International Journal of Molecular Sciences

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Prof. Dr. Anders Brahme

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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

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Keywords

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

Published Papers (1 paper)

Research

13 pages, 3214 KiB

Open AccessArticle

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 1323

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 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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