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Radiation-Induced DNA Damage, Repair and Responses
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Radiation-Induced DNA Damage, Repair and Responses

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 10 August 2024 | Viewed by 2110

Special Issue Editor

Prof. Dr. Anders Brahme

E-Mail Website
Guest Editor
Department of Oncology-Pathology, Karolinska Institutet, 10074 Stockholm, Sweden
Interests: simple and complex DSB´s; role of TP53; HR and NHEJ Repair; NHEJ and HR Interactions; histone modifications; low dose apoptosis; repair fidelity; misrepair

Special Issue Information

Dear Colleagues,

The field of radiation damage and repair is rapidly advancing, with many novel molecular tools enabling the detailed investigation of both molecular processes and the advanced radiation interaction codes that determine the type of molecular damage caused to DNA. The main structure of nuclear DNA has largely been clarified in recent decades, revealing that the tetra-nucleosomes are the key component of heterochromatic DNA; however, unfortunately, research has not yet reached the calculational stage in sufficient detail. The role of Histone modifications has also opened up new dimensions regarding the epigenetic machinery involved in the DNA repair processes, in combination with the classical DNA repair players. The scope of this Special Issue includes the interesting and essential express start of DSB repair according to the initial fast Ku-DNApkcs hetero dimer, and its possible switch to the slower and more flexible MRN dimer complex for HR repair when there is high flexibility in its homology.

This Special Issue focuses on advances in the study of radiation-induced damage and the repair of cells and biomolecules. The submission of both original research articles and comprehensive reviews is welcome.

Prof. Dr. Anders Brahme
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • MR, EM, and fish molecular imaging
  • influence of EU hetero-chromatin
  • radiation type influence
  • mutation and cancer incidence
  • therapeutic possibilities

Published Papers (2 papers)

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Research

14 pages, 4761 KiB  
Article
Genome-Wide Profile of Mutations Induced by Carbon Ion Beam Irradiation of Dehulled Rice Seeds
by Ying Ling, Yuming Zhang, Ming Huang, Tao Guo and Guili Yang
Int. J. Mol. Sci. 2024, 25(10), 5195; https://doi.org/10.3390/ijms25105195 - 10 May 2024
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Abstract
As a physical mutagen, carbon ion beam (CIB) irradiation can induce high-frequency mutation, which is user-friendly and environment-friendly in plant breeding. In this study, we resequenced eight mutant lines which were screened out from the progeny of the CIB-irradiated dehulled rice seeds. Among [...] Read more.
As a physical mutagen, carbon ion beam (CIB) irradiation can induce high-frequency mutation, which is user-friendly and environment-friendly in plant breeding. In this study, we resequenced eight mutant lines which were screened out from the progeny of the CIB-irradiated dehulled rice seeds. Among these mutants, CIB induced 135,535 variations, which include single base substitutions (SBSs), and small insertion and deletion (InDels). SBSs are the most abundant mutation, and account for 88% of all variations. Single base conversion is the main type of SBS, and the average ratio of transition and transversion is 1.29, and more than half of the InDels are short-segmented mutation (1–2 bp). A total of 69.2% of the SBSs and InDels induced by CIBs occurred in intergenic regions on the genome. Surprisingly, the average mutation frequency in our study is 9.8 × 10−5/bp and much higher than that of the previous studies, which may result from the relatively high irradiation dosage and the dehulling of seeds for irradiation. By analyzing the mutation of every 1 Mb in the genome of each mutant strain, we found some unusual high-frequency (HF) mutation regions, where SBSs and InDels colocalized. This study revealed the mutation mechanism of dehulled rice seeds by CIB irradiation on the genome level, which will enrich our understanding of the mutation mechanism of CIB radiation and improve mutagenesis efficiency. Full article
(This article belongs to the Special Issue Radiation-Induced DNA Damage, Repair and Responses)
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13 pages, 3214 KiB  
Article
Foci-Xpress: Automated and Fast Nuclear Foci Counting Tool
by Jae-I Moon, Woo-Jin Kim, Ki-Tae Kim, Hyun-Jung Kim, Hye-Rim Shin, Heein Yoon, Seung Gwa Park, Min-Sang Park, Young-Dan Cho, Pil-Jong Kim and Hyun-Mo Ryoo
Int. J. Mol. Sci. 2023, 24(19), 14465; https://doi.org/10.3390/ijms241914465 - 23 Sep 2023
Viewed by 1410
Abstract
In the nucleus, distinct, discrete spots or regions called “foci” have been identified, each harboring a specific molecular function. Accurate and efficient quantification of these foci is essential for understanding cellular dynamics and signaling pathways. In this study, we present an innovative automated [...] Read more.
In the nucleus, distinct, discrete spots or regions called “foci” have been identified, each harboring a specific molecular function. Accurate and efficient quantification of these foci is essential for understanding cellular dynamics and signaling pathways. In this study, we present an innovative automated image analysis method designed to precisely quantify subcellular foci within the cell nucleus. Manual foci counting methods can be tedious and time-consuming. To address these challenges, we developed an open-source software that automatically counts the number of foci from the indicated image files. We compared the foci counting efficiency, velocity, accuracy, and convenience of Foci-Xpress with those of other conventional methods in foci-induced models. We can adjust the brightness of foci to establish a threshold. The Foci-Xpress method was significantly faster than other conventional methods. Its accuracy was similar to that of conventional methods. The most significant strength of Foci-Xpress is automation, which eliminates the need for analyzing equipment while counting. This enhanced throughput facilitates comprehensive statistical analyses and supports robust conclusions from experiments. Furthermore, automation completely rules out biases caused by researchers, such as manual errors or daily variations. Thus, Foci-Xpress is a convincing, convenient, and easily accessible focus-counting tool for cell biologists. Full article
(This article belongs to the Special Issue Radiation-Induced DNA Damage, Repair and Responses)
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