical methods for the analysis of biological nanostructures and their dynamics in the interior of three-dimensionally (3D) conserved cells. Here, important structural parameters to be considered are the topology, i.e. the mutual positions and distances, as well as the sizes of the constituting subunits. This has become possible by the development of a novel method of far-field light fluorescence microscopy, spatially modulated illumination (SMI) microscopy. Using this approach, axial distances between fluorescence-labeled targets can be measured with an accuracy close to 1 nm; their sizes can be determined down to a few tens of nanometers. This approach can be extended to the determination of 3D positions and mutual 3D distances and sizes of any number of small objects/subunits that can be discriminated due to their spectral signatures. Consequently, the new approach allows an ‘in situ nanostructure elucidation, until now regarded to be beyond the possibilities of far-field light microscopy. Application examples discussed are: colocalization/nanosizing and topological analysis of large protein-protein complexes, of nucleic acid-protein complexes (such as transcription factories), or of the highly complex DNA-protein nanostructures of which active/ inactive gene regions in the eukaryotic cell nucleus are constituted. KW - Fluoreszenzmikroskopie Y1 - 2003 U6 - https://doi.org/https://doi.org/10.1159/000070464 SN - 1424-8492 VL - 1 IS - 2 SP - 77 EP - 88 PB - S. Karger AG ER - TY - JOUR A1 - Hildenbrand, Georg A1 - Rapp, Alexander A1 - Spöri, Udo A1 - Wagner, Christian A1 - Cremer, Christoph A1 - Hausmann, Michael T1 - Nano-Sizing of Specific Gene Domains in Intact Human Cell Nuclei by Spatially Modulated Illumination Light Microscopy JF - Biophysical Journal KW - Genom KW - Zellkern KW - Fluoreszenzmikroskopie Y1 - 2005 U6 - https://doi.org/https://doi.org/10.1529/biophysj.104.056796 SN - 0006-3495 VL - 88 IS - 6 SP - 4312 EP - 4318 PB - Elsevier BV ER - TY - JOUR A1 - Wagner, Christian A1 - Hildenbrand, Georg A1 - Spöri, Udo A1 - Cremer, Christoph T1 - Beyond nanosizing: an approach to shape analysis of fluorescent nanostructures by SMI-microscopy JF - Optik KW - Fluoreszenzmikroskopie Y1 - 2006 U6 - https://doi.org/https://doi.org/10.1016/j.ijleo.2005.05.006 SN - 0030-4026 VL - 117 IS - 1 SP - 26 EP - 32 PB - Elsevier BV ER - TY - JOUR A1 - Wiech, Thorsten A1 - Stein, Stefan A1 - Lachenmaier, Victoria A1 - Schmitt, Eberhard A1 - Schwarz-Finsterle, Jutta A1 - Wiech, Elisabeth A1 - Hildenbrand, Georg A1 - Werner, Martin A1 - Hausmann, Michael T1 - Spatial allelic imbalance of BCL2 genes and chromosome 18 territories in nonneoplastic and neoplastic cervical squamous epithelium JF - European Biophysics Journal KW - Genom KW - Krebs, Medizin Y1 - 2009 U6 - https://doi.org/https://doi.org/10.1007/s00249-009-0474-5 SN - 0175-7571 VL - 38 IS - 6 SP - 793 EP - 806 PB - Springer Science and Business Media LLC ER - TY - JOUR A1 - Kaufmann, Rainer A1 - Müller, P A1 - Hildenbrand, Georg A1 - Hausmann, Michael A1 - Cremer, Christoph T1 - Analysis of Her2/neu membrane protein clusters in different types of breast cancer cells using localization microscopy BT - ANALYSIS OF HER2/neu MEMBRANE PROTEIN CLUSTERS JF - Journal of Microscopy KW - Krebs, Medizin KW - Brustkrebs Y1 - 2010 U6 - https://doi.org/https://doi.org/10.1111/j.1365-2818.2010.03436.x SN - 0022-2720 VL - 242 IS - 1 SP - 46 EP - 54 PB - Wiley ER - TY - JOUR A1 - Müller, Patrick A1 - Lemmermann, Niels A. A1 - Kaufmann, Rainer A1 - Gunkel, Manuel A1 - Paech, Daniel A1 - Hildenbrand, Georg A1 - Holtappels, Rafaela A1 - Cremer, Christoph A1 - Hausmann, Michael T1 - Spatial distribution and structural arrangement of a murine cytomegalovirus glycoprotein detected by SPDM localization microscopy JF - Histochemistry and Cell Biology KW - Fluoreszenzmikroskopie Y1 - 2014 U6 - https://doi.org/https://doi.org/10.1007/s00418-014-1185-2 SN - 0948-6143 VL - 142 IS - 1 SP - 61 EP - 67 PB - Springer Science and Business Media LLC ER - TY - JOUR A1 - Falk, Martin A1 - Hausmann, Michael A1 - Lukasova, Emilie A1 - Biswas, Abin A1 - Hildenbrand, Georg A1 - Davidkova, Marie A1 - Krasavin, Evgeny A1 - Kleibl, Zdenek A1 - Falkova, Iva A1 - Jezkova, Lucie A1 - Stefancikova, Lenka A1 - Sevcik, Jan A1 - Hofer, Michal A1 - Bacikova, Alena A1 - Matula, Pavel A1 - Boreyko, Alla A1 - Vachelova, Jana A1 - Michaelidesova, Anna A1 - Kozubek, Stanislav T1 - Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: Part - Structuromics JF - Critical Reviews in Eukaryotic Gene Expression KW - Radiologie Y1 - 2014 U6 - https://doi.org/https://doi.org/10.1615/CritRevEukaryotGeneExpr.v24.i3.40 SN - 1045-4403 VL - 24 IS - 3 SP - 225 EP - 247 PB - Begell House ER - TY - JOUR A1 - Falk, Martin A1 - Hausmann, Michael A1 - Lukasova, Emilie A1 - Biswas, Abin A1 - Hildenbrand, Georg A1 - Davidkova, Marie A1 - Krasavin, Evgeny A1 - Kleibl, Zdenek A1 - Falkova, Iva A1 - Jezkova, Lucie A1 - Stefancikova, Lenka A1 - Sevcik, Jan A1 - Hofer, Michal A1 - Bacikova, Alena A1 - Matula, Pavel A1 - Boreyko, Alla A1 - Vachelova, Jana A1 - Michaelidesova, Anna A1 - Kozubek, Stanislav T1 - Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: PART A-Radiomics JF - Critical Reviews in Eukaryotic Gene Expression KW - Radiologie Y1 - 2014 U6 - https://doi.org/https://doi.org/10.1615/CritRevEukaryotGeneExpr.2014010313 SN - 1045-4403 VL - 24 IS - 3 SP - 205 EP - 223 PB - Begell House ER - TY - JOUR A1 - Burger, Nina A1 - Biswas, Abin A1 - Barzan, Daniel A1 - Kirchner, Anne A1 - Hosser, Hiltraud A1 - Hausmann, Michael A1 - Hildenbrand, Georg A1 - Herskind, Carsten A1 - Wenz, Frederik A1 - Veldwijk, Marlon R. T1 - A method for the efficient cellular uptake and retention of small modified gold nanoparticles for the radiosensitization of cells JF - Nanomedicine: Nanotechnology, Biology and Medicine KW - Gold KW - Nanopartikel Y1 - 2014 U6 - https://doi.org/https://doi.org/10.1016/j.nano.2014.03.011 SN - 1549-9634 VL - 10 IS - 6 SP - 1365 EP - 1373 PB - Elsevier BV ER - TY - CHAP A1 - Hausmann, Michael A1 - Lee, Jin-Ho A1 - Hildenbrand, Georg T1 - 3D DNA FISH for analyses of chromatin-nuclear architecture T2 - Epigenetics Methods KW - Genom Y1 - 2020 SN - 9780128194140 U6 - https://doi.org/https://doi.org/10.1016/B978-0-12-819414-0.00020-3 SP - 399 EP - 418 PB - Elsevier ER - TY - CHAP A1 - Hausmann, Michael A1 - Pilarczyk, Götz A1 - Maus, Emanuel A1 - Hesser, Jürgen A1 - Hildenbrand, Georg T1 - Super-resolution microscopy of nanogold-labelling T2 - Nanoparticle Enhanced Radiation Therapy KW - Krebs, Medizin KW - Strahlentherapie Y1 - 2020 SN - 9780750323963 U6 - https://doi.org/https://doi.org/10.1088/978-0-7503-2396-3ch11 SP - 11 EP - 1 PB - IOP Publishing ER - TY - CHAP A1 - Falk, Martin A1 - Wolinsky, Michael A1 - Veldwijk, Marlon R. A1 - Hildenbrand, Georg A1 - Hausmann, Michael T1 - Gold nanoparticle enhanced radiosensitivity of cells: considerations and contradictions from model systems and basic investigations of cell damaging for radiation therapy T2 - Nanoparticle Enhanced Radiation Therapy KW - Krebs, Medizin KW - Strahlentherapie Y1 - 2020 SN - 9780750323963 U6 - https://doi.org/https://doi.org/10.1088/978-0-7503-2396-3ch10 SP - 10 EP - 1 PB - IOP Publishing ER - TY - GEN A1 - Lee, Jin-Ho A1 - Bobkova, Elizaveta A1 - Gier, Theresa A1 - Gote, Martin A1 - Schmidt-kaler, Fanz A1 - Brieger, Emily A1 - Maus, Emanuel A1 - Krufczik, Matthias A1 - Chojowski, Robert A1 - Korn, Friederike A1 - Sarah, Schumann A1 - Scherthan, Harry A1 - Falkova, Iva A1 - Falk, Martin A1 - Hausmann, Michael A1 - Hildenbrand, Georg T1 - Mechanisms and Challenges for Understanding Radiation Induced Changes in Chromatin Nanoarchitecture T2 - DRO 2018 N2 - The three-dimensional architecture of genomes acts as an additional level of mode for fundamental biological processes such as DNA damage response. In this context, nanoprobing and super-resolution microscopy are powerful methods for structural analyses of genomic targets in native chromatin of single cells at resolutions of single antibodies, proteins, histones, short DNA stretches, etc. We used multi-color chromatin nanoprobing and single molecule localization microscopy of established DNA damage and chromatin markers in 3D-conserved nuclei of different cell types exposed to various types and doses of ionizing radiation. Similarly, effect of gold nanoparticles on extent and direction of cellular radiation response was assessed. Our studies revealed the nanoarchitecture of damage foci with respect to γH2AX, Mre11 or 53BP1 and their molecular rearrangements during repair processes. Nanoscopy of genomic Alu resulted in linear-quadratic dose-effects for low to higher dose ranges and in changes of H3K9me3 distribution around Alu clusters upon radiation exposure. Preliminary results show post-irradiation time dependent changes in Alu chromatin. Moreover, gold nanoparticles incorporated into cells seem to act by an interplay of radiation enhancement and chromatin remodeling leading to altered radiosensitivity. Our results contribute to the understanding of cellular radiation responses, thereby laying the basis for improved biological dosimetry and radiotherapies in future. N2 - Poster KW - Genom Y1 - 2019 U6 - https://doi.org/https://doi.org/10.13140/RG.2.2.31391.20647 ER - TY - JOUR A1 - Ngwa, Wilfred A1 - Boateng, Francis A1 - Kumar, Rajiv A1 - Irvine, Darrell J. A1 - Formenti, Silvia A1 - Ngoma, Twalib A1 - Herskind, Carsten A1 - Veldwijk, Marlon R. A1 - Hildenbrand, Georg A1 - Hausmann, Michael A1 - Wenz, Frederik A1 - Hesser, Jürgen T1 - Smart Radiation Therapy Biomaterials JF - International Journal of Radiation Oncology*Biology*Physics KW - Krebs, Medizin KW - Strahlentherapie Y1 - 2017 U6 - https://doi.org/https://doi.org/10.1016/j.ijrobp.2016.10.034 SN - 0360-3016 VL - 97 IS - 3 SP - 624 EP - 637 PB - Elsevier BV ER - TY - JOUR A1 - Stuhlmüller, Michael A1 - Schwarz-Finsterle, Jutta A1 - Fey, Evelyn A1 - Lux, Johannes A1 - Bach, Margund A1 - Cremer, Christoph A1 - Hinderhofer, Katrin A1 - Hausmann, Michael A1 - Hildenbrand, Georg T1 - In situ optical sequencing and structure analysis of a trinucleotide repeat genome region by localization microscopy after specific COMBO-FISH nano-probing JF - Nanoscale KW - Genom Y1 - 2015 U6 - https://doi.org/https://doi.org/10.1039/C5NR04141D SN - 2040-3364 VL - 7 IS - 42 SP - 17938 EP - 17946 PB - Royal Society of Chemistry (RSC) ER - TY - JOUR A1 - Moser, Felipe A1 - Hildenbrand, Georg A1 - Müller, Patrick A1 - Al Saroori, Alexander A1 - Biswas, Abin A1 - Bach, Margund A1 - Wenz, Frederik A1 - Cremer, Christoph A1 - Burger, Nina A1 - Veldwijk, Marlon R. A1 - Hausmann, Michael T1 - Cellular Uptake of Gold Nanoparticles and Their Behavior as Labels for Localization Microscopy JF - Biophysical Journal KW - Krebs, Medizin KW - Strahlentherapie Y1 - 2016 U6 - https://doi.org/https://doi.org/10.1016/j.bpj.2016.01.004 SN - 0006-3495 VL - 110 IS - 4 SP - 947 EP - 953 PB - Elsevier BV ER - TY - JOUR A1 - Bosiek, Katharina A1 - Hausmann, Michael A1 - Hildenbrand, Georg T1 - Perspectives on Comets, Comet-like Asteroids, and Their Predisposition to Provide an Environment That Is Friendly to Life JF - Astrobiology KW - Komet KW - Planetoid Y1 - 2016 U6 - https://doi.org/https://doi.org/10.1089/ast.2015.1354 SN - 1531-1074 VL - 16 IS - 4 SP - 311 EP - 323 PB - Mary Ann Liebert Inc ER - TY - JOUR A1 - Sievers, Aaron A1 - Bosiek, Katharina A1 - Bisch, Marc A1 - Dreessen, Chris A1 - Riedel, Jascha A1 - Froß, Patrick A1 - Hausmann, Michael A1 - Hildenbrand, Georg T1 - K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features JF - Genes N2 - In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4) on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of standard k-mer analysis. KW - Genom Y1 - 2017 U6 - https://doi.org/https://doi.org/10.3390/genes8040122 SN - 2073-4425 VL - 8 IS - 4 PB - MDPI AG ER - TY - JOUR A1 - Krufczik, Matthias A1 - Sievers, Aaron A1 - Hausmann, Annkathrin A1 - Lee, Jin-Ho A1 - Hildenbrand, Georg A1 - Schaufler, Wladimir A1 - Hausmann, Michael T1 - Combining Low Temperature Fluorescence DNA-Hybridization, Immunostaining, and Super-Resolution Localization Microscopy for Nano-Structure Analysis of ALU Elements and Their Influence on Chromatin Structure JF - International Journal of Molecular Sciences N2 - Immunostaining and fluorescence in situ hybridization (FISH) are well established methods for specific labelling of chromatin in the cell nucleus. COMBO-FISH (combinatorial oligonucleotide fluorescence in situ hybridization) is a FISH method using computer designed oligonucleotide probes specifically co-localizing at given target sites. In combination with super resolution microscopy which achieves spatial resolution far beyond the Abbe Limit, it allows new insights into the nano-scaled structure and organization of the chromatin of the nucleus. To avoid nano-structural changes of the chromatin, the COMBO-FISH labelling protocol was optimized omitting heat treatment for denaturation of the target. As an example, this protocol was applied to ALU elements—dispersed short stretches of DNA which appear in different kinds in large numbers in primate genomes. These ALU elements seem to be involved in gene regulation, genomic diversity, disease induction, DNA repair, etc. By computer search, we developed a unique COMBO-FISH probe which specifically binds to ALU consensus elements and combined this DNA–DNA labelling procedure with heterochromatin immunostainings in formaldehyde-fixed cell specimens. By localization microscopy, the chromatin network-like arrangements of ALU oligonucleotide repeats and heterochromatin antibody labelling sites were simultaneously visualized and quantified. This novel approach which simultaneously combines COMBO-FISH and immunostaining was applied to chromatin analysis on the nanoscale after low-linear-energy-transfer (LET) radiation exposure at different doses. Dose-correlated curves were obtained from the amount of ALU representing signals, and the chromatin re-arrangements during DNA repair after irradiation were quantitatively studied on the nano-scale. Beyond applications in radiation research, the labelling strategy of immunostaining and COMBO-FISH with localization microscopy will also offer new potentials for analyses of subcellular elements in combination with other specific chromatin targets. KW - Genom Y1 - 2017 U6 - https://doi.org/https://doi.org/10.3390/ijms18051005 SN - 1422-0067 VL - 18 IS - 5 PB - MDPI AG ER - TY - JOUR A1 - Hausmann, Michael A1 - Ilić, Nataša A1 - Pilarczyk, Götz A1 - Lee, Jin-Ho A1 - Logeswaran, Abiramy A1 - Borroni, Aurora A1 - Krufczik, Matthias A1 - Theda, Franziska A1 - Waltrich, Nadine A1 - Bestvater, Felix A1 - Hildenbrand, Georg A1 - Cremer, Christoph A1 - Blank, Michael T1 - Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research JF - International Journal of Molecular Sciences N2 - Understanding molecular interactions and regulatory mechanisms in tumor initiation, progression, and treatment response are key requirements towards advanced cancer diagnosis and novel treatment procedures in personalized medicine. Beyond decoding the gene expression, malfunctioning and cancer-related epigenetic pathways, investigations of the spatial receptor arrangements in membranes and genome organization in cell nuclei, on the nano-scale, contribute to elucidating complex molecular mechanisms in cells and tissues. By these means, the correlation between cell function and spatial organization of molecules or molecular complexes can be studied, with respect to carcinogenesis, tumor sensitivity or tumor resistance to anticancer therapies, like radiation or antibody treatment. Here, we present several new applications for bio-molecular nano-probes and super-resolution, laser fluorescence localization microscopy and their potential in life sciences, especially in biomedical and cancer research. By means of a tool-box of fluorescent antibodies, green fluorescent protein (GFP) tagging, or specific oligonucleotides, we present tumor relevant re-arrangements of Erb-receptors in membranes, spatial organization of Smad specific ubiquitin protein ligase 2 (Smurf2) in the cytosol, tumor cell characteristic heterochromatin organization, and molecular re-arrangements induced by radiation or antibody treatment. The main purpose of this article is to demonstrate how nano-scaled distance measurements between bio-molecules, tagged by appropriate nano-probes, can be applied to elucidate structures and conformations of molecular complexes which are characteristic of tumorigenesis and treatment responses. These applications open new avenues towards a better interpretation of the spatial organization and treatment responses of functionally relevant molecules, at the single cell level, in normal and cancer cells, offering new potentials for individualized medicine. KW - Krebs, Medizin KW - Strahlentherapie Y1 - 2017 U6 - https://doi.org/https://doi.org/10.3390/ijms18102066 SN - 1422-0067 VL - 18 IS - 10 PB - MDPI AG ER -