TY - JOUR A1 - Sievers, Aaron A1 - Sauer, Liane A1 - Bisch, Marc A1 - Sprengel, Jan A1 - Hausmann, Michael A1 - Hildenbrand, Georg T1 - Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes JF - Genes N2 - 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. KW - Genom Y1 - 2023 U6 - https://doi.org/https://doi.org/10.3390/genes14030755 SN - 2073-4425 VL - 14 IS - 3 PB - MDPI AG ER - TY - JOUR A1 - Henn, Lukas A1 - Sievers, Aaron A1 - Hausmann, Michael A1 - Hildenbrand, Georg T1 - Specific Patterns in Correlations of Super-Short Tandem Repeats (SSTRs) with G+C Content, Genic and Intergenic Regions, and Retrotransposons on All Human Chromosomes JF - Genes N2 - 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. KW - Genom KW - Genexpression Y1 - 2023 U6 - https://doi.org/https://doi.org/10.3390/genes15010033 SN - 2073-4425 VL - 15 IS - 1 PB - MDPI AG ER - TY - JOUR A1 - Solov’yov, Andrey V. A1 - Verkhovtsev, Alexey V. A1 - Mason, Nigel J. A1 - Amos, Richard A. A1 - Bald, Ilko A1 - Baldacchino, Gérard A1 - Dromey, Brendan A1 - Falk, Martin A1 - Fedor, Juraj A1 - Gerhards, Luca A1 - Hausmann, Michael A1 - Hildenbrand, Georg A1 - Hrabovský, Miloš A1 - Kadlec, Stanislav A1 - Kočišek, Jaroslav A1 - Lépine, Franck A1 - Ming, Siyi A1 - Nisbet, Andrew A1 - Ricketts, Kate A1 - Sala, Leo A1 - Schlathölter, Thomas A1 - Wheatley, Andrew E. H. A1 - Solov’yov, Ilia A. T1 - Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment JF - Chemical Reviews N2 - 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. KW - Kondensierte Materie KW - Strahlung Y1 - 2024 U6 - https://doi.org/https://doi.org/10.1021/acs.chemrev.3c00902 SN - 0009-2665 VL - 124 IS - 13 SP - 8014 EP - 8129 PB - American Chemical Society (ACS) ER - TY - JOUR A1 - Hikmat, Wisam Mohammed A1 - Sievers, Aaron A1 - Hausmann, Michael A1 - Hildenbrand, Georg T1 - Peculiar k-mer Spectra Are Correlated with 3D Contact Frequencies and Breakpoint Regions in the Human Genome JF - Genes KW - 3D genomics KW - Hi-C KW - k-mer KW - sequence analysis KW - Zellkern KW - Chromatin KW - Genom Y1 - U6 - https://doi.org/10.3390/genes15101247 VL - 15 IS - 10 ER - TY - GEN A1 - Eder, PA A1 - Jouanne-Diedrich, Holger K. von A1 - Rashid, A A1 - Soda, H T1 - Der präklinische 4 Item Stroke Scale (4I SS) und die Thrombektomie N2 - Der4I-SS zeigt eine moderate bis hohe diagnostische Genauigkeit in Bezug auf EVTs von Patienten mit akuten Schlaganfä̈llen. Die Implementierung kann zur Verbesserung der Patientenversorgung und Ressourcenallokation beitragen. N2 - Poster KW - Schlaganfall KW - Telemedizin Y1 - 2023 ER -