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 - 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 - 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 - JOUR A1 - Sievers, Aaron A1 - Wenz, Frederik A1 - Hausmann, Michael A1 - Hildenbrand, Georg T1 - Conservation of k-mer Composition and Correlation Contribution between Introns and Intergenic Regions of Animalia Genomes JF - Genes N2 - In this study, we pairwise-compared multiple genome regions, including genes, exons, coding DNA sequences (CDS), introns, and intergenic regions of 39 Animalia genomes, including Deuterostomia (27 species) and Protostomia (12 species), by applying established k-mer-based (alignment-free) comparison methods. We found strong correlations between the sequence structure of introns and intergenic regions, individual organisms, and within wider phylogenetical ranges, indicating the conservation of certain structures over the full range of analyzed organisms. We analyzed these sequence structures by quantifying the contribution of different sets of DNA words to the average correlation value by decomposing the correlation coefficients with respect to these word sets. We found that the conserved structures within introns, intergenic regions, and between the two were mainly a result of conserved tandem repeats with repeat units ≤ 2 bp (e.g., (AT)n), while other conserved sequence structures, such as those found between exons and CDS, were dominated by tandem repeats with repeat unit sizes of 3 bp in length and more complex DNA word patterns. We conclude that the conservation between intron and intergenic regions indicates a shared function of these sequence structures. Also, the similar differences in conserved structures with known origin, especially to the conservation between exons and CDS resulting from DNA codons, indicate that k-mer composition-based functional properties of introns and intergenic regions may differ from those of exons and CDS. KW - Genom Y1 - 2018 U6 - https://doi.org/https://doi.org/10.3390/genes9100482 SN - 2073-4425 VL - 9 IS - 10 PB - MDPI AG ER - TY - JOUR A1 - Eryilmaz, Marion A1 - Schmitt, Eberhard A1 - Krufczik, Matthias A1 - Theda, Franziska A1 - Lee, Jin-Ho A1 - Cremer, Christoph A1 - Bestvater, Felix A1 - Schaufler, Wladimir A1 - Hausmann, Michael A1 - Hildenbrand, Georg T1 - Localization Microscopy Analyses of MRE11 Clusters in 3D-Conserved Cell Nuclei of Different Cell Lines JF - Cancers N2 - In radiation biophysics, it is a subject of nowadays research to investigate DNA strand break repair in detail after damage induction by ionizing radiation. It is a subject of debate as to what makes up the cell’s decision to use a certain repair pathway and how the repair machinery recruited in repair foci is spatially and temporarily organized. Single-molecule localization microscopy (SMLM) allows super-resolution analysis by precise localization of single fluorescent molecule tags, resulting in nuclear structure analysis with a spatial resolution in the 10 nm regime. Here, we used SMLM to study MRE11 foci. MRE11 is one of three proteins involved in the MRN-complex (MRE11-RAD50-NBS1 complex), a prominent DNA strand resection and broken end bridging component involved in homologous recombination repair (HRR) and alternative non-homologous end joining (a-NHEJ). We analyzed the spatial arrangements of antibody-labelled MRE11 proteins in the nuclei of a breast cancer and a skin fibroblast cell line along a time-course of repair (up to 48 h) after irradiation with a dose of 2 Gy. Different kinetics for cluster formation and relaxation were determined. Changes in the internal nano-scaled structure of the clusters were quantified and compared between the two cell types. The results indicate a cell type-dependent DNA damage response concerning MRE11 recruitment and cluster formation. The MRE11 data were compared to H2AX phosphorylation detected by γH2AX molecule distribution. These data suggested modulations of MRE11 signal frequencies that were not directly correlated to DNA damage induction. The application of SMLM in radiation biophysics offers new possibilities to investigate spatial foci organization after DNA damaging and during subsequent repair. KW - Krebs, Medizin KW - Strahlentherapie KW - Brustkrebs Y1 - 2018 U6 - https://doi.org/https://doi.org/10.3390/cancers10010025 SN - 2072-6694 VL - 10 IS - 1 PB - MDPI AG ER - TY - JOUR A1 - Sievers, Aaron A1 - Sauer, Liane A1 - Hausmann, Michael A1 - Hildenbrand, Georg T1 - Eukaryotic Genomes Show Strong Evolutionary Conservation of k-mer Composition and Correlation Contributions between Introns and Intergenic Regions JF - Genes N2 - Several strongly conserved DNA sequence patterns in and between introns and intergenic regions (IIRs) consisting of short tandem repeats (STRs) with repeat lengths <3 bp have already been described in the kingdom of Animalia. In this work, we expanded the search and analysis of conserved DNA sequence patterns to a wider range of eukaryotic genomes. Our aims were to confirm the conservation of these patterns, to support the hypothesis on their functional constraints and/or the identification of unknown patterns. We pairwise compared genomic DNA sequences of genes, exons, CDS, introns and intergenic regions of 34 Embryophyta (land plants), 30 Protista and 29 Fungi using established k-mer-based (alignment-free) comparison methods. Additionally, the results were compared with values derived for Animalia in former studies. We confirmed strong correlations between the sequence structures of IIRs spanning over the entire domain of Eukaryotes. We found that the high correlations within introns, intergenic regions and between the two are a result of conserved abundancies of STRs with repeat units ≤2 bp (e.g., (AT)n). For some sequence patterns and their inverse complementary sequences, we found a violation of equal distribution on complementary DNA strands in a subset of genomes. Looking at mismatches within the identified STR patterns, we found specific preferences for certain nucleotides stable over all four phylogenetic kingdoms. We conclude that all of these conserved patterns between IIRs indicate a shared function of these sequence structures related to STRs. KW - Genom KW - Eukaryoten Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/genes12101571 SN - 2073-4425 VL - 12 IS - 10 PB - MDPI AG ER - TY - JOUR A1 - Paschek, Klaus A1 - Roßmann, Arthur A1 - Hausmann, Michael A1 - Hildenbrand, Georg T1 - Analysis of Tidal Accelerations in the Solar System and in Extrasolar Planetary Systems JF - Applied Sciences N2 - Volcanism powered by tidal forces inside celestial bodies can provide enough energy to keep important solvents for living systems in the liquid phase. A prerequisite to calculate such tidal interactions and consequences is depending on simulations for tidal accelerations in a multi-body system. Unfortunately, from measurements in many extrasolar planetary systems, only few physical and orbital parameters are well-known enough for investigated celestial bodies. For calculating tidal acceleration vectors under missing most orbital parameter exactly, a simulation method is developed that is only based on a few basic parameters, easily measurable even in extrasolar planetary systems. Such a method as the one presented here allows finding a relation between the tidal acceleration vectors and potential heating inside celestial objects. Using the values and results of our model approach to our solar system as a “gold standard” for feasibility allowed us to classify this heating in relation to different forms of volcanism. This “gold standard” approach gave us a classification measure for the relevance of tidal heating in other extrasolar systems with a reduced availability of exact physical parameters. We help to estimate conditions for the identification of potential candidates for further sophisticated investigations by more complex established methods such as viscoelastic multi-body theories. As a first example, we applied the procedures developed here to the extrasolar planetary system TRAPPIST-1 as an example to check our working hypothesis. KW - Sonnensystem KW - Vulkanismus Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/app11188624 SN - 2076-3417 VL - 11 IS - 18 PB - MDPI AG ER - TY - INPR A1 - Paschek, Klaus A1 - Roßmann, Arthur A1 - Hausmann, Michael A1 - Hildenbrand, Georg T1 - Analysis of Tidal Accelerations in the Solar System and in Extrasolar Planetary Systems N2 - Volcanism powered by tidal forces inside celestial bodies can provide enough energy to keep important solvents for living systems in the liquid phase. Moreover, tidal forces and their environmental consequences may strongly influence habitability of planets and other celestial bodies and may result in special forms of live and living conditions. A prerequisite to calculate such tidal interactions and consequences is depending on simulations for tidal accelerations in a multi-body system. Unfortunately, from measurements in many extrasolar planetary systems only few physical and orbital parameters are well enough known for investigated celestial bodies. For calculating tidal acceleration vectors under missing most orbital parameter exactly, a simulation method is developed that is only based on a few basic parameters, easily measurable even in extrasolar planetary systems. Such a method as being presented here, allows finding a relation between the tidal acceleration vectors and potential heating inside celestial objects. Using values and results of our model approach to our solar system as a “gold standard” for feasibility allowed us to classify this heating in relation to different forms of volcanism. This “gold standard” approach gave us a classification measure for the relevance of tidal heating in other extrasolar systems with a reduced availability of exact physical parameters. We would help to estimate conditions for the identification of potential candidates for further sophisticated investigations by more complex established methods like viscoelastic multi-body theories. As a first example, we applied the procedures developed here to the extrasolar planetary system TRAPPIST-1 as an example to check our working hypothesis. KW - Sonnensystem KW - Vulkanismus Y1 - 2021 U6 - https://doi.org/https://doi.org/10.20944/preprints202107.0408.v1 PB - MDPI AG ER - TY - CHAP A1 - Hausmann, Michael A1 - Neitzel, Charlotte A1 - Hahn, Hannes A1 - Winter, Ruth A1 - Falkova, Iva A1 - Heermann, Dieter W. A1 - Pilarczyk, Götz A1 - Hildenbrand, Georg A1 - Scherthan, Harry A1 - Falk, Martin T1 - Space and Time in the Universe of the Cell Nucleus after Ionizing Radiation Attacks: A Comparison of Cancer and Non-Cancer Cell Response T2 - The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response KW - Krebszelle KW - Strahlentherapie KW - Zellkern Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/IECC2021-09219 PB - MDPI CY - Basel Switzerland ER - 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 - 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 -