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Rafiepour P, Sina S, Amoli ZA, Shekarforoush SS, Farajzadeh E, Mortazavi SMJ. A mechanistic simulation of induced DNA damage in a bacterial cell by X- and gamma rays: a parameter study. Phys Eng Sci Med 2024; 47:1015-1035. [PMID: 38652348 DOI: 10.1007/s13246-024-01424-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 04/07/2024] [Indexed: 04/25/2024]
Abstract
Mechanistic Monte Carlo simulations calculating DNA damage caused by ionizing radiation are highly dependent on the simulation parameters. In the present study, using the Geant4-DNA toolkit, the impact of different parameters on DNA damage induced in a bacterial cell by X- and gamma-ray irradiation was investigated. Three geometry configurations, including the simple (without DNA details), the random (a random multiplication of identical DNA segments), and the fractal (a regular replication of DNA segments using fractal Hilbert curves), were simulated. Also, three physics constructors implemented in Geant4-DNA, i.e., G4EmDNAPhysics_option2, G4EmDNAPhysics_option4, and G4EmDNAPhysics_option6, with two energy thresholds of 17.5 eV and 5-37.5 eV were compared for direct DNA damage calculations. Finally, a previously developed mathematical model of cell repair called MEDRAS (Mechanistic DNA Repair and Survival) was employed to compare the impact of physics constructors on the cell survival curve. The simple geometry leads to undesirable results compared to the random and fractal ones, highlighting the importance of simulating complex DNA structures in mechanistic simulation studies. Under the same conditions, the DNA damage calculated in the fractal geometry was more consistent with the experimental data. All physics constructors can be used alternatively with the fractal geometry, provided that an energy threshold of 17.5 eV is considered for recording direct DNA damage. All physics constructors represent a similar behavior in generating cell survival curves, although the slopes of the curves are different. Since the inverse of the slope of a bacterial cell survival curve (i.e., the D10-value) is highly sensitive to the simulation parameters, it is not logical to determine an optimal set of parameters for calculating the D10-value by Monte Carlo simulation.
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Affiliation(s)
- Payman Rafiepour
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran
| | - Sedigheh Sina
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
- Radiation research center, School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
| | - Zahra Alizadeh Amoli
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Seyed Shahram Shekarforoush
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Ebrahim Farajzadeh
- Secondary Standard Dosimetry Laboratory (SSDL), Pars Isotope Co, Karaj, Iran
| | - Seyed Mohammad Javad Mortazavi
- Ionizing and Non-ionizing Radiation Protection Research Center (INIRPRC), Shiraz University of Medical Sciences, Shiraz, Iran
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2
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Akamatsu K, Endo T, Akagi H, Kono H, Itakura R. Specificity of DNA damage formation induced by femtosecond near-infrared laser filamentation in water. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 258:112994. [PMID: 39059070 DOI: 10.1016/j.jphotobiol.2024.112994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/16/2024] [Accepted: 07/22/2024] [Indexed: 07/28/2024]
Abstract
We investigated the deoxyribonucleic acid (DNA) damage induced by laser filamentation, which was generated by focusing femtosecond near-infrared Ti:Sapphire laser light in water at several repetition rates ranging from 1000 Hz to 10 Hz. Using plasmid DNA (pUC19), the single-strand break, double-strand break, nucleobase lesions, and the fragmented DNA were analyzed and quantified by agarose gel electrophoresis. Additionally, the H2O2 concentration after irradiation was determined. We observed that (1) the DNA damage per laser shot and (2) the enzyme-sensitive base lesions per total DNA damage decreased as the laser repetition rate increased. Furthermore, (3) extraordinarily short DNA fragments were likely to be produced, compared with those produced using X-rays, and (4) most OH radicals could be eliminated by recombination to generate H2O2, preventing them from damaging the DNA. The Monte-Carlo simulation of the strand break formation implies that the observed dependency of strand break efficiency on the laser repetition rate is mainly due to diffusion of DNA molecules. These findings quantitatively and qualitatively revealed that an intense laser pulse induces a specific DNA damage profile that is not induced by X-rays, a sparsely ionizing radiation source.
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Affiliation(s)
- Ken Akamatsu
- Kansai Institute for Photon Science, National Institutes for Quantum Science and Technology (QST), Kizugawa 619-0215, Japan.
| | - Tomoyuki Endo
- Kansai Institute for Photon Science, National Institutes for Quantum Science and Technology (QST), Kizugawa 619-0215, Japan
| | - Hiroshi Akagi
- Kansai Institute for Photon Science, National Institutes for Quantum Science and Technology (QST), Kizugawa 619-0215, Japan
| | - Hirohiko Kono
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Ryuji Itakura
- Kansai Institute for Photon Science, National Institutes for Quantum Science and Technology (QST), Kizugawa 619-0215, Japan
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3
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Tuan Anh L, Ngoc Hoang T, Thibaut Y, Chatzipapas K, Sakata D, Incerti S, Villagrasa C, Perrot Y. "dsbandrepair" - An updated Geant4-DNA simulation tool for evaluating the radiation-induced DNA damage and its repair. Phys Med 2024; 124:103422. [PMID: 38981169 DOI: 10.1016/j.ejmp.2024.103422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/07/2024] [Accepted: 06/29/2024] [Indexed: 07/11/2024] Open
Abstract
PURPOSE Interdisciplinary scientific communities have shown large interest to achieve a mechanistic description of radiation-induced biological damage, aiming to predict biological results produced by different radiation quality exposures. Monte Carlo track-structure simulations are suitable and reliable for the study of early DNA damage induction used as input for assessing DNA damage. This study presents the most recent improvements of a Geant4-DNA simulation tool named "dsbandrepair". METHODS "dsbandrepair" is a Monte Carlo simulation tool based on a previous code (FullSim) that estimates the induction of early DNA single-strand breaks (SSBs) and double-strand breaks (DSBs). It uses DNA geometries generated by the DNAFabric computational tool for simulating the induction of early single-strand breaks (SSBs) and double-strand breaks (DSBs). Moreover, the new tool includes some published radiobiological models for survival fraction and un-rejoined DSB. Its application for a human fibroblast cell and human umbilical vein endothelial cell containing both heterochromatin and euchromatin was conducted. In addition, this new version offers the possibility of using the new IRT-syn method for computing the chemical stage. RESULTS The direct and indirect strand breaks, SSBs, DSBs, and damage complexity obtained in this work are equivalent to those obtained with the previously published simulation tool when using the same configuration in the physical and chemical stages. Simulation results on survival fraction and un-rejoined DSB are in reasonable agreement with experimental data. CONCLUSIONS "dsbandrepair" is a tool for simulating DNA damage and repair, benchmarked against experimental data. It has been released as an advanced example in Geant4.11.2.
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Affiliation(s)
- Le Tuan Anh
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
| | - Tran Ngoc Hoang
- CNRS/IN2P3, CENBG, UMR 5797, Bordeaux University, 33170 Gradignan, France
| | - Yann Thibaut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
| | | | | | - Sébastien Incerti
- CNRS/IN2P3, CENBG, UMR 5797, Bordeaux University, 33170 Gradignan, France
| | - Carmen Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
| | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
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4
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Chattaraj A, Selvam TP. Radiation-induced DNA damage by proton, helium and carbon ions in human fibroblast cell: Geant4-DNA and MCDS-based study. Biomed Phys Eng Express 2024; 10:045059. [PMID: 38870909 DOI: 10.1088/2057-1976/ad57ce] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/13/2024] [Indexed: 06/15/2024]
Abstract
Background. Radiation-induced DNA damages such as Single Strand Break (SSB), Double Strand Break (DSB) and Complex DSB (cDSB) are critical aspects of radiobiology with implications in radiotherapy and radiation protection applications.Materials and Methods. This study presents a thorough investigation into the effects of protons (0.1-100 MeV/u), helium ions (0.13-100 MeV/u) and carbon ions (0.5-480 MeV/u) on DNA of human fibroblast cells using Geant4-DNA track structure code coupled with DBSCAN algorithm and Monte Carlo Damage Simulations (MCDS) code. Geant4-DNA-based simulations consider 1μm × 1μm × 0.5μm water box as the target to calculate energy deposition on event-by-event basis and the three-dimensional coordinates of the interaction location, and then DBSCAN algorithm is used to calculate yields of SSB, DSB and cDSB in human fibroblast cell. The study investigated the influence of Linear Energy Transfer (LET) of protons, helium ions and carbon ions on the yields of DNA damages. Influence of cellular oxygenation on DNA damage patterns is investigated using MCDS code.Results. The study shows that DSB and SSB yields are influenced by the LET of the particles, with distinct trends observed for different particles. The cellular oxygenation is a key factor, with anoxic cells exhibiting reduced SSB and DSB yields, underscoring the intricate relationship between cellular oxygen levels and DNA damage. The study introduced DSB/SSB ratio as an informative metric for evaluating the severity of radiation-induced DNA damage, particularly in higher LET regions.Conclusions. The study highlights the importance of considering particle type, LET, and cellular oxygenation in assessing the biological effects of ionizing radiation.
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Affiliation(s)
- Arghya Chattaraj
- Radiological Physics and Advisory Division, Health, Safety and Environment Group, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - T Palani Selvam
- Radiological Physics and Advisory Division, Health, Safety and Environment Group, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
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5
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Plante I, West DW, Weeks J, Risca VI. Simulation of Radiation-Induced DNA Damage and Protection by Histones Using the Code RITRACKS. BIOTECH 2024; 13:17. [PMID: 38921049 PMCID: PMC11201919 DOI: 10.3390/biotech13020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/10/2024] [Accepted: 05/31/2024] [Indexed: 06/27/2024] Open
Abstract
(1) Background: DNA damage is of great importance in the understanding of the effects of ionizing radiation. Various types of DNA damage can result from exposure to ionizing radiation, with clustered types considered the most important for radiobiological effects. (2) Methods: The code RITRACKS (Relativistic Ion Tracks), a program that simulates stochastic radiation track structures, was used to simulate DNA damage by photons and ions spanning a broad range of linear energy transfer (LET) values. To perform these simulations, the transport code was modified to include cross sections for the interactions of ions or electrons with DNA and amino acids for ionizations, dissociative electron attachment, and elastic collisions. The radiochemistry simulations were performed using a step-by-step algorithm that follows the evolution of all particles in time, including reactions between radicals and DNA structures and amino acids. Furthermore, detailed DNA damage events, such as base pair positions, DNA fragment lengths, and fragment yields, were recorded. (3) Results: We report simulation results using photons and the ions 1H+, 4He2+, 12C6+, 16O8+, and 56Fe26+ at various energies, covering LET values from 0.3 to 164 keV/µm, and performed a comparison with other codes and experimental results. The results show evidence of DNA protection from damage at its points of contacts with histone proteins. (4) Conclusions: RITRACKS can provide a framework for studying DNA damage from a variety of ionizing radiation sources with detailed representations of DNA at the atomic scale, DNA-associated proteins, and resulting DNA damage events and statistics, enabling a broader range of future comparisons with experiments such as those based on DNA sequencing.
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Affiliation(s)
| | - Devany W. West
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY 10065, USA; (D.W.W.); (V.I.R.)
| | - Jason Weeks
- NASA Johnson Space Center, Houston, TX 77058, USA;
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY 10065, USA; (D.W.W.); (V.I.R.)
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6
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Liu Y, Zhu K, Peng X, Luo S, Zhu J, Xiao W, He L, Wang X. Proton relative biological effectiveness for the induction of DNA double strand breaks based on Geant4. Biomed Phys Eng Express 2024; 10:035018. [PMID: 38181453 DOI: 10.1088/2057-1976/ad1bb9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/05/2024] [Indexed: 01/07/2024]
Abstract
Uncertainties in the relative biological effectiveness (RBE) of proton remains a major barrier to the biological optimization of proton therapy. A large amount of experimental data suggest that proton RBE is variable. As an evolving Monte Carlo code toolkit, Geant4-DNA is able to simulate the initial DNA damage caused by particle beams through physical and chemical interactions at the nanometer scale over a short period of time. This contributes to evaluating the radiobiological effects induced by ionizing radiation. Based on the Geant4-DNA toolkit, this study constructed a DNA geometric model containing 6.32Gbp, simulated the relationship between radiochemical yields (G-values) and their corresponding chemical constructors, and calculated a detailed calculation of the sources of damage and the complexity of damage in DNA strand breaks. The damage model constructed in this study can simulate the relative biological effectiveness (RBE) in the proton Bragg peak region. The results indicate that: (1) When the electron energy is below 400 keV, the yield of OH·account for 18.1% to 25.3% of the total water radiolysis yields. (2) Under the influence of histone clearance function, the yield of indirect damage account for over 72.93% of the yield of DNA strand breaks (SBs). When linear energy transfer (LET) increased from 29.79 (keV/μm) to 64.29 (keV/μm), the yield of double strand breaks (DSB) increased from 17.27% to 32.65%. (3) By investigating the effect of proton Bragg peak depth on the yield of direct DSB (DSBdirect) and total DSB (DSBtotal), theRBEDSBtotandRBEDSBdirlevels of cells show that the RBE value of protons reaches 2.2 in the Bragg peak region.
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Affiliation(s)
- Yuchen Liu
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
| | - Kun Zhu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou 215123, People's Republic of China
| | - Xiaoyu Peng
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
| | - Siyuan Luo
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
| | - Jin Zhu
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
| | - Wancheng Xiao
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
| | - Lie He
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
| | - Xiaodong Wang
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
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7
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Chatzipapas KP, Tran NH, Dordevic M, Zivkovic S, Zein S, Shin W, Sakata D, Lampe N, Brown JMC, Ristic‐Fira A, Petrovic I, Kyriakou I, Emfietzoglou D, Guatelli S, Incerti S. Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application. PRECISION RADIATION ONCOLOGY 2023. [DOI: 10.1002/pro6.1186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Affiliation(s)
| | - Ngoc Hoang Tran
- University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan France
| | - Milos Dordevic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Sara Zivkovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Sara Zein
- University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan France
| | - Wook‐Geun Shin
- Physics Division, Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School Boston Massachusetts USA
| | | | | | - Jeremy M. C. Brown
- Department of Physics and Astronomy Swinburne University of Technology Melbourne Australia
| | - Aleksandra Ristic‐Fira
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Ivan Petrovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Ioanna Kyriakou
- Medical Physics Laboratory Department of Medicine University of Ioannina Ioannina Greece
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory Department of Medicine University of Ioannina Ioannina Greece
| | - Susanna Guatelli
- Centre for Medical Radiation Physics University of Wollongong Wollongong New South Wales Australia
| | - Sébastien Incerti
- University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan France
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8
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Mansouri E, Mesbahi A, Hejazi MS, Montazersaheb S, Tarhriz V, Ghasemnejad T, Zarei M. Nanoscopic biodosimetry using plasmid DNA in radiotherapy with metallic nanoparticles. J Appl Clin Med Phys 2022; 24:e13879. [PMID: 36546569 PMCID: PMC9924121 DOI: 10.1002/acm2.13879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/08/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Nanoscopic lesions (complex damages), are the most lethal lesions for the cells. As nanoparticles have become increasingly popular in radiation therapy and the importance of analyzing nanoscopic dose enhancement has increased, a reliable tool for nanodosimetry has become indispensable. In this regard, the DNA plasmid is a widely used tool as a nanodosimetry probe in radiobiology and nano-radiosensitization studies. This approach is helpful for unraveling the radiosensitization role of nanoparticles in terms of physical and physicochemical effects and for quantifying radiation-induced biological damage. This review discusses the potential of using plasmid DNA assays for assessing the relative effects of nano-radiosensitizers, which can provide a theoretical basis for the development of nanoscopic biodosimetry and nanoparticle-based radiotherapy.
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Affiliation(s)
- Elham Mansouri
- Drug Applied Research CenterTabriz University of Medical SciencesTabrizIran
| | - Asghar Mesbahi
- Molecular Medicine Research CenterInstitute of BiomedicineTabriz University of Medical SciencesTabrizIran,Medical Physics DepartmentMedical SchoolTabriz University of Medical SciencesTabrizIran
| | - Mohammad Saied Hejazi
- Molecular Medicine Research CenterInstitute of BiomedicineTabriz University of Medical SciencesTabrizIran
| | - Soheila Montazersaheb
- Molecular Medicine Research CenterInstitute of BiomedicineTabriz University of Medical SciencesTabrizIran
| | - Vahideh Tarhriz
- Molecular Medicine Research CenterInstitute of BiomedicineTabriz University of Medical SciencesTabrizIran
| | - Tohid Ghasemnejad
- Molecular Medicine Research CenterInstitute of BiomedicineTabriz University of Medical SciencesTabrizIran
| | - Mojtaba Zarei
- Drug Applied Research CenterTabriz University of Medical SciencesTabrizIran
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9
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Souli MP, Nikitaki Z, Puchalska M, Brabcová KP, Spyratou E, Kote P, Efstathopoulos EP, Hada M, Georgakilas AG, Sihver L. Clustered DNA Damage Patterns after Proton Therapy Beam Irradiation Using Plasmid DNA. Int J Mol Sci 2022; 23:ijms232415606. [PMID: 36555249 PMCID: PMC9779025 DOI: 10.3390/ijms232415606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Modeling ionizing radiation interaction with biological matter is a major scientific challenge, especially for protons that are nowadays widely used in cancer treatment. That presupposes a sound understanding of the mechanisms that take place from the early events of the induction of DNA damage. Herein, we present results of irradiation-induced complex DNA damage measurements using plasmid pBR322 along a typical Proton Treatment Plan at the MedAustron proton and carbon beam therapy facility (energy 137-198 MeV and Linear Energy Transfer (LET) range 1-9 keV/μm), by means of Agarose Gel Electrophoresis and DNA fragmentation using Atomic Force Microscopy (AFM). The induction rate Mbp-1 Gy-1 for each type of damage, single strand breaks (SSBs), double-strand breaks (DSBs), base lesions and non-DSB clusters was measured after irradiations in solutions with varying scavenging capacity containing 2-amino-2-(hydroxymethyl)propane-1,3-diol (Tris) and coumarin-3-carboxylic acid (C3CA) as scavengers. Our combined results reveal the determining role of LET and Reactive Oxygen Species (ROS) in DNA fragmentation. Furthermore, AFM used to measure apparent DNA lengths provided us with insights into the role of increasing LET in the induction of highly complex DNA damage.
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Affiliation(s)
- Maria P Souli
- Atominstitut, Technische Universität Wien, 1020 Vienna, Austria
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 15780 Athens, Greece
| | - Zacharenia Nikitaki
- Atominstitut, Technische Universität Wien, 1020 Vienna, Austria
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 15780 Athens, Greece
| | | | | | - Ellas Spyratou
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 11517 Athens, Greece
| | - Panagiotis Kote
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 15780 Athens, Greece
| | - Efstathios P Efstathopoulos
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 11517 Athens, Greece
| | - Megumi Hada
- Radiation Institute for Science & Engineering, Prairie View A&M University, Prairie View, TX 77446, USA
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 15780 Athens, Greece
| | - Lembit Sihver
- Atominstitut, Technische Universität Wien, 1020 Vienna, Austria
- Nuclear Physics Institute, Czech Academy of Sciences, Na Truhlářce 39/64, 180 86 Prague, Czech Republic
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10
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Matsuya Y, Kai T, Parisi A, Yoshii Y, Sato T. Application of a simple DNA damage model developed for electrons to proton irradiation. Phys Med Biol 2022; 67. [DOI: 10.1088/1361-6560/ac9a20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/13/2022] [Indexed: 01/18/2023]
Abstract
Abstract
Proton beam therapy allows irradiating tumor volumes with reduced side effects on normal tissues with respect to conventional x-ray radiotherapy. Biological effects such as cell killing after proton beam irradiations depend on the proton kinetic energy, which is intrinsically related to early DNA damage induction. As such, DNA damage estimation based on Monte Carlo simulations is a research topic of worldwide interest. Such simulation is a mean of investigating the mechanisms of DNA strand break formations. However, past modellings considering chemical processes and DNA structures require long calculation times. Particle and heavy ion transport system (PHITS) is one of the general-purpose Monte Carlo codes that can simulate track structure of protons, meanwhile cannot handle radical dynamics simulation in liquid water. It also includes a simple model enabling the efficient estimation of DNA damage yields only from the spatial distribution of ionizations and excitations without DNA geometry, which was originally developed for electron track-structure simulations. In this study, we investigated the potential application of the model to protons without any modification. The yields of single-strand breaks, double-strand breaks (DSBs) and the complex DSBs were assessed as functions of the proton kinetic energy. The PHITS-based estimation showed that the DSB yields increased as the linear energy transfer (LET) increased, and reproduced the experimental and simulated yields of various DNA damage types induced by protons with LET up to about 30 keV μm−1. These results suggest that the current DNA damage model implemented in PHITS is sufficient for estimating DNA lesion yields induced after protons irradiation except at very low energies (below 1 MeV). This model contributes to evaluating early biological impacts in radiation therapy.
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11
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Assessing the DNA Damaging Effectiveness of Ionizing Radiation Using Plasmid DNA. Int J Mol Sci 2022; 23:ijms232012459. [PMID: 36293322 PMCID: PMC9604049 DOI: 10.3390/ijms232012459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/17/2022] Open
Abstract
Plasmid DNA is useful for investigating the DNA damaging effects of ionizing radiation. In this study, we have explored the feasibility of plasmid DNA-based detectors to assess the DNA damaging effectiveness of two radiotherapy X-ray beam qualities after undergoing return shipment of ~8000 km between two institutions. The detectors consisted of 18 μL of pBR322 DNA enclosed with an aluminum seal in nine cylindrical cavities drilled into polycarbonate blocks. We shipped them to Toronto, Canada for irradiation with either 100 kVp or 6 MV X-ray beams to doses of 10, 20, and 30 Gy in triplicate before being shipped back to San Diego, USA. The Toronto return shipment also included non-irradiated controls and we kept a separate set of controls in San Diego. In San Diego, we quantified DNA single strand breaks (SSBs), double strand breaks (DSBs), and applied Nth and Fpg enzymes to quantify oxidized base damage. The rate of DSBs/Gy/plasmid was 2.8±0.7 greater for the 100 kVp than the 6 MV irradiation. The 100 kVp irradiation also resulted in 5±2 times more DSBs/SSB than the 6 MV beam, demonstrating that the detector is sensitive enough to quantify relative DNA damage effectiveness, even after shipment over thousands of kilometers.
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12
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Zhu K, Wu C, Peng X, Ji X, Luo S, Liu Y, Wang X. Nanoscale Calculation of Proton-Induced DNA Damage Using a Chromatin Geometry Model with Geant4-DNA. Int J Mol Sci 2022; 23:ijms23116343. [PMID: 35683021 PMCID: PMC9181653 DOI: 10.3390/ijms23116343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Monte Carlo simulations can quantify various types of DNA damage to evaluate the biological effects of ionizing radiation at the nanometer scale. This work presents a study simulating the DNA target response after proton irradiation. A chromatin fiber model and new physics constructors with the ELastic Scattering of Electrons and Positrons by neutral Atoms (ELSEPA) model were used to describe the DNA geometry and the physical stage of water radiolysis with the Geant4-DNA toolkit, respectively. Three key parameters (the energy threshold model for strand breaks, the physics model and the maximum distance to distinguish DSB clusters) of scoring DNA damage were studied to investigate the impact on the uncertainties of DNA damage. On the basis of comparison of our results with experimental data and published findings, we were able to accurately predict the yield of various types of DNA damage. Our results indicated that the difference in physics constructor can cause up to 56.4% in the DNA double-strand break (DSB) yields. The DSB yields were quite sensitive to the energy threshold for strand breaks (SB) and the maximum distance to classify the DSB clusters, which were even more than 100 times and four times than the default configurations, respectively.
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Affiliation(s)
- Kun Zhu
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Chun Wu
- School of Nursing, University of South China, Hengyang 421001, China;
| | - Xiaoyu Peng
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Xuantao Ji
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Siyuan Luo
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Yuchen Liu
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Xiaodong Wang
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
- Correspondence:
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13
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Matsuya Y, Kai T, Sato T, Ogawa T, Hirata Y, Yoshii Y, Parisi A, Liamsuwan T. Track-structure modes in particle and heavy ion transport code system (PHITS): application to radiobiological research. Int J Radiat Biol 2021; 98:148-157. [PMID: 34930091 DOI: 10.1080/09553002.2022.2013572] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE In radiation physics, Monte Carlo radiation transport simulations are powerful tools to evaluate the cellular responses after irradiation. When investigating such radiation-induced biological effects, it is essential to perform track structure simulations by explicitly considering each atomic interaction in liquid water at the sub-cellular and DNA scales. The Particle and Heavy-Ion Transport code System (PHITS) is a Monte Carlo code which enables to calculate track structure at DNA scale by employing the track-structure modes for electrons, protons and carbon ions. In this paper, we review the recent development status and future prospects of the track-structure modes in the PHITS code. CONCLUSIONS To date, the physical features of these modes have been verified using the available experimental data and Monte Carlo simulation results reported in literature. These track-structure modes can be used for calculating microdosimetric distributions to estimate cell survival and for estimating initial DNA damage yields. The use of PHITS track-structure mode is expected not only to clarify the underlying mechanisms of radiation effects but also to predict curative effects in radiation therapy. The results of PHITS simulations coupled with biophysical models will contribute to the radiobiological studies by precisely predicting radiation-induced biological effects based on the Monte Carlo approach.
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Affiliation(s)
- Yusuke Matsuya
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, Tokai, Japan
| | - Takeshi Kai
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, Tokai, Japan
| | - Tatsuhiko Sato
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, Tokai, Japan
| | - Tatsuhiko Ogawa
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, Tokai, Japan
| | - Yuho Hirata
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, Tokai, Japan
| | - Yuji Yoshii
- Central Institute of Isotope Science, Hokkaido University, Sapporo, Japan
| | - Alessio Parisi
- Department of Radiation Oncology, Mayo Clinic, Jacksonville, Florida
| | - Thiansin Liamsuwan
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
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14
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Rucinski A, Biernacka A, Schulte R. Applications of nanodosimetry in particle therapy planning and beyond. Phys Med Biol 2021; 66. [PMID: 34731854 DOI: 10.1088/1361-6560/ac35f1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/03/2021] [Indexed: 12/28/2022]
Abstract
This topical review summarizes underlying concepts of nanodosimetry. It describes the development and current status of nanodosimetric detector technology. It also gives an overview of Monte Carlo track structure simulations that can provide nanodosimetric parameters for treatment planning of proton and ion therapy. Classical and modern radiobiological assays that can be used to demonstrate the relationship between the frequency and complexity of DNA lesion clusters and nanodosimetric parameters are reviewed. At the end of the review, existing approaches of treatment planning based on relative biological effectiveness (RBE) models or dose-averaged linear energy transfer are contrasted with an RBE-independent approach based on nandosimetric parameters. Beyond treatment planning, nanodosimetry is also expected to have applications and give new insights into radiation protection dosimetry.
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Affiliation(s)
| | - Anna Biernacka
- University of Gdansk, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdansk, 80-307 Gdansk, Poland
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15
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A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast. Cancers (Basel) 2021; 13:cancers13194940. [PMID: 34638425 PMCID: PMC8508455 DOI: 10.3390/cancers13194940] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/21/2021] [Accepted: 09/26/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary DNA damage caused by ionizing radiation in a human fibroblast cell evaluated by the Geant4-DNA Monte Carlo toolkit is presented. A validation study using a computational geometric human DNA model was then carried out, and the calculated DNA damage as a function of particle type and energy is presented. The results of this work showed a significant improvement on past work and were consistent with recent radiobiological experimental data, such as damage yields. This work and the developed methodology could impact a broad number of research fields in which the understanding of radiation effects is crucial, such as cancer radiotherapy, space science, and medical physics. Abstract Accurately modeling the radiobiological mechanisms responsible for the induction of DNA damage remains a major scientific challenge, particularly for understanding the effects of low doses of ionizing radiation on living beings, such as the induction of carcinogenesis. A computational approach based on the Monte Carlo technique to simulate track structures in a biological medium is currently the most reliable method for calculating the early effects induced by ionizing radiation on DNA, the primary cellular target of such effects. The Geant4-DNA Monte Carlo toolkit can simulate not only the physical, but also the physico-chemical and chemical stages of water radiolysis. These stages can be combined with simplified geometric models of biological targets, such as DNA, to assess direct and indirect early DNA damage. In this study, DNA damage induced in a human fibroblast cell was evaluated using Geant4-DNA as a function of incident particle type (gammas, protons, and alphas) and energy. The resulting double-strand break yields as a function of linear energy transfer closely reproduced recent experimental data. Other quantities, such as fragment length distribution, scavengeable damage fraction, and time evolution of damage within an analytical repair model also supported the plausibility of predicting DNA damage using Geant4-DNA.The complete simulation chain application “molecularDNA”, an example for users of Geant4-DNA, will soon be distributed through Geant4.
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16
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Sala L, Zerolová A, Rodriguez A, Reimitz D, Davídková M, Ebel K, Bald I, Kočišek J. Folding DNA into origami nanostructures enhances resistance to ionizing radiation. NANOSCALE 2021; 13:11197-11203. [PMID: 34142687 PMCID: PMC8247635 DOI: 10.1039/d1nr02013g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/04/2021] [Indexed: 05/22/2023]
Abstract
We report experimental results on damage induced by ionizing radiation to DNA origami triangles which are commonly used prototypes for scaffolded DNA origami nanostructures. We demonstrate extreme stability of DNA origami upon irradiation, which is caused by (i) the multi-row design holding the shape of the origami even after severe damage to the scaffold DNA and (ii) the reduction of damage to the scaffold DNA due to the protective effect of the folded structure. With respect to damage induced by ionizing radiation, the protective effect of the structure is superior to that of a naturally paired DNA double helix. Present results allow estimating the stability of scaffolded DNA origami nanostructures in applications such as nanotechnology, pharmacy or in singulo molecular studies where they are exposed to ionizing radiation from natural and artificial sources. Additionally, possibilities are opened for scaffolded DNA use in the design of radiation-resistant and radio-sensitive materials.
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Affiliation(s)
- Leo Sala
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 18223 Prague, Czech Republic.
| | - Agnes Zerolová
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 18223 Prague, Czech Republic. and Department of Chemistry, Technical University of Liberec, 46117, Liberec, Czech Republic
| | - Alvaro Rodriguez
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 18223 Prague, Czech Republic.
| | - Dan Reimitz
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 18223 Prague, Czech Republic.
| | - Marie Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, 180 00 Prague, Czech Republic
| | - Kenny Ebel
- Institute of Chemistry-Physical Chemistry, Universität Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam, Germany
| | - Ilko Bald
- Institute of Chemistry-Physical Chemistry, Universität Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam, Germany
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 18223 Prague, Czech Republic.
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17
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McConnell KA, Chang C, Giebeler A, Liu L, Zhu Qu L, Moiseenko V. Double-strand breaks measured along a 160 MeV proton Bragg curve using a novel FIESTA-DNA probe in a cell-free environment. Phys Med Biol 2021; 66:054001. [PMID: 33470972 DOI: 10.1088/1361-6560/abdd89] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Proton radiotherapy treatment planning systems use a constant relative biological effectiveness (RBE) = 1.1 to convert proton absorbed dose into biologically equivalent high-energy photon dose. This method ignores linear energy transfer (LET) distributions, and RBE is known to change as a function of LET. Variable RBE approaches have been proposed for proton planning optimization. Experimental validation of models underlying these approaches is a pre-requisite for their clinical implementation. This validation has to probe every level in the evolution of radiation-induced biological damage leading to cell death, starting from DNA double-strand breaks (DSB). Using a novel FIESTA-DNA probe, we measured the probability of double-strand break (P DSB) along a 160 MeV proton Bragg curve at two dose levels (30 and 60 Gy (RBE)) and compared it to measurements in a 6 MV photon beam. A machined setup that held an Advanced Markus parallel plate chamber for proton dose verification alongside the probes was fabricated. Each sample set consisted of five 10 μl probes suspended inside plastic microcapillary tubes. These were irradiated with protons to 30 Gy (RBE) at depths of 5-17.5 cm and 60 Gy (RBE) at depths of 10-17.2 cm with 1 mm resolution around Bragg peak. Sample sets were also irradiated using 6MV photons to 20, 40, 60, and 80 Gy. For the 30 Gy (RBE) measurements, increases in P DSB/Gy were observed at 17.0 cm followed by decreases at larger depth. For the 60 Gy (RBE) measurements, no increase in P DSB/Gy was observed, but there was a decrease after 17.0 cm. Dose-response for P DSB between 30 and 60 Gy (RBE) showed less than doubling of P DSB when dose was doubled. Proton RBE effect from DSB, RBEP,DSB, was <1 except at the Bragg peak. The experiment showed that the novel probe can be used to perform DNA DSB measurements in a proton beam. To establish relevance to clinical environment, further investigation of the probe's chemical scavenging needs to be performed.
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Affiliation(s)
- Kristen A McConnell
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California, United States of America. California Proton Cancer Therapy Center, San Diego, CA 92121, United States of America
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18
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Small KL, Henthorn NT, Angal-Kalinin D, Chadwick AL, Santina E, Aitkenhead A, Kirkby KJ, Smith RJ, Surman M, Jones J, Farabolini W, Corsini R, Gamba D, Gilardi A, Merchant MJ, Jones RM. Evaluating very high energy electron RBE from nanodosimetric pBR322 plasmid DNA damage. Sci Rep 2021; 11:3341. [PMID: 33558553 PMCID: PMC7870938 DOI: 10.1038/s41598-021-82772-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/07/2020] [Indexed: 01/18/2023] Open
Abstract
This paper presents the first plasmid DNA irradiations carried out with Very High Energy Electrons (VHEE) over 100-200 MeV at the CLEAR user facility at CERN to determine the Relative Biological Effectiveness (RBE) of VHEE. DNA damage yields were measured in dry and aqueous environments to determine that ~ 99% of total DNA breaks were caused by indirect effects, consistent with other published measurements for protons and photons. Double-Strand Break (DSB) yield was used as the biological endpoint for RBE calculation, with values found to be consistent with established radiotherapy modalities. Similarities in physical damage between VHEE and conventional modalities gives confidence that biological effects of VHEE will also be similar-key for clinical implementation. Damage yields were used as a baseline for track structure simulations of VHEE plasmid irradiation using GEANT4-DNA. Current models for DSB yield have shown reasonable agreement with experimental values. The growing interest in FLASH radiotherapy motivated a study into DSB yield variation with dose rate following VHEE irradiation. No significant variations were observed between conventional and FLASH dose rate irradiations, indicating that no FLASH effect is seen under these conditions.
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Affiliation(s)
- K L Small
- The University of Manchester, Manchester, UK.
- The Cockcroft Institute, Daresbury, UK.
| | - N T Henthorn
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - D Angal-Kalinin
- The University of Manchester, Manchester, UK
- The Cockcroft Institute, Daresbury, UK
- ASTeC, STFC Daresbury Laboratory, Daresbury, Warrington, UK
| | - A L Chadwick
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - E Santina
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - A Aitkenhead
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, UK
| | - K J Kirkby
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - R J Smith
- The Cockcroft Institute, Daresbury, UK
- ASTeC, STFC Daresbury Laboratory, Daresbury, Warrington, UK
| | - M Surman
- The Cockcroft Institute, Daresbury, UK
- ASTeC, STFC Daresbury Laboratory, Daresbury, Warrington, UK
| | - J Jones
- The Cockcroft Institute, Daresbury, UK
- ASTeC, STFC Daresbury Laboratory, Daresbury, Warrington, UK
| | - W Farabolini
- CERN, Geneva, Switzerland
- CEA Saclay, IRFU-DACM, Saclay, France
| | | | | | - A Gilardi
- CERN, Geneva, Switzerland
- Federico II, DIETI, University of Napoli, Napoli, Italy
| | - M J Merchant
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - R M Jones
- The University of Manchester, Manchester, UK
- The Cockcroft Institute, Daresbury, UK
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19
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Lee SW, Kwon YJ, Baek I, Choi HI, Ahn JW, Kim JB, Kang SY, Kim SH, Jo YD. Mutagenic Effect of Proton Beams Characterized by Phenotypic Analysis and Whole Genome Sequencing in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:752108. [PMID: 34777430 PMCID: PMC8581144 DOI: 10.3389/fpls.2021.752108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/05/2021] [Indexed: 05/19/2023]
Abstract
Protons may have contributed to the evolution of plants as a major component of cosmic-rays and also have been used for mutagenesis in plants. Although the mutagenic effect of protons has been well-characterized in animals, no comprehensive phenotypic and genomic analyses has been reported in plants. Here, we investigated the phenotypes and whole genome sequences of Arabidopsis M2 lines derived by irradiation with proton beams and gamma-rays, to determine unique characteristics of proton beams in mutagenesis. We found that mutation frequency was dependent on the irradiation doses of both proton beams and gamma-rays. On the basis of the relationship between survival and mutation rates, we hypothesized that there may be a mutation rate threshold for survived individuals after irradiation. There were no significant differences between the total mutation rates in groups derived using proton beam or gamma-ray irradiation at doses that had similar impacts on survival rate. However, proton beam irradiation resulted in a broader mutant phenotype spectrum than gamma-ray irradiation, and proton beams generated more DNA structural variations (SVs) than gamma-rays. The most frequent SV was inversion. Most of the inversion junctions contained sequences with microhomology and were associated with the deletion of only a few nucleotides, which implies that preferential use of microhomology in non-homologous end joining was likely to be responsible for the SVs. These results show that protons, as particles with low linear energy transfer (LET), have unique characteristics in mutagenesis that partially overlap with those of low-LET gamma-rays and high-LET heavy ions in different respects.
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Affiliation(s)
- Sang Woo Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Yu-Jeong Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
- Department of Horticulture, Chonbuk National University, Jeonju-si, South Korea
| | - Inwoo Baek
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Si-Yong Kang
- Department of Horticulture, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
- *Correspondence: Yeong Deuk Jo,
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20
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Sakata D, Belov O, Bordage MC, Emfietzoglou D, Guatelli S, Inaniwa T, Ivanchenko V, Karamitros M, Kyriakou I, Lampe N, Petrovic I, Ristic-Fira A, Shin WG, Incerti S. Fully integrated Monte Carlo simulation for evaluating radiation induced DNA damage and subsequent repair using Geant4-DNA. Sci Rep 2020; 10:20788. [PMID: 33247225 PMCID: PMC7695857 DOI: 10.1038/s41598-020-75982-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022] Open
Abstract
Ionising radiation induced DNA damage and subsequent biological responses to it depend on the radiation’s track-structure and its energy loss distribution pattern. To investigate the underlying biological mechanisms involved in such complex system, there is need of predicting biological response by integrated Monte Carlo (MC) simulations across physics, chemistry and biology. Hence, in this work, we have developed an application using the open source Geant4-DNA toolkit to propose a realistic “fully integrated” MC simulation to calculate both early DNA damage and subsequent biological responses with time. We had previously developed an application allowing simulations of radiation induced early DNA damage on a naked cell nucleus model. In the new version presented in this work, we have developed three additional important features: (1) modeling of a realistic cell geometry, (2) inclusion of a biological repair model, (3) refinement of DNA damage parameters for direct damage and indirect damage scoring. The simulation results are validated with experimental data in terms of Single Strand Break (SSB) yields for plasmid and Double Strand Break (DSB) yields for plasmid/human cell. In addition, the yields of indirect DSBs are compatible with the experimental scavengeable damage fraction. The simulation application also demonstrates agreement with experimental data of \documentclass[12pt]{minimal}
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\begin{document}$$\gamma$$\end{document}γ-H2AX yields for gamma ray irradiation. Using this application, it is now possible to predict biological response along time through track-structure MC simulations.
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Affiliation(s)
- Dousatsu Sakata
- Department of Accelerator and Medical Physics, National Institute of Radiological Sciences, QST, Chiba, Japan.
| | - Oleg Belov
- Joint Institute for Nuclear Research, Dubna, Russia.,Dubna State University, Dubna, Russia
| | - Marie-Claude Bordage
- INSERM, UMR 1037, CRCT, Université Paul Sabatier, Toulouse, France.,UMR 1037, CRCT, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, Medical School, University of Ioannina, 45110, Ioannina, Greece
| | - Susanna Guatelli
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | - Taku Inaniwa
- Department of Accelerator and Medical Physics, National Institute of Radiological Sciences, QST, Chiba, Japan
| | - Vladimir Ivanchenko
- Geant4 Associates International Ltd, Hebden Bridge, UK.,Tomsk State University, Tomsk, Russia
| | | | - Ioanna Kyriakou
- Medical Physics Laboratory, Medical School, University of Ioannina, 45110, Ioannina, Greece
| | | | - Ivan Petrovic
- Vinca Institute of Nuclear Science, University of Belgrade, Belgrade, Serbia
| | | | - Wook-Geun Shin
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, Gradignan, 33170, France
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21
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Tang J, Xiao Q, Gui Z, Li B, Zhang P. Simulation of Proton-Induced DNA Damage Patterns Using an Improved Clustering Algorithm. Radiat Res 2020; 194:363-378. [PMID: 32931557 DOI: 10.1667/rr15552.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 07/23/2020] [Indexed: 11/03/2022]
Abstract
Simulations of deoxyribonucleic acid (DNA) molecular damage use the traversal algorithm that has the disadvantages of being time-consuming, slowly converging, and requiring high-performance computer clusters. This work presents an improved version of the algorithm, "density-based spatial clustering of applications with noise" (DBSCAN), using a KD-tree approach to find neighbors of each point for calculating clustered DNA damage. The resulting algorithm considers the spatial distributions for sites of energy deposition and hydroxyl radical attack, yielding the statistical probability of (single and double) DNA strand breaks. This work achieves high accuracy and high speed at calculating clustered DNA damage that has been induced by proton treatment at the molecular level while running on an i7 quad-core CPU. The simulations focus on the indirect effect generated by hydroxyl radical attack on DNA. The obtained results are consistent with those of other published experiments and simulations. Due to the array of chemical processes triggered by proton treatment, it is possible to predict the effects that different track structures of various energy protons produce on eliciting direct and indirect damage of DNA.
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Affiliation(s)
- Jing Tang
- Shanxi Provincial Key Laboratory for Biomedical Imaging and Big Data, North University of China, Taiyuan, 030051, P.R. China
| | - Qinfeng Xiao
- School of Computer and Information Technology, Beijing Jiaotong University, Beijing, 100044, P.R. China
| | - Zhiguo Gui
- Shanxi Provincial Key Laboratory for Biomedical Imaging and Big Data, North University of China, Taiyuan, 030051, P.R. China
| | - Baosheng Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, P.R. China
| | - Pengcheng Zhang
- Shanxi Provincial Key Laboratory for Biomedical Imaging and Big Data, North University of China, Taiyuan, 030051, P.R. China
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22
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Dai T, Li Q, Liu X, Dai Z, He P, Ma Y, Shen G, Chen W, Zhang H, Meng Q, Zhang X. Nanodosimetric quantities and RBE of a clinically relevant carbon-ion beam. Med Phys 2019; 47:772-780. [PMID: 31705768 DOI: 10.1002/mp.13914] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/09/2019] [Accepted: 11/01/2019] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Although carbon-ion therapy is becoming increasingly attractive to the treatment of tumors, details about the ionization pattern formed by therapeutic carbon-ion beam in tissue have not been fully investigated. In this work, systematic calculations for the nanodosimetric quantities and relative biological effectiveness (RBE) of a clinically relevant carbon-ion beam were studied for the first time. METHODS The method combining both track structure and condensed history Monte Carlo (MC) simulations was adopted to calculate the nanodosimetric quantities. Fragments and energy spectra at different positions of the radiation field of a clinically relevant carbon-ion pencil beam were generated by means of MC simulations in water. Nanodosimetric quantities such as mean ionization cluster size ( M 1 ), the first moment of conditional cluster size ( M 1 C 2 ), cumulative probability ( F 2 ), and conditional cumulative probability ( F 3 C 2 ) at these positions were then acquired based on the spectra and the pre-calculated nanodosimetric database created by track structure MC simulations. What's more, a novel approach to calculate RBE based on the said nanodosimetric quantities was introduced. The RBE calculations were then conducted for the carbon-ion beam at different water-equivalent depths. RESULTS Lateral distributions at various water-equivalent depths of both the nanodosimetric quantities and RBE values were obtained. The values of M 1 , M 1 C 2 , F 2 , and F 3 C 2 were 1.49, 2.67, 0.30, and 0.38 at the plateau at the beam central axis and maximized at 2.79, 5.69, 0.47, and 0.68 at the depths around the Bragg peak, respectively. At a given depth, M 1 and F 2 decreased laterally with increasing the distance to the beam central axis while M 1 C 2 and F 3 C 2 remained nearly unchanged at first and then decreased except for M 1 C 2 at the rising edge of the Bragg peak. The calculated RBE values were 1.07 at the plateau and 3.13 around the Bragg peak. Good agreement between the calculated RBE values and experimental data was obtained. CONCLUSIONS Different nanodosimetric quantities feature the track structure of therapeutic carbon-ion beam in different manners. Detailed ionization patterns generated by carbon-ion beam could be characterized by nanodosimetric quantities. Moreover the combined method adopted in this work to calculate nanodosimetric quantities is not only valid but also convenient. Nanodosimetric quantities are significantly helpful for the RBE calculations in carbon-ion therapy.
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Affiliation(s)
- Tianyuan Dai
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinguo Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongying Dai
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengbo He
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyuan Ma
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guosheng Shen
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiqiang Chen
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qianqian Meng
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofang Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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Sakata D, Lampe N, Karamitros M, Kyriakou I, Belov O, Bernal MA, Bolst D, Bordage MC, Breton V, Brown JM, Francis Z, Ivanchenko V, Meylan S, Murakami K, Okada S, Petrovic I, Ristic-Fira A, Santin G, Sarramia D, Sasaki T, Shin WG, Tang N, Tran HN, Villagrasa C, Emfietzoglou D, Nieminen P, Guatelli S, Incerti S. Evaluation of early radiation DNA damage in a fractal cell nucleus model using Geant4-DNA. Phys Med 2019; 62:152-157. [DOI: 10.1016/j.ejmp.2019.04.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/25/2019] [Accepted: 04/13/2019] [Indexed: 11/26/2022] Open
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24
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Petković VD, Keta OD, Vidosavljević MZ, Incerti S, Ristić Fira AM, Petrović IM. Biological outcomes of γ-radiation induced DNA damages in breast and lung cancer cells pretreated with free radical scavengers. Int J Radiat Biol 2019; 95:274-285. [PMID: 30451568 DOI: 10.1080/09553002.2019.1549753] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE Investigation of effects on DNA of γ-irradiated human cancer cells pretreated with free radical scavengers is aimed to create reference data which would enable assessment of the relative efficiency of high linear energy transfer (LET) radiations used in hadron therapy, i.e. protons and carbon ions. MATERIALS AND METHODS MCF-7 breast and HTB177 lung cancer cells are irradiated with γ-rays. To minimize indirect effects of irradiation, dimethyl sulfoxide (DMSO) or glycerol are applied as free radical scavengers. Biological response to irradiation is evaluated through clonogenic cell survival, immunocytochemical and cell cycle analysis, as well as expression of proteins involved in DNA damage response. RESULTS Examined cell lines reveal similar level of radioresistance. Application of scavengers leads to the rise of cell survival and decreases the number of DNA double strand breaks in irradiated cells. Differences in cell cycle and protein expression between the two cell lines are probably caused by different DNA damage repair mechanisms that are activated. CONCLUSION The obtained results show that DMSO and glycerol have good scavenging capacity, and may be used to minimize DNA damage induced by free radicals. Therefore, they will be used as the reference for comparison with high LET irradiations, as well as good experimental data suitable for validation of numerical simulations.
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Affiliation(s)
- Vladana D Petković
- a Vinča Institute of Nuclear Sciences , University of Belgrade , Belgrade , Serbia
| | - Otilija D Keta
- a Vinča Institute of Nuclear Sciences , University of Belgrade , Belgrade , Serbia
| | | | | | | | - Ivan M Petrović
- a Vinča Institute of Nuclear Sciences , University of Belgrade , Belgrade , Serbia
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25
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Panek A, Miszczyk J, Swakoń J. Biological effects and inter-individual variability in peripheral blood lymphocytes of healthy donors exposed to 60 MeV proton radiotherapeutic beam. Int J Radiat Biol 2018; 94:1085-1094. [PMID: 30273081 DOI: 10.1080/09553002.2019.1524941] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Purpose: The aim of our study was to investigate the amount of initial DNA damage and cellular repair capacity of human peripheral blood lymphocytes exposed to the therapeutic proton beam and compare it to X-rays. Materials and methods: Lymphocytes from 10 healthy donors were irradiated in the Spread Out Bragg Peak of the 60 MeV proton beam or, as a reference, exposed to 250 kV X-rays. DNA damage level was assessed using the alkaline version of the comet assay method. For both sources of radiation, dose-DNA damage response (0-4 Gy) and DNA repair kinetics (0-120 min) were estimated. The observed DNA damage was then used to calculate the relative biological effectiveness (RBE) of the proton beam in comparison to that of X-rays. Results: Dose-response relationships for the DNA damage level showed linear dependence for both proton beam and X-rays (R2 = 0.995 for protons and R2 = 0.993 for X-rays). Within the dose range of 1-4 Gy, protons were significantly more effective in inducing DNA damage than were X-rays (p < .05). The average RBE, calculated from the proton and X-ray doses required for the iso-effective, internally standardized tail DNA parameter (sT-DNA) was 1.28 ± 0.57. Similar half-life time of residual damage and repair efficiency of induced DNA damage for both radiation types were observed. In the X-irradiated group, significant inter-individual differences were observed. Conclusions: Proton therapy was more effective at high radiation doses. However, DNA damage repair mechanism after proton irradiation seems to differ from that following X-rays.
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Affiliation(s)
- Agnieszka Panek
- a Institute of Nuclear Physics Polish Academy of Sciences , Krakow , Poland
| | - Justyna Miszczyk
- a Institute of Nuclear Physics Polish Academy of Sciences , Krakow , Poland
| | - Jan Swakoń
- a Institute of Nuclear Physics Polish Academy of Sciences , Krakow , Poland
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26
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Šefl M, Pachnerová Brabcová K, Štěpán V. Dosimetry as a Catch in Radiobiology Experiments. Radiat Res 2018; 190:404-411. [PMID: 30016217 DOI: 10.1667/rr15020.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Experimental radiobiological studies in which the effects of ionizing radiation on a biological model are examined often highlight the biological aspects while missing detailed descriptions of the geometry, sample and dosimetric methods used. Such omissions can hinder the reproducibility and comparability of the experimental data. An application based on the Geant4 simulation toolkit was developed to design experiments using a biological solution placed in a microtube. The application was used to demonstrate the influence of the type of microtube, sample volume and energy of a proton source on the dose distribution across the sample, and on the mean dose in the whole sample. The results shown here are for samples represented by liquid water in the 0.4-, 1.5- and 2.0-ml microtubes irradiated with 20, 30 and 100 MeV proton beams. The results of this work demonstrate that the mean dose and homogeneity of the dose distribution within the sample strongly depend on all three parameters. Furthermore, this work shows how the dose uncertainty propagates into the scored primary DNA damages in plasmid DNA studies using agarose gel electrophoresis. This application is provided freely to assist users in verifying their experimental setup prior to the experiment.
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Affiliation(s)
- Martin Šefl
- a Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic.,b Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Prague, Czech Republic
| | | | - Václav Štěpán
- a Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
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27
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Forster JC, Douglass MJJ, Phillips WM, Bezak E. Monte Carlo Simulation of the Oxygen Effect in DNA Damage Induction by Ionizing Radiation. Radiat Res 2018; 190:248-261. [PMID: 29953346 DOI: 10.1667/rr15050.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
DNA damage induced by ionizing radiation exposure is enhanced in the presence of oxygen (the "oxygen effect"). Despite its practical importance in radiotherapy, the oxygen effect has largely been excluded from models that predict DNA damage from radiation tracks. A Monte Carlo-based algorithm was developed in MATLAB software to predict DNA damage from physical and chemical tracks through a cell nucleus simulated in Geant4-DNA, taking into account the effects of cellular oxygenation (pO2) on DNA radical chemistry processes. An initial spatial distribution of DNA base and sugar radicals was determined by spatially clustering direct events (that deposited at least 10.79 eV) and hydroxyl radical (•OH) interactions. The oxygen effect was modeled by increasing the efficiency with which sugar radicals from direct-type effects were converted to strand breaks from 0.6 to 1, the efficiency with which sugar radicals from the indirect effect were converted to strand breaks from 0.28 to 1 and the efficiency of base-to-sugar radical transfer from •OH-mediated base radicals from 0 to 0.03 with increasing pO2 from 0 to 760 mmHg. The DNA damage induction algorithm was applied to tracks from electrons, protons and alphas with LET values from 0.2 to 150 keV/μm under different pO2 conditions. The oxygen enhancement ratio for double-strand break induction was 3.0 for low-LET radiation up to approximately 15 keV/μm, after which it gradually decreased to a value of 1.3 at 150 keV/μm. These values were consistent with a range of experimental data published in the literature. The DNA damage yields were verified using experimental data in the literature and results from other theoretical models. The spatial clustering approach developed in this work has low memory requirements and may be suitable for particle tracking simulations with a large number of cells.
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Affiliation(s)
- Jake C Forster
- a Department of Physics, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia.,b Department of Medical Physics, Royal Adelaide Hospital, North Terrace, Adelaide, South Australia 5000, Australia
| | - Michael J J Douglass
- a Department of Physics, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia.,b Department of Medical Physics, Royal Adelaide Hospital, North Terrace, Adelaide, South Australia 5000, Australia
| | - Wendy M Phillips
- a Department of Physics, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia.,b Department of Medical Physics, Royal Adelaide Hospital, North Terrace, Adelaide, South Australia 5000, Australia
| | - Eva Bezak
- a Department of Physics, University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia.,c Cancer Research Institute and School of Health Sciences, University of South Australia, Adelaide, South Australia, Australia
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28
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Mechanistic DNA damage simulations in Geant4-DNA Part 2: Electron and proton damage in a bacterial cell. Phys Med 2018; 48:146-155. [DOI: 10.1016/j.ejmp.2017.12.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 11/29/2017] [Accepted: 12/08/2017] [Indexed: 11/18/2022] Open
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29
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Vyšín L, Burian T, Ukraintsev E, Davídková M, Grisham ME, Heinbuch S, Rocca JJ, Juha L. Dose-Rate Effects in Breaking DNA Strands by Short Pulses of Extreme Ultraviolet Radiation. Radiat Res 2018; 189:466-476. [PMID: 29505347 DOI: 10.1667/rr14825.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this study, we examined dose-rate effects on strand break formation in plasmid DNA induced by pulsed extreme ultraviolet (XUV) radiation. Dose delivered to the target molecule was controlled by attenuating the incident photon flux using aluminum filters as well as by changing the DNA/buffer-salt ratio in the irradiated sample. Irradiated samples were examined using agarose gel electrophoresis. Yields of single- and double-strand breaks (SSBs and DSBs) were determined as a function of the incident photon fluence. In addition, electrophoresis also revealed DNA cross-linking. Damaged DNA was inspected by means of atomic force microscopy (AFM). Both SSB and DSB yields decreased with dose rate increase. Quantum yields of SSBs at the highest photon fluence were comparable to yields of DSBs found after synchrotron irradiation. The average SSB/DSB ratio decreased only slightly at elevated dose rates. In conclusion, complex and/or clustered damages other than cross-links do not appear to be induced under the radiation conditions applied in this study.
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Affiliation(s)
- Luděk Vyšín
- a Institute of Physics.,e Department of Nuclear Chemistry, Czech Technical University in Prague, Prague, Czech Republic
| | - Tomáš Burian
- a Institute of Physics.,c Institute of Plasma Physics.,d J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | | | | | - Michael E Grisham
- f Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado
| | - Scott Heinbuch
- f Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado
| | - Jorge J Rocca
- f Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado
| | - Libor Juha
- a Institute of Physics.,c Institute of Plasma Physics
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30
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Henthorn NT, Warmenhoven JW, Sotiropoulos M, Mackay RI, Kirkby KJ, Merchant MJ. Nanodosimetric Simulation of Direct Ion-Induced DNA Damage Using Different Chromatin Geometry Models. Radiat Res 2017; 188:690-703. [PMID: 28792846 DOI: 10.1667/rr14755.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Monte Carlo based simulation has proven useful in investigating the effect of proton-induced DNA damage and the processes through which this damage occurs. Clustering of ionizations within a small volume can be related to DNA damage through the principles of nanodosimetry. For simulation, it is standard to construct a small volume of water and determine spatial clusters. More recently, realistic DNA geometries have been used, tracking energy depositions within DNA backbone volumes. Traditionally a chromatin fiber is built within the simulation and identically replicated throughout a cell nucleus, representing the cell in interphase. However, the in vivo geometry of the chromatin fiber is still unknown within the literature, with many proposed models. In this work, the Geant4-DNA toolkit was used to build three chromatin models: the solenoid, zig-zag and cross-linked geometries. All fibers were built to the same chromatin density of 4.2 nucleosomes/11 nm. The fibers were then irradiated with protons (LET 5-80 keV/μm) or alpha particles (LET 63-226 keV/μm). Nanodosimetric parameters were scored for each fiber after each LET and used as a comparator among the models. Statistically significant differences were observed in the double-strand break backbone size distributions among the models, although nonsignificant differences were noted among the nanodosimetric parameters. From the data presented in this article, we conclude that selection of the solenoid, zig-zag or cross-linked chromatin model does not significantly affect the calculated nanodosimetric parameters. This allows for a simulation-based cell model to make use of any of these chromatin models for the scoring of direct ion-induced DNA damage.
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Affiliation(s)
- N T Henthorn
- a Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - J W Warmenhoven
- a Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - M Sotiropoulos
- a Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - R I Mackay
- b Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, United Kingdom; and
| | - K J Kirkby
- a Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom.,c The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - M J Merchant
- a Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom.,c The Christie NHS Foundation Trust, Manchester, United Kingdom
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31
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Mavragani IV, Nikitaki Z, Souli MP, Aziz A, Nowsheen S, Aziz K, Rogakou E, Georgakilas AG. Complex DNA Damage: A Route to Radiation-Induced Genomic Instability and Carcinogenesis. Cancers (Basel) 2017; 9:cancers9070091. [PMID: 28718816 PMCID: PMC5532627 DOI: 10.3390/cancers9070091] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/06/2017] [Accepted: 07/14/2017] [Indexed: 12/26/2022] Open
Abstract
Cellular effects of ionizing radiation (IR) are of great variety and level, but they are mainly damaging since radiation can perturb all important components of the cell, from the membrane to the nucleus, due to alteration of different biological molecules ranging from lipids to proteins or DNA. Regarding DNA damage, which is the main focus of this review, as well as its repair, all current knowledge indicates that IR-induced DNA damage is always more complex than the corresponding endogenous damage resulting from endogenous oxidative stress. Specifically, it is expected that IR will create clusters of damage comprised of a diversity of DNA lesions like double strand breaks (DSBs), single strand breaks (SSBs) and base lesions within a short DNA region of up to 15–20 bp. Recent data from our groups and others support two main notions, that these damaged clusters are: (1) repair resistant, increasing genomic instability (GI) and malignant transformation and (2) can be considered as persistent “danger” signals promoting chronic inflammation and immune response, causing detrimental effects to the organism (like radiation toxicity). Last but not least, the paradigm shift for the role of radiation-induced systemic effects is also incorporated in this picture of IR-effects and consequences of complex DNA damage induction and its erroneous repair.
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Affiliation(s)
- Ifigeneia V Mavragani
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece.
| | - Zacharenia Nikitaki
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece.
| | - Maria P Souli
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece.
| | - Asef Aziz
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA.
| | - Somaira Nowsheen
- Mayo Medical Scientist Training Program, Mayo Medical School and Mayo Graduate School, Mayo Clinic, Rochester, MN 55905, USA.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.
| | - Khaled Aziz
- Mayo Medical Scientist Training Program, Mayo Medical School and Mayo Graduate School, Mayo Clinic, Rochester, MN 55905, USA.
| | - Emmy Rogakou
- First Department of Pediatrics, "Aghia Sophia" Children's Hospital, Medical School, University of Athens, 11527 Athens, Greece.
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece.
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32
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Souici M, Khalil TT, Muller D, Raffy Q, Barillon R, Belafrites A, Champion C, Fromm M. Single- and Double-Strand Breaks of Dry DNA Exposed to Protons at Bragg-Peak Energies. J Phys Chem B 2017; 121:497-507. [DOI: 10.1021/acs.jpcb.6b11060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mounir Souici
- Université de Bourgogne Franche-Comté, UMR CNRS 6249 Chrono-Environnement, 16 Route de Gray, 25030 Besançon Cedex, France
- Laboratoire
de Physique des Rayonnements et Applications, Université de Jijel, BP 98, Ouled Aissa, Jijel 18000, Algérie
| | - Talat T. Khalil
- Université de Bourgogne Franche-Comté, UMR CNRS 6249 Chrono-Environnement, 16 Route de Gray, 25030 Besançon Cedex, France
| | - Dominique Muller
- Laboratoire
ICube, CNRS-Université de Strasbourg, 23 rue du Loess, 67037 Strasbourg, France
| | - Quentin Raffy
- Institut Pluridisciplinaire Hubert Curien, UMR CNRS 7178, 23 rue du Loess, BP 28, 67037 Strasbourg Cedex 2, France
| | - Rémi Barillon
- Institut Pluridisciplinaire Hubert Curien, UMR CNRS 7178, 23 rue du Loess, BP 28, 67037 Strasbourg Cedex 2, France
| | - Abdelfettah Belafrites
- Laboratoire
de Physique des Rayonnements et Applications, Université de Jijel, BP 98, Ouled Aissa, Jijel 18000, Algérie
| | - Christophe Champion
- Université de Bordeaux, CNRS/IN2P3, Centre d’Etudes Nucléaires de Bordeaux Gradignan, CENBG, Chemin du Solarium, BP 120, 33175 Gradignan, France
| | - Michel Fromm
- Université de Bourgogne Franche-Comté, UMR CNRS 6249 Chrono-Environnement, 16 Route de Gray, 25030 Besançon Cedex, France
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Satyamitra MM, DiCarlo AL, Taliaferro L. Understanding the Pathophysiology and Challenges of Development of Medical Countermeasures for Radiation-Induced Vascular/Endothelial Cell Injuries: Report of a NIAID Workshop, August 20, 2015. Radiat Res 2016; 186:99-111. [PMID: 27387859 DOI: 10.1667/rr14436.1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
After the events of September 11, 2001, a decade of research on the development of medical countermeasures (MCMs) to treat victims of a radiological incident has yielded two FDA-approved agents to mitigate acute radiation syndrome. These licensed agents specifically target the mitigation of radiation-induced neutropenia and infection potential, while the ramifications of the exposure event in a public health emergency incident could include the entire body, causing additional acute and/or delayed organ/tissue injuries. Anecdotal data as well as recent findings from both radiation accident survivors and animal experiments implicate radiation-induced injury or dysfunction of the vascular endothelium leading to tissue and organ injuries. There are significant gaps in our understanding of the disease processes and progression, as well as the optimum approaches to develop medical countermeasures to mitigate radiation vascular injury. To address this issue, the Radiation and Nuclear Countermeasures Program of the National Institute of Allergy and Infectious Diseases (NIAID) organized a one-day workshop to examine the current state of the science in radiation-induced vascular injuries and organ dysfunction, the natural history of the pathophysiology and the product development maturity of potential medical countermeasures to treat these injuries. Meeting presentations were followed by a NIAID-led open discussion among academic investigators, industry researchers and government agency representatives. This article provides a summary of these presentations and subsequent discussion from the workshop.
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Affiliation(s)
- Merriline M Satyamitra
- Division of Allergy Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
| | - Andrea L DiCarlo
- Division of Allergy Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
| | - Lanyn Taliaferro
- Division of Allergy Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
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Pachnerová Brabcová K, Štěpán V, Karamitros M, Karabín M, Dostálek P, Incerti S, Davídková M, Sihver L. Contribution of indirect effects to clustered damage in DNA irradiated with protons. RADIATION PROTECTION DOSIMETRY 2015; 166:44-48. [PMID: 25897140 DOI: 10.1093/rpd/ncv159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protons are the dominant particles both in galactic cosmic rays and in solar particle events and, furthermore, proton irradiation becomes increasingly used in tumour treatment. It is believed that complex DNA damage is the determining factor for the consequent cellular response to radiation. DNA plasmid pBR322 was irradiated at U120-M cyclotron with 30 MeV protons and treated with two Escherichia coli base excision repair enzymes. The yields of SSBs and DSBs were analysed using agarose gel electrophoresis. DNA has been irradiated in the presence of hydroxyl radical scavenger (coumarin-3-carboxylic acid) in order to distinguish between direct and indirect damage of the biological target. Pure scavenger solution was used as a probe for measurement of induced OH· radical yields. Experimental OH· radical yield kinetics was compared with predictions computed by two theoretical models-RADAMOL and Geant4-DNA. Both approaches use Geant4-DNA for description of physical stages of radiation action, and then each of them applies a distinct model for description of the pre-chemical and chemical stage.
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Affiliation(s)
- K Pachnerová Brabcová
- Department of Applied Physics, Chalmers University of Technology, Fysikgränd 3, Göteborg SE-412 96, Sweden Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, Prague 180 00, Czech Republic
| | - V Štěpán
- Université de Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucléaires de Bordeaux-Gradignan, CENBG, Chemin du Solarium, BP 120, 33175 Gradignan, France Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, Prague 180 00, Czech Republic
| | - M Karamitros
- Université de Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucléaires de Bordeaux-Gradignan, CENBG, Chemin du Solarium, BP 120, 33175 Gradignan, France
| | - M Karabín
- Department of Biotechnology, Institute of Chemical Technology Prague, Technická 5, Prague 166 28, Czech Republic
| | - P Dostálek
- Department of Biotechnology, Institute of Chemical Technology Prague, Technická 5, Prague 166 28, Czech Republic
| | - S Incerti
- Université de Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucléaires de Bordeaux-Gradignan, CENBG, Chemin du Solarium, BP 120, 33175 Gradignan, France
| | - M Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, Prague 180 00, Czech Republic
| | - L Sihver
- Department of Applied Physics, Chalmers University of Technology, Fysikgränd 3, Göteborg SE-412 96, Sweden Atominstitut, TU Wien, Stadionallee 2, 1020 Vienna, Austria
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Vyšín L, Pachnerová Brabcová K, Štěpán V, Moretto-Capelle P, Bugler B, Legube G, Cafarelli P, Casta R, Champeaux JP, Sence M, Vlk M, Wagner R, Štursa J, Zach V, Incerti S, Juha L, Davídková M. Proton-induced direct and indirect damage of plasmid DNA. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2015; 54:343-352. [PMID: 26007308 DOI: 10.1007/s00411-015-0605-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 05/15/2015] [Indexed: 06/04/2023]
Abstract
Clustered DNA damage induced by 10, 20 and 30 MeV protons in pBR322 plasmid DNA was investigated. Besides determination of strand breaks, additional lesions were detected using base excision repair enzymes. The plasmid was irradiated in dry form, where indirect radiation effects were almost fully suppressed, and in water solution containing only minimal residual radical scavenger. Simultaneous irradiation of the plasmid DNA in the dry form and in the solution demonstrated the contribution of the indirect effect as prevalent. The damage composition slightly differed when comparing the results for liquid and dry samples. The obtained data were also subjected to analysis concerning different methodological approaches, particularly the influence of irradiation geometry, models used for calculation of strand break yields and interpretation of the strand breaks detected with the enzymes. It was shown that these parameters strongly affect the results.
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Affiliation(s)
- Luděk Vyšín
- Institute of Physics CAS, Na Slovance 1999/2, 182 21, Prague, Czech Republic
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Abstract
In addition to the physical advantages (Bragg peak), the use of charged particles in cancer therapy can be associated with distinct biological effects compared to X-rays. While heavy ions (densely ionizing radiation) are known to have an energy- and charge-dependent increased Relative Biological Effectiveness (RBE), protons should not be very different from sparsely ionizing photons. A slightly increased biological effectiveness is taken into account in proton treatment planning by assuming a fixed RBE of 1.1 for the whole radiation field. However, data emerging from recent studies suggest that, for several end points of clinical relevance, the biological response is differentially modulated by protons compared to photons. In parallel, research in the field of medical physics highlighted how variations in RBE that are currently neglected might actually result in deposition of significant doses in healthy organs. This seems to be relevant in particular for normal tissues in the entrance region and for organs at risk close behind the tumor. All these aspects will be considered and discussed in this review, highlighting how a re-discussion of the role of a variable RBE in proton therapy might be well-timed.
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Pachnerová Brabcová K, Sihver L, Yasuda N, Matuo Y, Stěpán V, Davídková M. Clustered DNA damage on subcellular level: effect of scavengers. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2014; 53:705-712. [PMID: 25034012 DOI: 10.1007/s00411-014-0557-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/08/2014] [Indexed: 06/03/2023]
Abstract
Clustered DNA damages are induced by ionizing radiation, particularly of high linear energy transfer (LET). Compared to isolated DNA damage sites, their biological effects can be more severe. We investigated a clustered DNA damage induced by high LET radiation (C 290 MeV u(-1) and Fe 500 MeV u(-1)) in pBR322 plasmid DNA. The plasmid is dissolved in pure water or in aqueous solution of one of the three scavengers (coumarin-3-carboxylic acid, dimethylsulfoxide, and glycylglycine). The yield of double strand breaks (DSB) induced in the DNA plasmid-scavenger system by heavy ion radiation was found to decrease with increasing scavenging capacity due to reaction with hydroxyl radical, linearly with high correlation coefficients. The yield of non-DSB clusters was found to occur twice as much as the DSB. Their decrease with increasing scavenging capacity had lower linear correlation coefficients. This indicates that the yield of non-DSB clusters depends on more factors, which are likely connected to the chemical properties of individual scavengers.
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Pang D, Nico JS, Karam L, Timofeeva O, Blakely WF, Dritschilo A, Dizdaroglu M, Jaruga P. Significant disparity in base and sugar damage in DNA resulting from neutron and electron irradiation. JOURNAL OF RADIATION RESEARCH 2014; 55:1081-1088. [PMID: 25034731 PMCID: PMC4229924 DOI: 10.1093/jrr/rru059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 05/20/2014] [Accepted: 06/08/2014] [Indexed: 06/03/2023]
Abstract
In this study, a comparison of the effects of neutron and electron irradiation of aqueous DNA solutions was investigated to characterize potential neutron signatures in DNA damage induction. Ionizing radiation generates numerous lesions in DNA, including base and sugar lesions, lesions involving base-sugar combinations (e.g. 8,5'-cyclopurine-2'-deoxynucleosides) and DNA-protein cross-links, as well as single- and double-strand breaks and clustered damage. The characteristics of damage depend on the linear energy transfer (LET) of the incident radiation. Here we investigated DNA damage using aqueous DNA solutions in 10 mmol/l phosphate buffer from 0-80 Gy by low-LET electrons (10 Gy/min) and the specific high-LET (∼0.16 Gy/h) neutrons formed by spontaneous (252)Cf decay fissions. 8-hydroxy-2'-deoxyguanosine (8-OH-dG), (5'R)-8,5'-cyclo-2'-deoxyadenosine (R-cdA) and (5'S)-8,5'-cyclo-2'-deoxyadenosine (S-cdA) were quantified using liquid chromatography-isotope-dilution tandem mass spectrometry to demonstrate a linear dose dependence for induction of 8-OH-dG by both types of radiation, although neutron irradiation was ∼50% less effective at a given dose compared with electron irradiation. Electron irradiation resulted in an exponential increase in S-cdA and R-cdA with dose, whereas neutron irradiation induced substantially less damage and the amount of damage increased only gradually with dose. Addition of 30 mmol/l 2-amino-2-(hydroxymethyl)-1,3-propanediol (TRIS), a free radical scavenger, to the DNA solution before irradiation reduced lesion induction to background levels for both types of radiation. These results provide insight into the mechanisms of DNA damage by high-LET (252)Cf decay neutrons and low-LET electrons, leading to enhanced understanding of the potential biological effects of these types of irradiation.
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Affiliation(s)
- Dalong Pang
- Department of Radiation Medicine, Georgetown University Hospital, 3800 Reservoir Road, LL Bles, Washington, DC 20007, USA
| | - Jeffrey S Nico
- Radiation Physics Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Lisa Karam
- Radiation Physics Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Olga Timofeeva
- Department of Radiation Medicine, Georgetown University Hospital, 3800 Reservoir Road, LL Bles, Washington, DC 20007, USA
| | - William F Blakely
- Scientific Research Department, Armed Forces Radiobiological Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD 20889, USA
| | - Anatoly Dritschilo
- Department of Radiation Medicine, Georgetown University Hospital, 3800 Reservoir Road, LL Bles, Washington, DC 20007, USA
| | - Miral Dizdaroglu
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Pawel Jaruga
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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Paganetti H. Relative biological effectiveness (RBE) values for proton beam therapy. Variations as a function of biological endpoint, dose, and linear energy transfer. Phys Med Biol 2014; 59:R419-72. [PMID: 25361443 DOI: 10.1088/0031-9155/59/22/r419] [Citation(s) in RCA: 616] [Impact Index Per Article: 61.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proton therapy treatments are based on a proton RBE (relative biological effectiveness) relative to high-energy photons of 1.1. The use of this generic, spatially invariant RBE within tumors and normal tissues disregards the evidence that proton RBE varies with linear energy transfer (LET), physiological and biological factors, and clinical endpoint. Based on the available experimental data from published literature, this review analyzes relationships of RBE with dose, biological endpoint and physical properties of proton beams. The review distinguishes between endpoints relevant for tumor control probability and those potentially relevant for normal tissue complication. Numerous endpoints and experiments on sub-cellular damage and repair effects are discussed. Despite the large amount of data, considerable uncertainties in proton RBE values remain. As an average RBE for cell survival in the center of a typical spread-out Bragg peak (SOBP), the data support a value of ~1.15 at 2 Gy/fraction. The proton RBE increases with increasing LETd and thus with depth in an SOBP from ~1.1 in the entrance region, to ~1.15 in the center, ~1.35 at the distal edge and ~1.7 in the distal fall-off (when averaged over all cell lines, which may not be clinically representative). For small modulation widths the values could be increased. Furthermore, there is a trend of an increase in RBE as (α/β)x decreases. In most cases the RBE also increases with decreasing dose, specifically for systems with low (α/β)x. Data on RBE for endpoints other than clonogenic cell survival are too diverse to allow general statements other than that the RBE is, on average, in line with a value of ~1.1. This review can serve as a source for defining input parameters for applying or refining biophysical models and to identify endpoints where additional radiobiological data are needed in order to reduce the uncertainties to clinically acceptable levels.
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Affiliation(s)
- Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, 30 Fruit Street, Boston, MA 02114, USA
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Grant JD, Chang JY. Proton-based stereotactic ablative radiotherapy in early-stage non-small-cell lung cancer. BIOMED RESEARCH INTERNATIONAL 2014; 2014:389048. [PMID: 25136582 PMCID: PMC4124720 DOI: 10.1155/2014/389048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/30/2014] [Accepted: 06/21/2014] [Indexed: 12/12/2022]
Abstract
Stereotactic ablative radiotherapy (SABR), a recent implementation in the practice of radiation oncology, has been shown to confer high rates of local control in the treatment of early stage non-small-cell lung cancer (NSCLC). This technique, which involves limited invasive procedures and reduced treatment intervals, offers definitive treatment for patients unable or unwilling to undergo an operation. The use of protons in SABR delivery confers the added physical advantage of normal tissue sparing due to the absence of collateral radiation dose delivered to regions distal to the target. This may translate into clinical benefit and a decreased risk of clinical toxicity in patients with nearby critical structures or limited pulmonary reserve. In this review, we present the rationale for proton-based SABR, principles relating to the delivery and planning of this modality, and a summary of published clinical studies.
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Affiliation(s)
- Jonathan D. Grant
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Joe Y. Chang
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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Sanderson BA, Araki N, Lilley JL, Guerrero G, Lewis LK. Modification of gel architecture and TBE/TAE buffer composition to minimize heating during agarose gel electrophoresis. Anal Biochem 2014; 454:44-52. [PMID: 24637158 PMCID: PMC4021863 DOI: 10.1016/j.ab.2014.03.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/04/2014] [Accepted: 03/05/2014] [Indexed: 11/29/2022]
Abstract
Agarose gel electrophoresis of DNA and RNA is routinely performed using buffers containing either Tris, acetate, and EDTA (TAE) or Tris, borate, and EDTA (TBE). Gels are run at a low, constant voltage (∼10 V/cm) to minimize current and asymmetric heating effects, which can induce band artifacts and poor resolution. In this study, alterations of gel structure and conductive media composition were analyzed to identify factors causing higher electrical currents during horizontal slab gel electrophoresis. Current was reduced when thinner gels and smaller chamber buffer volumes were used, but was not influenced by agarose concentration or the presence of ethidium bromide. Current was strongly dependent on the amount and type of EDTA used and on the concentrations of the major acid-base components of each buffer. Interestingly, resolution and the mobilities of circular versus linear plasmid DNAs were also affected by the chemical form and amount of EDTA. With appropriate modifications to gel structure and buffer constituents, electrophoresis could be performed at high voltages (20-25 V/cm), reducing run times by up to 3-fold. The most striking improvements were observed with small DNAs and RNAs (10-100 bp): high voltages and short run times produced sharper bands and higher resolution.
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Affiliation(s)
- Brian A Sanderson
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Naoko Araki
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Jennifer L Lilley
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Gilberto Guerrero
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - L Kevin Lewis
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
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Saloua KS, Sonia G, Pierre C, Léon S, Darel HJ. The relative contributions of DNA strand breaks, base damage and clustered lesions to the loss of DNA functionality induced by ionizing radiation. Radiat Res 2014; 181:99-110. [PMID: 24397439 DOI: 10.1667/rr13450.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The majority of studies on lethal radiobiological damage have focused on double-strand breaks (DSBs), a type of clustered DNA damage and the evaluation of their toxicity, while other types of clustered DNA damage have received much less attention. The main purpose of this study is to evaluate the contribution of different lesions induced by ionizing radiation to the loss of plasmid DNA functionality. We employed a simple model system comprising E. coli transformed with an irradiated plasmid [pGEM-3Zf (-)] to determine the effect of DSBs and other lesions including base damage and clustered lesions on the functionality ("viability") of the plasmid. The yields of γ-radiation-induced single-strand breaks (SSBs) and DSBs were measured by gel electrophoresis. We found that the transformation efficiency decreases with radiation dose, but this decrease cannot be explained by the formation of DSBs. For example, at doses of 500 and 700 Gy, the relative transformation efficiency falls from 100% to 53% and 26%, respectively, while only 5.7% and 9.1% of the plasmids contain a DSB. In addition, it is also unlikely that randomly distributed base lesions could explain the loss of functionality of the plasmid, since cells can repair them efficiently. However, clustered lesions other than DSBs, which are difficult to repair and result in the loss of information on both DNA strands, have the potential to induce the loss of plasmid functionality. We therefore measured the yields of γ-radiation-induced base lesions and cluster damage, which are respectively converted into SSBs and DSBs by the base excision repair enzymes endonuclease III (Nth) and formamidopyrimidine-DNA glycosylase (Fpg). Our data demonstrate that the yield of cluster damage (i.e., lesions that yield DSBs following digestion) is 31 times higher than that of frank DSBs. This finding suggests that frank DSBs make a relatively minor contribution to the loss of DNA functionality induced by ionizing radiation, while other toxic lesions formed at a much higher frequencies than DSBs must be responsible for the loss of plasmid functionality. These lesions may be clustered lesions/locally multiply damaged sites (LMDS), including base damage, SSBs and/or intrastrand and interstrand crosslinks, leading to the loss of vital information in the DNA. Using a mathematical model, we estimate that at least three toxic lesions are required for the inactivation of plasmid functionality, in part because even these complex lesions can be repaired.
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Affiliation(s)
- Kouass Sahbani Saloua
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
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Kedracka-Krok S, Jankowska U, Elas M, Sowa U, Swakon J, Cierniak A, Olko P, Romanowska-Dixon B, Urbanska K. Proteomic analysis of proton beam irradiated human melanoma cells. PLoS One 2014; 9:e84621. [PMID: 24392146 PMCID: PMC3879347 DOI: 10.1371/journal.pone.0084621] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/26/2013] [Indexed: 12/19/2022] Open
Abstract
Proton beam irradiation is a form of advanced radiotherapy providing superior distributions of a low LET radiation dose relative to that of photon therapy for the treatment of cancer. Even though this clinical treatment has been developing for several decades, the proton radiobiology critical to the optimization of proton radiotherapy is far from being understood. Proteomic changes were analyzed in human melanoma cells treated with a sublethal dose (3 Gy) of proton beam irradiation. The results were compared with untreated cells. Two-dimensional electrophoresis was performed with mass spectrometry to identify the proteins. At the dose of 3 Gy a minimal slowdown in proliferation rate was seen, as well as some DNA damage. After allowing time for damage repair, the proteomic analysis was performed. In total 17 protein levels were found to significantly (more than 1.5 times) change: 4 downregulated and 13 upregulated. Functionally, they represent four categories: (i) DNA repair and RNA regulation (VCP, MVP, STRAP, FAB-2, Lamine A/C, GAPDH), (ii) cell survival and stress response (STRAP, MCM7, Annexin 7, MVP, Caprin-1, PDCD6, VCP, HSP70), (iii) cell metabolism (TIM, GAPDH, VCP), and (iv) cytoskeleton and motility (Moesin, Actinin 4, FAB-2, Vimentin, Annexin 7, Lamine A/C, Lamine B). A substantial decrease (2.3 x) was seen in the level of vimentin, a marker of epithelial to mesenchymal transition and the metastatic properties of melanoma.
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Affiliation(s)
- Sylwia Kedracka-Krok
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
- Malopolska Centre of Biotechnology, Krakow, Poland
| | - Urszula Jankowska
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
- Malopolska Centre of Biotechnology, Krakow, Poland
| | - Martyna Elas
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Urszula Sowa
- Institute of Nuclear Physics, PAS, Kraków, Poland
| | - Jan Swakon
- Institute of Nuclear Physics, PAS, Kraków, Poland
| | - Agnieszka Cierniak
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Pawel Olko
- Institute of Nuclear Physics, PAS, Kraków, Poland
| | - Bozena Romanowska-Dixon
- Department of Ophthalmology and Ophthalmic Oncology, Jagiellonian University Medical College, Kraków, Poland
| | - Krystyna Urbanska
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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46
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Girdhani S, Sachs R, Hlatky L. Biological Effects of Proton Radiation: What We Know and Don't Know. Radiat Res 2013; 179:257-72. [DOI: 10.1667/rr2839.1] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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47
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Girdhani S, Lamont C, Hahnfeldt P, Abdollahi A, Hlatky L. Proton Irradiation Suppresses Angiogenic Genes and Impairs Cell Invasion and Tumor Growth. Radiat Res 2012; 178:33-45. [DOI: 10.1667/rr2724.1] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Swati Girdhani
- Center of Cancer Systems Biology, St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, Massachusetts 02135
| | - Clare Lamont
- Center of Cancer Systems Biology, St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, Massachusetts 02135
| | - Philip Hahnfeldt
- Center of Cancer Systems Biology, St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, Massachusetts 02135
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Ushigome T, Shikazono N, Fujii K, Watanabe R, Suzuki M, Tsuruoka C, Tauchi H, Yokoya A. Yield of Single- and Double-Strand Breaks and Nucleobase Lesions in Fully Hydrated Plasmid DNA Films Irradiated with High-LET Charged Particles. Radiat Res 2012; 177:614-27. [DOI: 10.1667/rr2701.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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49
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Merrigan TL, Timson DJ, Hunniford CA, Catney M, McCullough RW. Plume characteristics and dynamics of UV and IR laser-desorbed oligonucleotides. Int J Biol Macromol 2012; 50:1081-90. [PMID: 22465754 DOI: 10.1016/j.ijbiomac.2012.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 03/05/2012] [Accepted: 03/12/2012] [Indexed: 11/29/2022]
Abstract
Laser desorption of dye-tagged oligonucleotides was studied using laser-induced fluorescence imaging. Desorption with ultra violet (UV) and infra-red (IR) lasers resulted in forward directed plumes of molecules. In the case of UV desorption, the initial shot desorbed approximately seven-fold more material than subsequent shots. In contrast, the initial shot in IR desorption resulted in the ejection of less material compared to subsequent shots and these plumes had a component directed along the path of the laser. Thermal equilibrium of the molecules in the plume was achieved after approximately 25 μs with a spread in molecular temperature which was described by a modified Maxwell-Boltzmann equation.
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Affiliation(s)
- Tony L Merrigan
- Centre for Plasma Physics, School of Mathematics and Physics, Queen's University Belfast, Belfast, Northern Ireland, UK
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50
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Francis Z, Incerti S, Ivanchenko V, Champion C, Karamitros M, Bernal MA, Bitar ZE. Monte Carlo simulation of energy-deposit clustering for ions of the same LET in liquid water. Phys Med Biol 2011; 57:209-24. [DOI: 10.1088/0031-9155/57/1/209] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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