Article
Chemistry, Physical
Cate S. Anstoter, Mark DelloStritto, Michael L. Klein, Spiridoula Matsika
Summary: This paper explores the interaction between low-energy electrons and DNA in solution, focusing on the behavior of electronic states of solvated uracil anion through a combination of molecular dynamics and high-level electronic structure study. The dominant role of solvent reorganization followed by relaxation of the uracil core in stabilizing the solvated uracil anion is highlighted.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Cell Biology
Md Akram Hossain, Yunfeng Lin, Garrett Driscoll, Jia Li, Anne McMahon, Joshua Matos, Haichao Zhao, Daisuke Tsuchimoto, Yusaku Nakabeppu, Jianjun Zhao, Shan Yan
Summary: APE2 is essential for activating the ATR DDR pathway in response to various stressful conditions in Xenopus laevis egg extracts and human pancreatic cancer cells. Inhibition of APE2 leads to increased DNA damage and sensitizes cancer cells to chemotherapy drugs, indicating its crucial role in maintaining genome integrity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Kevin M. Wernke, Alina Tirla, Mengzhao Xue, Yulia Surovtseva, Fabian S. Menges, Seth B. Herzon
Summary: Colibactin is a genotoxic metabolite produced by commensal-pathogenic members of the human microbiome, potentially linked to tumorigenesis. Researchers synthesized and studied colibactin 742 (4), finding that it induces DNA interstrand-cross-links and activates DNA repair pathways, providing a new approach to study the genotoxic effects of colibactin.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Genevieve Trombly, Afaf Milad Said, Alexei P. Kudin, Viktoriya Peeva, Janine Altmueller, Kerstin Becker, Karl Koehrer, Gabor Zsurka, Wolfram S. Kunz
Summary: The study investigated the effects of hydrogen peroxide on mitochondrial DNA integrity. The results showed that hydrogen peroxide treatment resulted in DNA breaks, which were then repaired through rapid repair of single-strand breaks and degradation of double-strand breaks-generated linear fragments. Inactivation of mitochondrial DNA degradation resulted in the persistence of linear fragments in mutant cells without affecting the repair of single-strand breaks. These findings highlight the interplay between DNA repair and degradation processes, and the potential generation of somatic mitochondrial DNA deletions.
Article
Oncology
Qunsong Tan, Kaifeng Niu, Yuqi Zhu, Zixiang Chen, Yueyang Li, Mengge Li, Di Wei, Adayabalam S. Balajee, Hongbo Fang, Yongliang Zhao
Summary: The study demonstrates that RNF8 ubiquitinates RecQL4 protein, facilitating its dissociation from DSB sites and hindering the recruitment of downstream DSB repair proteins. RecQL4 also interacts with WRAP53 beta, which enhances its association with RNF8. Overall, the ubiquitination event mediated by RNF8 is essential for RecQL4's function in DSB repair.
Article
Biochemistry & Molecular Biology
Ricardo Peraza-Vega, Mahara Valverde, Emilio Rojas
Summary: The repair of DNA damage is crucial for maintaining genetic information and cell functioning. Double-strand breaks (DSBs) are the most harmful type of DNA damage, and their repair involves two main mechanisms: non-homologous end joining (NHEJ) and homologous recombination repair (HRR). MiRNAs have been shown to play an important role in regulating genes involved in NHEJ and HRR, and alterations in miRNA expression can impact the ability of cells to repair DSBs and affect cancer therapy sensitivity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Kyle B. Vrtis, James M. Dewar, Gheorghe Chistol, R. Alex Wu, Thomas G. W. Graham, Johannes C. Walter
Summary: Research has shown that collisions between the replicative CMG helicase and nicks in DNA templates can lead to different forms of double-strand breaks, causing replisome disassembly.
Review
Nanoscience & Nanotechnology
Adam M. Kabza, Nandini Kundu, Wenrui Zhong, Jonathan T. Sczepanski
Summary: This article summarizes the recent progress in integrating chemically modified nucleotides with DNA strand displacement reactions to develop robust systems and devices that operate in living organisms. It also discusses the factors to consider when applying modified oligonucleotides to living cells.
WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Shaolong Zhang, Pengzhao Shang, Kun Gao, Guomeng Zhao, Jingping Zhou, Rong Chen, Xiaoju Ning, Changying Guo
Summary: The DNA repair machinery plays a role in estrogen-dependent transactivation. The study reveals that mechanisms underlying estrogen-induced DNA damage are complex. It is found that the process of 17 beta-estradiol (E2)-induced ROS production can be divided into two phases, and oxidative DNA damage occurs at different temporal and spatial locations due to intracellular Ca2+ fluctuation and ER alpha-dependent transcription. The study also shows that DNA oxidation is not necessary for estrogen-responsive gene expression, while topoisomerase-mediated DNA strand breaks are essential in estrogen signaling.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Immunology
Daniel de Oliveira Patricio, Greicy Brisa Malaquias Dias, Lucilene Wildner Granella, Ben Trigg, Helena Claire Teague, Dina Bittencourt, Andre Bafica, Alfeu Zanotto-Filho, Brian Ferguson, Daniel Santos Mansur
Summary: DNA-PKcs plays a role in restricting the spread of Zika virus infection in human cells by influencing the transcription of interferons and related genes. This mechanism is independent of DNA breaks.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Erwan Goy, Maxime Tomezak, Caterina Facchin, Nathalie Martin, Emmanuel Bouchaert, Jerome Benoit, Clementine de Schutter, Joe Nassour, Laure Saas, Claire Drullion, Priscille M. Brodin, Alexandre Vandeputte, Olivier Molendi-Coste, Laurent Pineau, Gautier Goormachtigh, Olivier Pluquet, Albin Pourtier, Fabrizio Cleri, Eric Lartigau, Nicolas Penel, Corinne Abbadie
Summary: Induction of second primary cancers is a rare but severe complication of curative-intent radiation therapy. Research shows that normal human or mouse dermal fibroblasts exposed to out-of-field radiation dose at the margin of the target volume do not die, but enter a long-lived senescent state, leading to the accumulation of unrepaired DNA single-strand breaks. Some of these senescent cells eventually escape cell cycle arrest and give rise to daughter cells with mutations and invasive properties. This discovery highlights the role of single-strand break-induced senescence as the mechanism of second primary cancer initiation, with potential implications for prevention.
Article
Biochemistry & Molecular Biology
Sijie Liu, Yu Hua, Jingna Wang, Lingyan Li, Junjie Yuan, Bo Zhang, Ziyang Wang, Jianguo Ji, Daochun Kong
Summary: Protection of 30 overhangs in DNA double-strand breaks (DSBs) repair is achieved through the transient formation of RNA-DNA hybrids, with RNA polymerase III (RNAPIII) responsible for synthesizing the RNA strand. CtIP and MRN nuclease activity are required for initiating RNAPIII-mediated RNA synthesis at DSBs. Reduced RNAPIII levels suppress homologous recombination (HR) and lead to genetic loss > 30 bp at DSBs.
Article
Biochemistry & Molecular Biology
Juliette Restier-Verlet, Aurelie Joubert, Melanie L. Ferlazzo, Adeline Granzotto, Laurene Sonzogni, Joelle Al-Choboq, Laura El Nachef, Eymeric Le Reun, Michel Bourguignon, Nicolas Foray
Summary: Radiation-induced bystander effects (RIBE) refer to biological events occurring in non-targeted cells. It has been found that medium transfer-induced RIBE can result in DNA double-strand breaks, while micro-irradiation-induced RIBE shows the same temporal occurrence. The effects of RIBE on surrounding tissues can be beneficial or deleterious depending on their radiosensitivity and ability to release Ca2+ ions.
Article
Biochemistry & Molecular Biology
Laurene Sonzogni, Melanie L. Ferlazzo, Adeline Granzotto, Beatrice Fervers, Laurent Charlet, Nicolas Foray
Summary: The mechanistic model RIANS from radiobiology is crucial for understanding the recognition, repair and genotoxic stress response of DNA double-strand breaks induced by radiation. This model also applies to exposure to metal ions. Our study found that the induction of DSB by pesticides depends on their concentration and the RIANS status of cells. Impaired DSB recognition and repair, leading to toxicity, can occur when the nucleo-shuttling of ATM is delayed. Additionally, the combination of certain metal ions and pesticides can have additive or supra-additive effects on DSB recognition and/or repair.
Review
Cell Biology
Ksenia G. Kolobynina, Alexander Rapp, M. Cristina Cardoso
Summary: Chromatin serves as the background for all DNA-based molecular processes in the cell nucleus. The initial chromatin structure at the site of DNA damage determines lesion generation and activation of the DNA damage response pathway. Ubiquitination, as an important chromatin post-translational modification, is involved in chromatin changes at the damaged site and throughout the genome.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Materials Science, Multidisciplinary
Joas Grossi, Jorge Kohanoff, Eduardo M. Bringa
MATERIALS RESEARCH EXPRESS
(2020)
Article
Chemistry, Physical
Bin Gu, Brian Cunningham, Daniel Munoz Santiburcio, Fabiana Da Pieve, Emilio Artacho, Jorge Kohanoff
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Geochemistry & Geophysics
F. Da Pieve, G. Gronoff, J. Guo, C. J. Mertens, L. Neary, B. Gu, N. E. Koval, J. Kohanoff, A. C. Vandaele, F. Cleri
Summary: This study investigates the radiation environment induced by galactic and solar radiation at Oxia Planum and Mawrth Vallis on Mars, revealing similar conditions at different sites during solar minimum and maximum, with slightly enhanced gamma-ray contribution in water-rich regolith. The exposure estimates for different locations show reasonable to large safety margins for long stays and low risk for short stays, with the influence of ground composition on radiation levels highlighted.
JOURNAL OF GEOPHYSICAL RESEARCH-PLANETS
(2021)
Article
Materials Science, Multidisciplinary
Javier F. Troncoso, Piotr Chudzinski, Tchavdar N. Todorov, Pablo Aguado-Puente, Myrta Gruening, Jorge J. Kohanoff
Summary: PbTe is a leading thermoelectric material at intermediate temperatures due to its low lattice thermal conductivity, but its efficiency can be enhanced by designing nanostructures. The presence of grain boundaries and voids can reduce thermal conductivity and impede grain growth kinetics.
PHYSICAL REVIEW MATERIALS
(2021)
Article
Green & Sustainable Science & Technology
Xiaoli Liu, Ruchita Jani, Esther Orisakwe, Conrad Johnston, Piotr Chudzinski, Ming Qu, Brian Norton, Niall Holmes, Jorge Kohanoff, Lorenzo Stella, Hongxi Yin, Kazuaki Yazawa
Summary: Thermoelectric cement is a composite material with the potential to enhance ordinary cement's thermoelectric performance, allowing for electricity generation from waste heat, reducing fossil fuel usage, and supplementing other renewable energy sources.
RENEWABLE & SUSTAINABLE ENERGY REVIEWS
(2021)
Article
Optics
Lorenzo Stella, Jonathan Smyth, Brendan Dromey, Jorge Kohanoff
Summary: This study models the relaxation of free electron-hole pairs generated after proton irradiation using a simplified set of hydrodynamic equations, and finds both ultrafast and long relaxation times in amorphous SiO2, indicating the necessity of considering factors such as Coulomb screening and thermal detrapping of self-trapped excitons (STEs).
EUROPEAN PHYSICAL JOURNAL D
(2021)
Article
Optics
Jorge Kohanoff, Alfredo A. Correa, Gleb Gribakin, Conrad Johnston, Andres Saul
Summary: Cement, as a barrier for nuclear waste disposal, may be contaminated with radioactive products, particularly Sr-90. Research has shown that beta-decay events in cement can lead to a series of non-equilibrium processes, causing perturbations in surrounding electronic charge and chemical/structural changes.
EUROPEAN PHYSICAL JOURNAL D
(2021)
Article
Chemistry, Physical
Bin Gu, Daniel Munoz-Santiburcio, Fabrizio Cleri, Emilio Artacho, Jorge Kohanoff, Fabiana Da Pieve
Summary: The electronic stopping power (Se) of water vapor, hydrogen, and oxygen gases for protons was calculated using real-time time-dependent density functional theory. The results were compared to experimental and SRIM data, and the applicability of the Bragg's Additivity Rule was validated. The contributions of hydrogen and oxygen atoms to the electronic stopping power were also analyzed, revealing slight differences due to the neglected bond contributions in SRIM.
RADIATION PHYSICS AND CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Natalia E. E. Koval, Peter Koval, Fabiana Da Pieve, Jorge Kohanoff, Emilio Artacho, Dimitris Emfietzoglou
Summary: This work presents ab initio calculations of the energy loss function (ELF) and inelastic scattering cross sections in liquid water using linear-response time-dependent density functional theory. The results show good agreement with recent calculations and experimental data. The study also provides an analysis of the contributions of different molecular orbitals, species, and orbital angular momenta to the total ELF, as well as single-differential cross sections for each molecular orbital channel, which can be useful for Monte Carlo track-structure simulations.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Construction & Building Technology
Xiaoli Liu, Kazuaki Yazawa, Ming Qu, Orkan Kurtulus, Brian Norton, Niall Holmes, Ruchita Jani, Jorge Kohanoff, Lorenzo Stella, Conrad Johnston, Hongxi Yin
Summary: The thermoelectric building envelope (TBE) integrates thermoelectric materials with the building envelope for active space heating and cooling. This study experimentally evaluates the heating and cooling performance of a TBE prototype under various operating conditions and provides critical guidance for TBE applications.
ENERGY AND BUILDINGS
(2022)
Article
Polymer Science
Ruchita Jani, Niall Holmes, Roger West, Kevin Gaughan, Xiaoli Liu, Ming Qu, Esther Orisakwe, Lorenzo Stella, Jorge Kohanoff, Hongxi Yin, Bartlomiej Wojciechowski
Summary: Thermoelectric materials can convert thermal energy into electrical energy, and can be used to harvest the heat energy generated by temperature differences between the inside and outside of buildings. This paper presents research on the development and characterization of a cement-based thermoelectric material, which is doped with metal oxides to enhance its thermoelectric properties. The study also discusses the positive impact of moisture content on the electrical conductivity of the material.
Editorial Material
Optics
Tzveta Apostolova, Jorge Kohanoff, Nikita Medvedev, Eduardo Oliva, Antonio Rivera
Summary: This topical issue gathers recent developments and specific applications of combined and multi-scale modeling in the field of intense electronic excitation of matter, and discusses the paradigm of hybrid models and the motivation behind developing such combined approaches.
EUROPEAN PHYSICAL JOURNAL D
(2022)
Article
Optics
Alejandro Prada, Francisco Sanchez-Perez, Mathieu Bailly-Grandvaux, Eduardo Bringa, Maria Jose Caturla, Jose Manuel Perlado, Jorge Kohanoff, Ovidio Pena-Rodriguez, Antonio Rivera
Summary: We studied the thermal evolution of surface atoms in amorphous silica under high electronic excitation produced by irradiation with swift heavy ions using a validated atomistic model based on molecular dynamics. Three mechanisms, including ejection, collective and flow mechanisms, were found to be responsible for the evolution of the surface region, explaining the experimental observations of angular distributions of emitted atoms, total sputtering yield, and changes in density, residual stress, defect formation, and optical properties.
EUROPEAN PHYSICAL JOURNAL D
(2023)
Article
Materials Science, Multidisciplinary
Johannes L. Teunissen, Thomas Jarrin, Nicolas Richard, Natalia E. Koval, Daniel Munoz Santiburcio, Jorge Kohanoff, Emilio Artacho, Fabrizio Cleri, Fabiana Da Pieve
Summary: Understanding the generation and evolution of defects induced by ion irradiation is vital for estimating the degradation of material properties. This study investigates collision cascades in GaAs and demonstrates the significant impact of electronic stopping on the number of defects. The results also contribute to discussions on estimating material degradation using nonionizing energy loss models.
PHYSICAL REVIEW MATERIALS
(2023)
Article
Physics, Multidisciplinary
Natalia E. Koval, Fabiana Da Pieve, Bin Gu, Daniel Munoz-Santiburcio, Jorge Kohanoff, Emilio Artacho
Summary: We conducted real-time time-dependent density-functional-theory calculations on the electronic stopping power of negative and positive projectiles moving through liquid water, including electrons, protons, antiprotons, and muons. Our results, after accounting for finite mass effects, show significant differences compared to previously known semiempirical calculations using the dielectric response formalism. We found discrepancies between the linear and nonlinear stopping power, both in terms of the maximum value and the position of the Bragg peak. Our findings highlight the importance of accounting for nonlinearity in electronic processes, particularly for electron projectiles modeled as classical point charges, and confirm the expected substantial influence of the quantum nature of electron projectiles on stopping power around and below the Bragg peak.
PHYSICAL REVIEW RESEARCH
(2023)
