@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} }