@article{SchaeferHildenbrandHausmann2024, author = {Sch{\"a}fer, Myriam and Hildenbrand, Georg and Hausmann, Michael}, title = {Impact of Gold Nanoparticles and Ionizing Radiation on Whole Chromatin Organization as Detected by Single-Molecule Localization Microscopy}, series = {International Journal of Molecular Sciences}, volume = {25}, journal = {International Journal of Molecular Sciences}, number = {23}, publisher = {MDPI AG}, issn = {1422-0067}, doi = {https://doi.org/10.3390/ijms252312843}, year = {2024}, abstract = {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.}, subject = {Krebs, Medizin}, language = {en} } @article{FaillaAlbrechtSpoerietal.2003, author = {Failla, Antonio Virgillo and Albrecht, Benno and Sp{\"o}ri, U. and Schweitzer, A. and Kroll, A. and Hildenbrand, Georg and Bach, M. and Cremer, Christoph}, title = {Nanostructure Analysis Using Spatially Modulated Illumination Microscopy}, series = {Complexus}, volume = {1}, journal = {Complexus}, number = {2}, publisher = {S. Karger AG}, issn = {1424-8492}, doi = {https://doi.org/10.1159/000070464}, pages = {77 -- 88}, year = {2003}, abstract = {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.}, subject = {Fluoreszenzmikroskopie}, language = {en} } @article{HildenbrandRappSpoerietal.2005, author = {Hildenbrand, Georg and Rapp, Alexander and Sp{\"o}ri, Udo and Wagner, Christian and Cremer, Christoph and Hausmann, Michael}, title = {Nano-Sizing of Specific Gene Domains in Intact Human Cell Nuclei by Spatially Modulated Illumination Light Microscopy}, series = {Biophysical Journal}, volume = {88}, journal = {Biophysical Journal}, number = {6}, publisher = {Elsevier BV}, issn = {0006-3495}, doi = {https://doi.org/10.1529/biophysj.104.056796}, pages = {4312 -- 4318}, year = {2005}, subject = {Genom}, language = {en} } @article{WagnerHildenbrandSpoerietal.2006, author = {Wagner, Christian and Hildenbrand, Georg and Sp{\"o}ri, Udo and Cremer, Christoph}, title = {Beyond nanosizing: an approach to shape analysis of fluorescent nanostructures by SMI-microscopy}, series = {Optik}, volume = {117}, journal = {Optik}, number = {1}, publisher = {Elsevier BV}, issn = {0030-4026}, doi = {https://doi.org/10.1016/j.ijleo.2005.05.006}, pages = {26 -- 32}, year = {2006}, subject = {Fluoreszenzmikroskopie}, language = {en} } @article{WiechSteinLachenmaieretal.2009, author = {Wiech, Thorsten and Stein, Stefan and Lachenmaier, Victoria and Schmitt, Eberhard and Schwarz-Finsterle, Jutta and Wiech, Elisabeth and Hildenbrand, Georg and Werner, Martin and Hausmann, Michael}, title = {Spatial allelic imbalance of BCL2 genes and chromosome 18 territories in nonneoplastic and neoplastic cervical squamous epithelium}, series = {European Biophysics Journal}, volume = {38}, journal = {European Biophysics Journal}, number = {6}, publisher = {Springer Science and Business Media LLC}, issn = {0175-7571}, doi = {https://doi.org/10.1007/s00249-009-0474-5}, pages = {793 -- 806}, year = {2009}, subject = {Genom}, language = {en} } @article{KaufmannMuellerHildenbrandetal.2010, author = {Kaufmann, Rainer and M{\"u}ller, P and Hildenbrand, Georg and Hausmann, Michael and Cremer, Christoph}, title = {Analysis of Her2/neu membrane protein clusters in different types of breast cancer cells using localization microscopy}, series = {Journal of Microscopy}, volume = {242}, journal = {Journal of Microscopy}, number = {1}, publisher = {Wiley}, issn = {0022-2720}, doi = {https://doi.org/10.1111/j.1365-2818.2010.03436.x}, pages = {46 -- 54}, year = {2010}, subject = {Krebs, Medizin}, language = {en} } @article{MuellerLemmermannKaufmannetal.2014, author = {M{\"u}ller, Patrick and Lemmermann, Niels A. and Kaufmann, Rainer and Gunkel, Manuel and Paech, Daniel and Hildenbrand, Georg and Holtappels, Rafaela and Cremer, Christoph and Hausmann, Michael}, title = {Spatial distribution and structural arrangement of a murine cytomegalovirus glycoprotein detected by SPDM localization microscopy}, series = {Histochemistry and Cell Biology}, volume = {142}, journal = {Histochemistry and Cell Biology}, number = {1}, publisher = {Springer Science and Business Media LLC}, issn = {0948-6143}, doi = {https://doi.org/10.1007/s00418-014-1185-2}, pages = {61 -- 67}, year = {2014}, subject = {Fluoreszenzmikroskopie}, language = {en} } @article{FalkHausmannLukasovaetal.2014, author = {Falk, Martin and Hausmann, Michael and Lukasova, Emilie and Biswas, Abin and Hildenbrand, Georg and Davidkova, Marie and Krasavin, Evgeny and Kleibl, Zdenek and Falkova, Iva and Jezkova, Lucie and Stefancikova, Lenka and Sevcik, Jan and Hofer, Michal and Bacikova, Alena and Matula, Pavel and Boreyko, Alla and Vachelova, Jana and Michaelidesova, Anna and Kozubek, Stanislav}, title = {Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: Part - Structuromics}, series = {Critical Reviews in Eukaryotic Gene Expression}, volume = {24}, journal = {Critical Reviews in Eukaryotic Gene Expression}, number = {3}, publisher = {Begell House}, issn = {1045-4403}, doi = {https://doi.org/10.1615/CritRevEukaryotGeneExpr.v24.i3.40}, pages = {225 -- 247}, year = {2014}, subject = {Radiologie}, language = {en} } @article{FalkHausmannLukasovaetal.2014, author = {Falk, Martin and Hausmann, Michael and Lukasova, Emilie and Biswas, Abin and Hildenbrand, Georg and Davidkova, Marie and Krasavin, Evgeny and Kleibl, Zdenek and Falkova, Iva and Jezkova, Lucie and Stefancikova, Lenka and Sevcik, Jan and Hofer, Michal and Bacikova, Alena and Matula, Pavel and Boreyko, Alla and Vachelova, Jana and Michaelidesova, Anna and Kozubek, Stanislav}, title = {Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: PART A-Radiomics}, series = {Critical Reviews in Eukaryotic Gene Expression}, volume = {24}, journal = {Critical Reviews in Eukaryotic Gene Expression}, number = {3}, publisher = {Begell House}, issn = {1045-4403}, doi = {https://doi.org/10.1615/CritRevEukaryotGeneExpr.2014010313}, pages = {205 -- 223}, year = {2014}, subject = {Radiologie}, language = {en} } @article{BurgerBiswasBarzanetal.2014, author = {Burger, Nina and Biswas, Abin and Barzan, Daniel and Kirchner, Anne and Hosser, Hiltraud and Hausmann, Michael and Hildenbrand, Georg and Herskind, Carsten and Wenz, Frederik and Veldwijk, Marlon R.}, title = {A method for the efficient cellular uptake and retention of small modified gold nanoparticles for the radiosensitization of cells}, series = {Nanomedicine: Nanotechnology, Biology and Medicine}, volume = {10}, journal = {Nanomedicine: Nanotechnology, Biology and Medicine}, number = {6}, publisher = {Elsevier BV}, issn = {1549-9634}, doi = {https://doi.org/10.1016/j.nano.2014.03.011}, pages = {1365 -- 1373}, year = {2014}, subject = {Gold}, language = {en} } @incollection{HausmannLeeHildenbrand2020, author = {Hausmann, Michael and Lee, Jin-Ho and Hildenbrand, Georg}, title = {3D DNA FISH for analyses of chromatin-nuclear architecture}, series = {Epigenetics Methods}, booktitle = {Epigenetics Methods}, publisher = {Elsevier}, isbn = {9780128194140}, doi = {https://doi.org/10.1016/B978-0-12-819414-0.00020-3}, pages = {399 -- 418}, year = {2020}, subject = {Genom}, language = {en} } @incollection{HausmannPilarczykMausetal.2020, author = {Hausmann, Michael and Pilarczyk, G{\"o}tz and Maus, Emanuel and Hesser, J{\"u}rgen and Hildenbrand, Georg}, title = {Super-resolution microscopy of nanogold-labelling}, series = {Nanoparticle Enhanced Radiation Therapy}, booktitle = {Nanoparticle Enhanced Radiation Therapy}, publisher = {IOP Publishing}, isbn = {9780750323963}, doi = {https://doi.org/10.1088/978-0-7503-2396-3ch11}, pages = {11 -- 1}, year = {2020}, subject = {Krebs, Medizin}, language = {en} } @incollection{FalkWolinskyVeldwijketal.2020, author = {Falk, Martin and Wolinsky, Michael and Veldwijk, Marlon R. and Hildenbrand, Georg and Hausmann, Michael}, title = {Gold nanoparticle enhanced radiosensitivity of cells: considerations and contradictions from model systems and basic investigations of cell damaging for radiation therapy}, series = {Nanoparticle Enhanced Radiation Therapy}, booktitle = {Nanoparticle Enhanced Radiation Therapy}, publisher = {IOP Publishing}, isbn = {9780750323963}, doi = {https://doi.org/10.1088/978-0-7503-2396-3ch10}, pages = {10 -- 1}, year = {2020}, subject = {Krebs, Medizin}, language = {en} } @misc{LeeBobkovaGieretal.2019, author = {Lee, Jin-Ho and Bobkova, Elizaveta and Gier, Theresa and Gote, Martin and Schmidt-kaler, Fanz and Brieger, Emily and Maus, Emanuel and Krufczik, Matthias and Chojowski, Robert and Korn, Friederike and Sarah, Schumann and Scherthan, Harry and Falkova, Iva and Falk, Martin and Hausmann, Michael and Hildenbrand, Georg}, title = {Mechanisms and Challenges for Understanding Radiation Induced Changes in Chromatin Nanoarchitecture}, series = {DRO 2018}, journal = {DRO 2018}, doi = {https://doi.org/10.13140/RG.2.2.31391.20647}, year = {2019}, abstract = {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.}, subject = {Genom}, language = {en} } @article{NgwaBoatengKumaretal.2017, author = {Ngwa, Wilfred and Boateng, Francis and Kumar, Rajiv and Irvine, Darrell J. and Formenti, Silvia and Ngoma, Twalib and Herskind, Carsten and Veldwijk, Marlon R. and Hildenbrand, Georg and Hausmann, Michael and Wenz, Frederik and Hesser, J{\"u}rgen}, title = {Smart Radiation Therapy Biomaterials}, series = {International Journal of Radiation Oncology*Biology*Physics}, volume = {97}, journal = {International Journal of Radiation Oncology*Biology*Physics}, number = {3}, publisher = {Elsevier BV}, issn = {0360-3016}, doi = {https://doi.org/10.1016/j.ijrobp.2016.10.034}, pages = {624 -- 637}, year = {2017}, subject = {Krebs, Medizin}, language = {en} } @article{StuhlmuellerSchwarzFinsterleFeyetal.2015, author = {Stuhlm{\"u}ller, Michael and Schwarz-Finsterle, Jutta and Fey, Evelyn and Lux, Johannes and Bach, Margund and Cremer, Christoph and Hinderhofer, Katrin and Hausmann, Michael and Hildenbrand, Georg}, title = {In situ optical sequencing and structure analysis of a trinucleotide repeat genome region by localization microscopy after specific COMBO-FISH nano-probing}, series = {Nanoscale}, volume = {7}, journal = {Nanoscale}, number = {42}, publisher = {Royal Society of Chemistry (RSC)}, issn = {2040-3364}, doi = {https://doi.org/10.1039/C5NR04141D}, pages = {17938 -- 17946}, year = {2015}, subject = {Genom}, language = {en} } @article{MoserHildenbrandMuelleretal.2016, author = {Moser, Felipe and Hildenbrand, Georg and M{\"u}ller, Patrick and Al Saroori, Alexander and Biswas, Abin and Bach, Margund and Wenz, Frederik and Cremer, Christoph and Burger, Nina and Veldwijk, Marlon R. and Hausmann, Michael}, title = {Cellular Uptake of Gold Nanoparticles and Their Behavior as Labels for Localization Microscopy}, series = {Biophysical Journal}, volume = {110}, journal = {Biophysical Journal}, number = {4}, publisher = {Elsevier BV}, issn = {0006-3495}, doi = {https://doi.org/10.1016/j.bpj.2016.01.004}, pages = {947 -- 953}, year = {2016}, subject = {Krebs, Medizin}, language = {en} } @article{BosiekHausmannHildenbrand2016, author = {Bosiek, Katharina and Hausmann, Michael and Hildenbrand, Georg}, title = {Perspectives on Comets, Comet-like Asteroids, and Their Predisposition to Provide an Environment That Is Friendly to Life}, series = {Astrobiology}, volume = {16}, journal = {Astrobiology}, number = {4}, publisher = {Mary Ann Liebert Inc}, issn = {1531-1074}, doi = {https://doi.org/10.1089/ast.2015.1354}, pages = {311 -- 323}, year = {2016}, subject = {Komet}, language = {en} } @article{SieversBosiekBischetal.2017, author = {Sievers, Aaron and Bosiek, Katharina and Bisch, Marc and Dreessen, Chris and Riedel, Jascha and Froß, Patrick and Hausmann, Michael and Hildenbrand, Georg}, title = {K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features}, series = {Genes}, volume = {8}, journal = {Genes}, number = {4}, publisher = {MDPI AG}, issn = {2073-4425}, doi = {https://doi.org/10.3390/genes8040122}, year = {2017}, abstract = {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.}, subject = {Genom}, language = {en} } @article{KrufczikSieversHausmannetal.2017, author = {Krufczik, Matthias and Sievers, Aaron and Hausmann, Annkathrin and Lee, Jin-Ho and Hildenbrand, Georg and Schaufler, Wladimir and Hausmann, Michael}, title = {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}, series = {International Journal of Molecular Sciences}, volume = {18}, journal = {International Journal of Molecular Sciences}, number = {5}, publisher = {MDPI AG}, issn = {1422-0067}, doi = {https://doi.org/10.3390/ijms18051005}, year = {2017}, abstract = {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.}, subject = {Genom}, language = {en} } @article{HausmannIlićPilarczyketal.2017, author = {Hausmann, Michael and Ilić, Nataša and Pilarczyk, G{\"o}tz and Lee, Jin-Ho and Logeswaran, Abiramy and Borroni, Aurora and Krufczik, Matthias and Theda, Franziska and Waltrich, Nadine and Bestvater, Felix and Hildenbrand, Georg and Cremer, Christoph and Blank, Michael}, title = {Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research}, series = {International Journal of Molecular Sciences}, volume = {18}, journal = {International Journal of Molecular Sciences}, number = {10}, publisher = {MDPI AG}, issn = {1422-0067}, doi = {https://doi.org/10.3390/ijms18102066}, year = {2017}, abstract = {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.}, subject = {Krebs, Medizin}, language = {en} } @article{HildenbrandMetzlerPilarczyketal.2018, author = {Hildenbrand, Georg and Metzler, Philipp and Pilarczyk, G{\"o}tz and Bobu, Vladimir and Kriz, Wilhelm and Hosser, Hiltraud and Fleckenstein, Jens and Krufczik, Matthias and Bestvater, Felix and Wenz, Frederik and Hausmann, Michael}, title = {Dose enhancement effects of gold nanoparticles specifically targeting RNA in breast cancer cells}, series = {PLOS ONE}, volume = {13}, journal = {PLOS ONE}, number = {1}, editor = {Baptista, Pedro V.}, publisher = {Public Library of Science (PLoS)}, issn = {1932-6203}, doi = {https://doi.org/10.1371/journal.pone.0190183}, year = {2018}, subject = {Krebs, Medizin}, language = {en} } @article{EryilmazSchmittKrufcziketal.2018, author = {Eryilmaz, Marion and Schmitt, Eberhard and Krufczik, Matthias and Theda, Franziska and Lee, Jin-Ho and Cremer, Christoph and Bestvater, Felix and Schaufler, Wladimir and Hausmann, Michael and Hildenbrand, Georg}, title = {Localization Microscopy Analyses of MRE11 Clusters in 3D-Conserved Cell Nuclei of Different Cell Lines}, series = {Cancers}, volume = {10}, journal = {Cancers}, number = {1}, publisher = {MDPI AG}, issn = {2072-6694}, doi = {https://doi.org/10.3390/cancers10010025}, year = {2018}, abstract = {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.}, subject = {Krebs, Medizin}, language = {en} } @article{SieversWenzHausmannetal.2018, author = {Sievers, Aaron and Wenz, Frederik and Hausmann, Michael and Hildenbrand, Georg}, title = {Conservation of k-mer Composition and Correlation Contribution between Introns and Intergenic Regions of Animalia Genomes}, series = {Genes}, volume = {9}, journal = {Genes}, number = {10}, publisher = {MDPI AG}, issn = {2073-4425}, doi = {https://doi.org/10.3390/genes9100482}, year = {2018}, abstract = {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.}, subject = {Genom}, language = {en} } @article{HausmannWinklerHildenbrandetal.2003, author = {Hausmann, Michael and Winkler, Ralph and Hildenbrand, Georg and Finsterle, Jutta and Weisel, Andrea and Rapp, Alexander and Schmitt, Eberhard and Janz, Siegfried and Cremer, Christoph}, title = {COMBO-FISH: specific labeling of nondenatured chromatin targets by computer-selected DNA oligonucleotide probe combinations}, series = {BioTechniques}, volume = {35}, journal = {BioTechniques}, number = {3}, publisher = {Informa UK Limited}, issn = {0736-6205}, doi = {https://doi.org/10.2144/03353rr03}, pages = {564 -- 577}, year = {2003}, subject = {Genom}, language = {en} } @article{BobkovaDepesLeeetal.2018, author = {Bobkova, Elizaveta and Depes, Daniel and Lee, Jin-Ho and Jezkova, Lucie and Falkova, Iva and Pagacova, Eva and Kopecna, Olga and Zadneprianetc, Mariia and Bacikova, Alena and Kulikova, Elena and Smirnova, Elena and Bulanova, Tatiana and Boreyko, Alla and Krasavin, Evgeny and Wenz, Frederik and Bestvater, Felix and Hildenbrand, Georg and Hausmann, Michael and Falk, Martin}, title = {Recruitment of 53BP1 Proteins for DNA Repair and Persistence of Repair Clusters Differ for Cell Types as Detected by Single Molecule Localization Microscopy}, series = {International Journal of Molecular Sciences}, volume = {19}, journal = {International Journal of Molecular Sciences}, number = {12}, publisher = {MDPI AG}, issn = {1422-0067}, doi = {https://doi.org/10.3390/ijms19123713}, year = {2018}, abstract = {DNA double stranded breaks (DSBs) are the most serious type of lesions introduced into chromatin by ionizing radiation. During DSB repair, cells recruit different proteins to the damaged sites in a manner dependent on local chromatin structure, DSB location in the nucleus, and the repair pathway entered. 53BP1 is one of the important players participating in repair pathway decision of the cell. Although many molecular biology details have been investigated, the architecture of 53BP1 repair foci and its development during the post-irradiation time, especially the period of protein recruitment, remains to be elucidated. Super-resolution light microscopy is a powerful new tool to approach such studies in 3D-conserved cell nuclei. Recently, we demonstrated the applicability of single molecule localization microscopy (SMLM) as one of these highly resolving methods for analyses of dynamic repair protein distribution and repair focus internal nano-architecture in intact cell nuclei. In the present study, we focused our investigation on 53BP1 foci in differently radio-resistant cell types, moderately radio-resistant neonatal human dermal fibroblasts (NHDF) and highly radio-resistant U87 glioblastoma cells, exposed to high-LET 15N-ion radiation. At given time points up to 24 h post irradiation with doses of 1.3 Gy and 4.0 Gy, the coordinates and spatial distribution of fluorescently tagged 53BP1 molecules was quantitatively evaluated at the resolution of 10-20 nm. Clusters of these tags were determined as sub-units of repair foci according to SMLM parameters. The formation and relaxation of such clusters was studied. The higher dose generated sufficient numbers of DNA breaks to compare the post-irradiation dynamics of 53BP1 during DSB processing for the cell types studied. A perpendicular (90°) irradiation scheme was used with the 4.0 Gy dose to achieve better separation of a relatively high number of particle tracks typically crossing each nucleus. For analyses along ion-tracks, the dose was reduced to 1.3 Gy and applied in combination with a sharp angle irradiation (10° relative to the cell plane). The results reveal a higher ratio of 53BP1 proteins recruited into SMLM defined clusters in fibroblasts as compared to U87 cells. Moreover, the speed of foci and thus cluster formation and relaxation also differed for the cell types. In both NHDF and U87 cells, a certain number of the detected and functionally relevant clusters remained persistent even 24 h post irradiation; however, the number of these clusters again varied for the cell types. Altogether, our findings indicate that repair cluster formation as determined by SMLM and the relaxation (i.e., the remaining 53BP1 tags no longer fulfill the cluster definition) is cell type dependent and may be functionally explained and correlated to cell specific radio-sensitivity. The present study demonstrates that SMLM is a highly appropriate method for investigations of spatiotemporal protein organization in cell nuclei and how it influences the cell decision for a particular repair pathway at a given DSB site.}, subject = {Genom}, language = {en} } @article{PagačovaŠtefančikovaSchmidtKaleretal.2019, author = {Pag{\´a}čov{\´a}, Eva and Štefanč{\´i}kov{\´a}, Lenka and Schmidt-Kaler, Franz and Hildenbrand, Georg and Vičar, Tom{\´a}š and Depeš, Daniel and Lee, Jin-Ho and Bestvater, Felix and Lacombe, Sandrine and Porcel, Erika and Roux, St{\´e}phane and Wenz, Frederik and Kopecna, Olga and Falkov{\´a}, Iva and Hausmann, Michael and Falk, Martin}, title = {Challenges and Contradictions of Metal Nano-Particle Applications for Radio-Sensitivity Enhancement in Cancer Therapy}, series = {International Journal of Molecular Sciences}, volume = {20}, journal = {International Journal of Molecular Sciences}, number = {3}, publisher = {MDPI AG}, issn = {1422-0067}, doi = {https://doi.org/10.3390/ijms20030588}, year = {2019}, abstract = {From the very beginnings of radiotherapy, a crucial question persists with how to target the radiation effectiveness into the tumor while preserving surrounding tissues as undamaged as possible. One promising approach is to selectively pre-sensitize tumor cells by metallic nanoparticles. However, though the "physics" behind nanoparticle-mediated radio-interaction has been well elaborated, practical applications in medicine remain challenging and often disappointing because of limited knowledge on biological mechanisms leading to cell damage enhancement and eventually cell death. In the present study, we analyzed the influence of different nanoparticle materials (platinum (Pt), and gold (Au)), cancer cell types (HeLa, U87, and SKBr3), and doses (up to 4 Gy) of low-Linear Energy Transfer (LET) ionizing radiation (γ- and X-rays) on the extent, complexity and reparability of radiation-induced γH2AX + 53BP1 foci, the markers of double stand breaks (DSBs). Firstly, we sensitively compared the focus presence in nuclei during a long period of time post-irradiation (24 h) in spatially (three-dimensionally, 3D) fixed cells incubated and non-incubated with Pt nanoparticles by means of high-resolution immunofluorescence confocal microscopy. The data were compared with our preliminary results obtained for Au nanoparticles and recently published results for gadolinium (Gd) nanoparticles of approximately the same size (2-3 nm). Next, we introduced a novel super-resolution approach—single molecule localization microscopy (SMLM)—to study the internal structure of the repair foci. In these experiments, 10 nm Au nanoparticles were used that could be also visualized by SMLM. Altogether, the data show that different nanoparticles may or may not enhance radiation damage to DNA, so multi-parameter effects have to be considered to better interpret the radiosensitization. Based on these findings, we discussed on conclusions and contradictions related to the effectiveness and presumptive mechanisms of the cell radiosensitization by nanoparticles. We also demonstrate that SMLM offers new perspectives to study internal structures of repair foci with the goal to better evaluate potential differences in DNA damage patterns.}, subject = {Krebs, Medizin}, language = {en} } @incollection{HausmannLeeSieversetal.2020, author = {Hausmann, Michael and Lee, Jin-Ho and Sievers, Aaron and Krufczik, Matthias and Hildenbrand, Georg}, title = {COMBinatorial Oligonucleotide FISH (COMBO-FISH) with Uniquely Binding Repetitive DNA Probes}, series = {The Nucleus}, booktitle = {The Nucleus}, publisher = {Springer US}, address = {New York, NY}, isbn = {9781071607626}, issn = {1064-3745}, doi = {https://doi.org/10.1007/978-1-0716-0763-3_6}, pages = {65 -- 77}, year = {2020}, subject = {Genom}, language = {en} } @article{HausmannNeitzelBobkovaetal.2020, author = {Hausmann, Michael and Neitzel, Charlotte and Bobkova, Elizaveta and Nagel, David and Hofmann, Andreas and Chramko, Tatyana and Smirnova, Elena and Kopecna, Olga and Pag{\´a}čov{\´a}, Eva and Boreyko, Alla and Krasavin, Evgeny and Falkova, Iva and Heermann, Dieter W. and Pilarczyk, G{\"o}tz and Hildenbrand, Georg and Bestvater, Felix and Falk, Martin}, title = {Single Molecule Localization Microscopy Analyses of DNA-Repair Foci and Clusters Detected Along Particle Damage Tracks}, series = {Frontiers in Physics}, volume = {8}, journal = {Frontiers in Physics}, publisher = {Frontiers Media SA}, issn = {2296-424X}, doi = {https://doi.org/10.3389/fphy.2020.578662}, year = {2020}, subject = {Krebszelle}, language = {en} } @inproceedings{HausmannNeitzelHahnetal.2021, author = {Hausmann, Michael and Neitzel, Charlotte and Hahn, Hannes and Winter, Ruth and Falkova, Iva and Heermann, Dieter W. and Pilarczyk, G{\"o}tz and Hildenbrand, Georg and Scherthan, Harry and Falk, Martin}, title = {Space and Time in the Universe of the Cell Nucleus after Ionizing Radiation Attacks: A Comparison of Cancer and Non-Cancer Cell Response}, series = {The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response}, booktitle = {The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response}, publisher = {MDPI}, address = {Basel Switzerland}, doi = {https://doi.org/10.3390/IECC2021-09219}, year = {2021}, subject = {Krebszelle}, language = {en} } @article{HausmannFalkNeitzeletal.2021, author = {Hausmann, Michael and Falk, Martin and Neitzel, Charlotte and Hofmann, Andreas and Biswas, Abin and Gier, Theresa and Falkova, Iva and Heermann, Dieter W. and Hildenbrand, Georg}, title = {Elucidation of the Clustered Nano-Architecture of Radiation-Induced DNA Damage Sites and Surrounding Chromatin in Cancer Cells: A Single Molecule Localization Microscopy Approach}, series = {International Journal of Molecular Sciences}, volume = {22}, journal = {International Journal of Molecular Sciences}, number = {7}, publisher = {MDPI AG}, issn = {1422-0067}, doi = {https://doi.org/10.3390/ijms22073636}, year = {2021}, abstract = {In cancer therapy, the application of (fractionated) harsh radiation treatment is state of the art for many types of tumors. However, ionizing radiation is a "double-edged sword"—it can kill the tumor but can also promote the selection of radioresistant tumor cell clones or even initiate carcinogenesis in the normal irradiated tissue. Individualized radiotherapy would reduce these risks and boost the treatment, but its development requires a deep understanding of DNA damage and repair processes and the corresponding control mechanisms. DNA double strand breaks (DSBs) and their repair play a critical role in the cellular response to radiation. In previous years, it has become apparent that, beyond genetic and epigenetic determinants, the structural aspects of damaged chromatin (i.e., not only of DSBs themselves but also of the whole damage-surrounding chromatin domains) form another layer of complex DSB regulation. In the present article, we summarize the application of super-resolution single molecule localization microscopy (SMLM) for investigations of these structural aspects with emphasis on the relationship between the nano-architecture of radiation-induced repair foci (IRIFs), represented here by γH2AX foci, and their chromatin environment. Using irradiated HeLa cell cultures as an example, we show repair-dependent rearrangements of damaged chromatin and analyze the architecture of γH2AX repair clusters according to topological similarities. Although HeLa cells are known to have highly aberrant genomes, the topological similarity of γH2AX was high, indicating a functional, presumptively genome type-independent relevance of structural aspects in DSB repair. Remarkably, nano-scaled chromatin rearrangements during repair depended both on the chromatin domain type and the treatment. Based on these results, we demonstrate how the nano-architecture and topology of IRIFs and chromatin can be determined, point to the methodological relevance of SMLM, and discuss the consequences of the observed phenomena for the DSB repair network regulation or, for instance, radiation treatment outcomes.}, subject = {Krebszelle}, language = {en} } @article{BartosovaSchaeferZhangetal.2021, author = {Bartosova, Maria and Schaefer, Betti and Zhang, Conghui and Herzog, Rebecca and Ridinger, David and Damgov, Ivan and Levai, Eszter and Marinovic, Iva and Eckert, Christoph and Romero, Philipp and Sallay, Peter and Ujszaszi, Akos and Unterwurzacher, Markus and Wagner, Anja and Hildenbrand, Georg and Warady, Bradley and Schaefer, Franz and Zarogiannis, Sotirios G. and Kratochwill, Klaus and Schmitt, Claus Peter}, title = {Glucose Derivative Induced Vasculopathy in Children on Chronic Peritoneal Dialysis}, series = {Nephrology Dialysis Transplantation}, volume = {36}, journal = {Nephrology Dialysis Transplantation}, number = {Supplement_1}, publisher = {Oxford University Press (OUP)}, issn = {0931-0509}, doi = {https://doi.org/10.1093/ndt/gfab126.004}, year = {2021}, abstract = {Abstract Background and Aims Patients with chronic kidney disease patients (CKD) have an exceedingly high cardiovascular risk. While vasculopathy is further accelerated during peritoneal dialysis (PD), the pathophysiological role of reactive metabolites such as glucose degradation products (GDP) is uncertain. Method Omental and parietal peritoneal tissues from 100 non-CKD individuals, 107 children with CKD5, 60 children treated with neutral pH, low GDP, and 30 children treated with acidic pH, high GDP PD fluids underwent standardized digital histomorphometry. Omental arterioles localized within the fat tissue, protected from direct PD fluid exposure were microdissected for multi-omics analysis. Key regulated pathways were validated by quantitative immunostaining, with localization microscopy in peritoneal tissues of matched cohorts and in vitro in human umbilical vein endothelial cells. Results Arterioles from children with CKD5 exhibited reduced lumen to vessel ratio (L/V) and reduced endothelial telomere length compared to non-CKD individuals; gene ontology analysis identified enrichment of arteriolar genes associated with nuclear telomere cap complex and focal adhesion. Pathway analysis of arteriolar cross-omics identified top canonical pathways including telomere extension by telomerase, actin cytoskeleton, integrin and tight junction signalling. Peritoneal vasculopathy progressed with PD vintage and was more pronounced with high versus low GDP exposure (p\&lt;0.001). Compared to CKD5, low GDP-PD upregulated 145/110 and downregulated 38/34 arteriolar genes/proteins, high GDP-PD upregulated 684/137 and supressed 1560/55 genes/proteins (p\&lt;0.01). High GDP milieu induced upregulation of arteriolar genes involved in cell death/apoptosis and suppressed genes related to cell viability/survival, cytoskeleton organization and immune response biofunctions. Vasculopathy associated canonical pathways concordantly regulated on arteriolar gene and protein level with high GDP exposure included cell death/proliferation, apoptosis, cytoskeleton organization, metabolism and detoxification, cell junction signalling, and immune response. Quantitative validation in PD cohorts with similar PD vintage, dialytic glucose exposure and age (n=15 / group) verified increased proapoptotic activity and cytoskeleton disintegration with high-GDP exposure; single-molecule-localization microscopy demonstrated arteriolar endothelial zonula occludens-1 (ZO-1) disruption. Absolute and relative to endoluminal surface length, arteriolar endothelial cell counts were inversely correlated with GDP exposure, with apoptosis marker caspase-3, TGF-ß induced pSMAD2/3, interleukin-6, ZO-1 protein abundance and the degree of vasculopathy. In vitro, exposure to GDP 3,4-dideoxyglucosone-3-ene dose-dependently reduced nuclear endothelial lamin-A/C and membrane ZO-1 assembly. Transendothelial electrical resistance was decreased. ZO-1 and sealing tight junction claudin-5 protein abundance were decreased in cells after incubation with high GDP compared to low GDP PD fluid and culture media. On nanoscale level GDP reduced junction cluster formation in the membrane area. Conclusion Multi-omics analysis of omental arterioles from children without pre-existing vasculopathy and life-style related confounders identified key mechanisms of vascular aging in CKD5 and the major contribution of GDP to accelerated vasculopathy during PD, i.e. disruption of endothelial cell junctions and cytoskeleton and induction of apoptosis.}, subject = {Peritonealdialyse}, language = {en} } @article{BartosovaZhangSchaeferetal.2021, author = {Bartosova, Maria and Zhang, Conghui and Schaefer, Betti and Herzog, Rebecca and Ridinger, David and Damgov, Ivan and Levai, Eszter and Marinovic, Iva and Eckert, Christoph and Romero, Philipp and Sallay, Peter and Ujszaszi, Akos and Unterwurzacher, Markus and Wagner, Anja and Hildenbrand, Georg and Warady, Bradley A. and Schaefer, Franz and Zarogiannis, Sotirios G. and Kratochwill, Klaus and Schmitt, Claus Peter}, title = {Glucose Derivative Induced Vasculopathy in Children on Chronic Peritoneal Dialysis}, series = {Circulation Research}, volume = {129}, journal = {Circulation Research}, number = {5}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, issn = {0009-7330}, doi = {https://doi.org/10.1161/CIRCRESAHA.121.319310}, year = {2021}, abstract = {Rationale: Patients with chronic kidney disease (CKD) have an exceedingly high cardiovascular risk; which further increases in patients on peritoneal dialysis (PD). The pathophysiological role of reactive metabolites accumulating in CKD such as glucose degradation products (GDP) is uncertain. Objective: Delineating the impact of GDP present in PD fluids in accelerated vasculopathy development in patients with CKD. Methods and Results: Omental and parietal peritoneal tissues were obtained from 107 children with CKD before dialysis and 90 children on chronic PD with PD fluids containing very low or high concentrations of GDP. Omental arterioles, protected from local PD fluid exposure by surrounding fat, were microdissected for multiomics analyses. High-GDP exposed omental arterioles exhibited 3-fold higher advanced glycation endproduct concentrations and upregulated genes involved in cell death/apoptosis and suppressed genes related to cell viability/survival, cytoskeleton organization, and immune response biofunctions. Vasculopathy-associated canonical pathways concordantly regulated on gene and protein level with high-GDP exposure included cell death/proliferation, apoptosis, cytoskeleton organization, metabolism and detoxification, cell junction signaling, and immune response. Parietal peritoneal arterioles of patients exposed to high-GDP fluids exhibited lumen narrowing compared to patients with CKD stage 5 (end-stage kidney disease) and patients on low-GDP PD, intima thickness was increased. Protein quantification verified increased proapoptotic activity and cytoskeleton disintegration, single-molecule-localization microscopy demonstrated arteriolar endothelial ZO-1 (zonula occludens-1) disruption. Absolute and per endoluminal surface length, arteriolar endothelial cell counts inversely correlated with GDP exposure, caspase-3, TGF (transforming growth factor)-β-induced pSMAD2/3 (phosphorylated SMAD2/3), interleukin-6, ZO-1 abundance, and lumen narrowing. In vitro, 3,4-dideoxyglucosone-3-ene reduced lamin-A/C and membrane ZO-1 assembly, increased pSMAD2/3, and ionic and 4 and 10 kDa permeability of arterial endothelial cells. Conclusions: Our findings indicate a fundamental role of GDP in PD-associated vasculopathy, exerted by endothelial cell junction and cytoskeleton disruption, and induction of apoptosis. They should redirect the focus of research and intervention on targeting reactive metabolite overload in CKD and PD. Registration: URL: https://www.clinicaltrials.gov ; Unique identifier: NCT01893710.}, subject = {Peritonealdialyse}, language = {en} } @unpublished{PaschekRossmannHausmannetal.2021, author = {Paschek, Klaus and Roßmann, Arthur and Hausmann, Michael and Hildenbrand, Georg}, title = {Analysis of Tidal Accelerations in the Solar System and in Extrasolar Planetary Systems}, publisher = {MDPI AG}, doi = {https://doi.org/10.20944/preprints202107.0408.v1}, year = {2021}, abstract = {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.}, subject = {Sonnensystem}, language = {en} } @article{BartosovaRidingerMarinovicetal.2021, author = {Bartosova, Maria and Ridinger, David and Marinovic, Iva and Heigwer, Jana and Zhang, Conghui and Levai, Eszter and Westhoff, Jens H. and Schaefer, Franz and Terjung, Stefan and Hildenbrand, Georg and Krunic, Damir and Bestvater, Felix and Hausmann, Michael and Schmitt, Claus Peter and Zarogiannis, Sotirios G.}, title = {An Experimental Workflow for Studying Barrier Integrity, Permeability, and Tight Junction Composition and Localization in a Single Endothelial Cell Monolayer: Proof of Concept}, series = {International Journal of Molecular Sciences}, volume = {22}, journal = {International Journal of Molecular Sciences}, number = {15}, publisher = {MDPI AG}, issn = {1422-0067}, doi = {https://doi.org/10.3390/ijms22158178}, year = {2021}, abstract = {Endothelial and epithelial barrier function is crucial for the maintenance of physiological processes. The barrier paracellular permeability depends on the composition and spatial distribution of the cell-to-cell tight junctions (TJ). Here, we provide an experimental workflow that yields several layers of physiological data in the setting of a single endothelial cell monolayer. Human umbilical vein endothelial cells were grown on Transwell filters. Transendothelial electrical resistance (TER) and 10 kDa FITC dextran flux were measured using Alanyl-Glutamine (AlaGln) as a paracellular barrier modulator. Single monolayers were immunolabelled for Zonula Occludens-1 (ZO-1) and Claudin-5 (CLDN5) and used for automated immunofluorescence imaging. Finally, the same monolayers were used for single molecule localization microscopy (SMLM) of ZO-1 and CLDN5 at the nanoscale for spatial clustering analysis. The TER increased and the paracellular dextran flux decreased after the application of AlaGln and these functional changes of the monolayer were mediated by an increase in the ZO-1 and CLDN5 abundance in the cell-cell interface. At the nanoscale level, the functional and protein abundance data were accompanied by non-random increased clustering of CLDN5. Our experimental workflow provides multiple data from a single monolayer and has wide applicability in the setting of paracellular studies in endothelia and epithelia.}, subject = {Endothelzelle}, language = {en} } @article{PaschekRossmannHausmannetal.2021, author = {Paschek, Klaus and Roßmann, Arthur and Hausmann, Michael and Hildenbrand, Georg}, title = {Analysis of Tidal Accelerations in the Solar System and in Extrasolar Planetary Systems}, series = {Applied Sciences}, volume = {11}, journal = {Applied Sciences}, number = {18}, publisher = {MDPI AG}, issn = {2076-3417}, doi = {https://doi.org/10.3390/app11188624}, year = {2021}, abstract = {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.}, subject = {Sonnensystem}, language = {en} } @article{SieversSauerHausmannetal.2021, author = {Sievers, Aaron and Sauer, Liane and Hausmann, Michael and Hildenbrand, Georg}, title = {Eukaryotic Genomes Show Strong Evolutionary Conservation of k-mer Composition and Correlation Contributions between Introns and Intergenic Regions}, series = {Genes}, volume = {12}, journal = {Genes}, number = {10}, publisher = {MDPI AG}, issn = {2073-4425}, doi = {https://doi.org/10.3390/genes12101571}, year = {2021}, abstract = {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.}, subject = {Genom}, language = {en} } @article{DobešovaGierKopecnaetal.2022, author = {Dobešov{\´a}, Lucie and Gier, Theresa and Kopecna, Olga and Pag{\´a}čov{\´a}, Eva and Vičar, Tom{\´a}š and Bestvater, Felix and Toufar, Jiř{\´i} and Bač{\´i}kov{\´a}, Alena and Kopel, Pavel and Fedr, Radek and Hildenbrand, Georg and Falkov{\´a}, Iva and Falk, Martin and Hausmann, Michael}, title = {Incorporation of Low Concentrations of Gold Nanoparticles: Complex Effects on Radiation Response and Fate of Cancer Cells}, series = {Pharmaceutics}, volume = {14}, journal = {Pharmaceutics}, number = {1}, publisher = {MDPI AG}, issn = {1999-4923}, doi = {https://doi.org/10.3390/pharmaceutics14010166}, year = {2022}, abstract = {(1) Background: In oncology research, a long-standing discussion exists about pros and cons of metal nanoparticle-enhanced radiotherapy and real mechanisms behind the tumor cell response to irradiation (IR) in presence of gold nanoparticles (GNPs). A better understanding of this response is, however, necessary to develop more efficient and safety nanoparticle (NP) types designed to disturb specific processes in tumor cells. (2) Aims and Methods: We combined 3D confocal microscopy and super-resolution single molecule localization microscopy (SMLM) to analyze, at the multiscale, the early and late effects of 10 nm-GNPs on DNA double strand break (DSB) induction and repair in tumor cells exposed to different doses of photonic low-LET (linear energy transfer) radiation. The results were correlated to different aspects of short and long-term cell viability. SkBr3 breast cancer cells (selected for the highest incidence of this cancer type among all cancers in women, and because most breast tumors are treated with IR) were incubated with low concentrations of GNPs and irradiated with 60Co γ-rays or 6 MV X-rays. In numerous post-irradiation (PI) times, ranging from 0.5 to 24 h PI, the cells were spatially (3D) fixed and labeled with specific antibodies against γH2AX, 53BP1 and H3K9me3. The extent of DSB induction, multi-parametric micro- and nano-morphology of γH2AX and 53BP1 repair foci, DSB repair kinetics, persistence of unrepaired DSBs, nanoscale clustering of γH2AX and nanoscale (hetero)chromatin re-organization were measured by means of the mentioned microscopy techniques in dependence of radiation dose and GNP concentration. (3) Results: The number of γH2AX/53BP1 signals increased after IR and an additional increase was observed in GNP-treated (GNP(+)) cells compared to untreated controls. However, this phenomenon reflected slight expansion of the G2-phase cell subpopulation in irradiated GNP(+) specimens instead of enhanced DNA damage induction by GNPs. This statement is further supported by some micro- and nano-morphological parameters of γH2AX/53BP1 foci, which slightly differed for cells irradiated in absence or presence of GNPs. At the nanoscale, Ripley's distance frequency analysis of SMLM signal coordinate matrices also revealed relaxation of heterochromatin (H3K9me3) clusters upon IR. These changes were more prominent in presence of GNPs. The slight expansion of radiosensitive G2 cells correlated with mostly insignificant but systematic decrease in post-irradiation survival of GNP(+) cells. Interestingly, low GNP concentrations accelerated DSB repair kinetics; however, the numbers of persistent γH2AX/53BP1 repair foci were slightly increased in GNP(+) cells. (4) Conclusions: Low concentrations of 10-nm GNPs enhanced the G2/M cell cycle arrest and the proportion of radiosensitive G2 cells, but not the extent of DNA damage induction. GNPs also accelerated DSB repair kinetics and slightly increased presence of unrepaired γH2AX/53BP1 foci at 24 h PI. GNP-mediated cell effects correlated with slight radiosensitization of GNP(+) specimens, significant only for the highest radiation dose tested (4 Gy).}, subject = {Strahlentherapie}, language = {en} } @incollection{HildenbrandPaschekSchaeferetal.2022, author = {Hildenbrand, Georg and Paschek, Klaus and Sch{\"a}fer, Myriam and Hausmann, Michael}, title = {Cryovolcanism in the Solar System and beyond: Considerations on Energy Sources, Geological Aspects, and Astrobiological Perspectives}, series = {Astronomy and Planetary Science - From Cryovolcanism to Black Holes and Galactic Evolution}, booktitle = {Astronomy and Planetary Science - From Cryovolcanism to Black Holes and Galactic Evolution}, publisher = {IntechOpen}, isbn = {9781803561196}, doi = {https://doi.org/10.5772/intechopen.105067}, year = {2022}, abstract = {Volcanism based on melting rocks (silicate volcanism) is long known on Earth and has also been found on Jupiter's moon Io. Remnants of this type of volcanism have been identified also on other bodies in the solar system. Energy sources powered by accretion and the decay of radioactive isotopes seem to be dominant mainly inside larger bodies, which have enough volume to accumulate and retain this energy in significant amounts. On the other hand, the impact of tidal forces allows even tiny bodies to melt up and pass into the stage of cryovolcanism. The dependence of tidal heating on the size of the object is minor, but the masses of and the distances to accompanying bodies as well as the inner compositions of the heated body are central factors. Even though Io as an example of a body supporting silicate volcanism is striking, the physics of tidal forces might suggest a relatively high probability for cryovolcanism. This chapter aims at considering the parameters known and objects found so far in our solar system to give insights into where in our system and other planetary systems cryovolcanism might be expected.}, subject = {Sonnensystem}, language = {en} } @article{RodenerSchaeferHausmannetal.2022, author = {Rodener, Daniel and Sch{\"a}fer, Myriam and Hausmann, Michael and Hildenbrand, Georg}, title = {Assessing the Potential for Liquid Solvents from X-ray Sources: Considerations on Bodies Orbiting Active Galactic Nuclei}, series = {Galaxies}, volume = {10}, journal = {Galaxies}, number = {5}, publisher = {MDPI AG}, issn = {2075-4434}, doi = {https://doi.org/10.3390/galaxies10050101}, year = {2022}, abstract = {We aim to establish a rough first prospect on the potential of certain biorelevant solvents (water, ammonia, and methane) being present in liquid form inside the uppermost few meters of several modeled rocky and icy surfaces of hypothetical bodies orbiting active galactic nuclei (AGNs) and investigate under which constraints this might occur. For this, we adjust and average X-ray spectra from a sample of 20 Type-1 Seyfert galaxies to calculate the mean snowline of the sample used. We then vary the hypothetical body's orbit between 10\% and 100\% of the snowline radius and calculate a sub-surface attenuation within four different model surface compositions for each. We then use this as a continuous source term for a thermal model. Example bodies are systematically investigated with sizes between 1/30 and 20 earth radii, with further variations also considered (such as possible bound rotation), to end up with a perspective of solvent phases under a wide slew of different conditions. We find that liquid solvents are possible under a multitude of parameters, with temperature being the main constraint to liquid water whereas body size and pressure are the main constraint to liquid methane and ammonia.}, subject = {L{\"o}sungsmittel}, language = {en} } @incollection{HausmannHildenbrandPilarczyk2022, author = {Hausmann, Michael and Hildenbrand, Georg and Pilarczyk, G{\"o}tz}, title = {Networks and Islands of Genome Nano-architecture and Their Potential Relevance for Radiation Biology}, series = {Results and Problems in Cell Differentiation}, booktitle = {Results and Problems in Cell Differentiation}, publisher = {Springer International Publishing}, address = {Cham}, isbn = {9783031065729}, issn = {0080-1844}, doi = {https://doi.org/10.1007/978-3-031-06573-6_1}, pages = {3 -- 34}, year = {2022}, abstract = {The cell nucleus is a complex biological system in which simultaneous reactions and functions take place to keep the cell as an individualized, specialized system running well. The cell nucleus contains chromatin packed in various degrees of density and separated in volumes of chromosome territories and subchromosomal domains. Between the chromatin, however, there is enough "free" space for floating RNA, proteins, enzymes, ATPs, ions, water molecules, etc. which are trafficking by super- and supra-diffusion to the interaction points where they are required. It seems that this trafficking works somehow automatically and drives the system perfectly. After exposure to ionizing radiation causing DNA damage from single base damage up to chromatin double-strand breaks, the whole system "cell nucleus" responds, and repair processes are starting to recover the fully functional and intact system. In molecular biology, many individual epigenetic pathways of DNA damage response or repair of single and double-strand breaks are described. How these responses are embedded into the response of the system as a whole is often out of the focus of consideration. In this article, we want to follow the hypothesis of chromatin architecture's impact on epigenetic pathways and vice versa. Based on the assumption that chromatin acts like an "aperiodic solid state within a limited volume," functionally determined networks and local topologies ("islands") can be defined that drive the appropriate repair process at a given damage site. Experimental results of investigations of the chromatin nano-architecture and DNA repair clusters obtained by means of single-molecule localization microscopy offer hints and perspectives that may contribute to verifying the hypothesis.}, subject = {Zellkern}, language = {en} } @article{ErenpreisaGiulianiYoshikawaetal.2023, author = {Erenpreisa, Jekaterina and Giuliani, Alessandro and Yoshikawa, Kenichi and Falk, Martin and Hildenbrand, Georg and Salmina, Kristine and Freivalds, Talivaldis and Vainshelbaum, Ninel and Weidner, Jonas and Sievers, Aaron and Pilarczyk, G{\"o}tz and Hausmann, Michael}, title = {Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change}, series = {International Journal of Molecular Sciences}, volume = {24}, journal = {International Journal of Molecular Sciences}, number = {3}, publisher = {MDPI AG}, issn = {1422-0067}, doi = {https://doi.org/10.3390/ijms24032658}, year = {2023}, abstract = {Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers. Under environmental stress or during cell development, differentiation towards specialized cell types, or to dysfunctional tumor, the cell nucleus seems to react as a whole through coordinated changes at all levels of control. This implies the need for a framework in which biological, chemical, and physical manifestations can serve as a basis for a coherent theory of gene self-organization. An international symposium held at the Biomedical Research and Study Center in Riga, Latvia, on 25 July 2022 addressed novel aspects of the abovementioned topic. The present article reviews the most recent results and conclusions of the state-of-the-art research in this multidisciplinary field of science, which were delivered and discussed by scholars at the Riga symposium.}, subject = {Zellkern}, language = {en} } @article{SieversSauerBischetal.2023, author = {Sievers, Aaron and Sauer, Liane and Bisch, Marc and Sprengel, Jan and Hausmann, Michael and Hildenbrand, Georg}, title = {Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes}, series = {Genes}, volume = {14}, journal = {Genes}, number = {3}, publisher = {MDPI AG}, issn = {2073-4425}, doi = {https://doi.org/10.3390/genes14030755}, year = {2023}, abstract = {Dinucleotides are known as determinants for various structural and physiochemical properties of DNA and for binding affinities of proteins to DNA. These properties (e.g., stiffness) and bound proteins (e.g., transcription factors) are known to influence important biological functions, such as transcription regulation and 3D chromatin organization. Accordingly, the question arises of how the considerable variations in dinucleotide contents of eukaryotic chromosomes could still provide consistent DNA properties resulting in similar functions and 3D conformations. In this work, we investigate the hypothesis that coupled dinucleotide contents influence DNA properties in opposite directions to moderate each other's influences. Analyzing all 2478 chromosomes of 155 eukaryotic species, considering bias from coding sequences and enhancers, we found sets of correlated and anti-correlated dinucleotide contents. Using computational models, we estimated changes of DNA properties resulting from this coupling. We found that especially pure A/T dinucleotides (AA, TT, AT, TA), known to influence histone positioning and AC/GT contents, are relevant moderators and that, e.g., the Roll property, which is known to influence histone affinity of DNA, is preferably moderated. We conclude that dinucleotide contents might indirectly influence transcription and chromatin 3D conformation, via regulation of histone occupancy and/or other mechanisms.}, subject = {Genom}, language = {en} } @article{HennSieversHausmannetal.2023, author = {Henn, Lukas and Sievers, Aaron and Hausmann, Michael and Hildenbrand, Georg}, title = {Specific Patterns in Correlations of Super-Short Tandem Repeats (SSTRs) with G+C Content, Genic and Intergenic Regions, and Retrotransposons on All Human Chromosomes}, series = {Genes}, volume = {15}, journal = {Genes}, number = {1}, publisher = {MDPI AG}, issn = {2073-4425}, doi = {https://doi.org/10.3390/genes15010033}, year = {2023}, abstract = {The specific characteristics of k-mer words (2 ≤ k ≤ 11) regarding genomic distribution and evolutionary conservation were recently found. Among them are, in high abundance, words with a tandem repeat structure (repeat unit length of 1 bp to 3 bp). Furthermore, there seems to be a class of extremely short tandem repeats (≤12 bp), so far overlooked, that are non-random-distributed and, therefore, may play a crucial role in the functioning of the genome. In the following article, the positional distributions of these motifs we call super-short tandem repeats (SSTRs) were compared to other functional elements, like genes and retrotransposons. We found length- and sequence-dependent correlations between the local SSTR density and G+C content, and also between the density of SSTRs and genes, as well as correlations with retrotransposon density. In addition to many general interesting relations, we found that SINE Alu has a strong influence on the local SSTR density. Moreover, the observed connection of SSTR patterns to pseudogenes and -exons might imply a special role of SSTRs in gene expression. In summary, our findings support the idea of a special role and the functional relevance of SSTRs in the genome.}, subject = {Genom}, language = {en} } @article{Solov’yovVerkhovtsevMasonetal.2024, author = {Solov'yov, Andrey V. and Verkhovtsev, Alexey V. and Mason, Nigel J. and Amos, Richard A. and Bald, Ilko and Baldacchino, G{\´e}rard and Dromey, Brendan and Falk, Martin and Fedor, Juraj and Gerhards, Luca and Hausmann, Michael and Hildenbrand, Georg and Hrabovsk{\´y}, Miloš and Kadlec, Stanislav and Kočišek, Jaroslav and L{\´e}pine, Franck and Ming, Siyi and Nisbet, Andrew and Ricketts, Kate and Sala, Leo and Schlath{\"o}lter, Thomas and Wheatley, Andrew E. H. and Solov'yov, Ilia A.}, title = {Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment}, series = {Chemical Reviews}, volume = {124}, journal = {Chemical Reviews}, number = {13}, publisher = {American Chemical Society (ACS)}, issn = {0009-2665}, doi = {https://doi.org/10.1021/acs.chemrev.3c00902}, pages = {8014 -- 8129}, year = {2024}, abstract = {This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.}, subject = {Kondensierte Materie}, language = {en} } @article{HikmatSieversHausmannetal., author = {Hikmat, Wisam Mohammed and Sievers, Aaron and Hausmann, Michael and Hildenbrand, Georg}, title = {Peculiar k-mer Spectra Are Correlated with 3D Contact Frequencies and Breakpoint Regions in the Human Genome}, series = {Genes}, volume = {15}, journal = {Genes}, number = {10}, doi = {10.3390/genes15101247}, subject = {Zellkern}, language = {de} } @misc{EderJouanneDiedrichRashidetal.2023, author = {Eder, PA and Jouanne-Diedrich, Holger K. von and Rashid, A and Soda, H}, title = {Der pr{\"a}klinische 4 Item Stroke Scale (4I SS) und die Thrombektomie}, year = {2023}, abstract = {Der4I-SS zeigt eine moderate bis hohe diagnostische Genauigkeit in Bezug auf EVTs von Patienten mit akuten Schlaganf{\"a}̈llen. Die Implementierung kann zur Verbesserung der Patientenversorgung und Ressourcenallokation beitragen.}, subject = {Schlaganfall}, language = {de} }