In our last paper, we have reported the direct interact between energetic ions and DNA, and its components, pointing out that damage to DNA is actually of highest biological consequence, as the integrity of DNA sequence is essential for biological function. Proteins are another kind of important biomolecules. Although much recent attention has been payed to ion irradiation initiated reaction cascades leading to DNA damage, the protein lesions induced by energetic ions remain virtually unexplored at the molecular scale (maybe because there are usually many copies of each protein, so a comparable level of damage is of much less biological impact). Except for DNA damage, an understanding of nascent events leading to radiolytic protein damage is also required in order to achieve a complete description of ionizing radiation effects on living cells.
It has been reported that damage of genome in a living cell by ionizing radiation is about one-third direct and two-thirds indirect. The former which has been introduced in our last paper, concerns direct energy deposition and ionizing reactions in the biomolecules; the latter results from radiation induced reactive species (mainly radicals) in the medium (mainly water) surrounding the biomolecules. In this review, a short description of ion implantation induced radical formation in water is presented. Then we summarize the aqueous radical reaction chemistry of DNA, protein and their component…
Ion beams have been widely applied in a few biological research fields such as radioactive breeding, health protection, and tumor therapy. Up to now many interesting and impressive achievements in biology and agriculture have been made. Over the past several decades, scientists in biology, physics, and chemistry have pursued investigations focused on understanding the mechanisms of these radiobiological effects of ion beams. From the chemical point of view, these effects are due to the ion irradiation induced biomolecular damage, direct or indirect. In this review, we will present a chemical o…
We propose a mathematical model for estimating biological damage caused by low-dose irradiation. We understand that the Linear Non Threshold (LNT) hypothesis is realized only in the case of no recovery effects. In order to treat the realistic living objects, our model takes into account various types of recovery as well as proliferation mechanism, which may change the resultant damage, especially for the case of lower dose rate irradiation. It turns out that the lower the radiation dose rate, the safer the irradiated system of living object (which is called symbolically "tissue" hereafter) can…
The multiscale approach to the assessment of biodamage resulting upon irradiation of biological media with ions is reviewed, explained and compared to other approaches. The processes of ion propagation in the medium concurrent with ionization and excitation of molecules, transport of secondary products, dynamics of the medium, and biological damage take place on a number of different temporal, spatial and energy scales. The multiscale approach, a physical phenomenon-based analysis of the scenario that leads to radiation damage, has been designed to consider all relevant effects on a variety of…
Over the past thirty years, researchers have highlighted the role played by a class of proteins or polypeptides that forms pathogenic amyloid aggregates in vivo, including i) the amyloid Abeta peptide, which is known to form senile plaques in Alzheimer's disease; ii) alpha-synuclein, responsible for Lewy body formation in Parkinson's disease and iii) IAPP, which is the protein component of type 2 diabetes-associated islet amyloids. These proteins, known as intrinsically disordered proteins (IDPs), are present as highly dynamic conformational ensembles. IDPs can partially (mis) fold into (dys) …
In the present work, we develop a general spatial stochastic model to describe the formation and repair of radiation-induced DNA damage. The model is described mathematically as a measure-valued particle-based stochastic system and extends in several directions the model developed in Cordoni et.al. 2021, Cordoni et.al. 2022a, Cordoni et.al. 2022b. In this new spatial formulation, radiation-induced DNA damage in the cell nucleus can undergo different pathways to either repair or lead to cell inactivation. The main novelty of the work is to rigorously define a spatial model that considers the pa…
ECM components, such as the Perineuronal net (PNN), one of the most prevalent parts surrounding the neuronal cell. PNN is a protective net-like structure regulating neuronal activity such as neurotransmission, charge balance and generates an action potential. Shock induced damage of this essential component may cause neuronal cell death and potentially leads to CTE, AD diseases, PTSD, etc. The shock generated possibly during an accident, improvised devie explosion or collision between NFL players may lead to damage to this safety net. The goal is to investigate the mechanics of PNN under shock…
How a nano-searcher finds its nano-target is a general problem in non-equilibrium statistical physics. It becomes vital when the searcher is a damaged DNA fragment trying to find its counterpart on the intact homologous chromosome. If the two copies are paired, that intact homologous sequence serves as a template to reconstitute the damaged DNA sequence, enabling the cell to survive without genetic mutations. To succeed, the search must stop only when the perfect homology is found. The biological process that ensures such a genomic integrity is called Homologous Recombination and is promoted b…
We develop and study the evolution of a model of radiation induced apoptosis in cells using stochastic simulations, and identified key protein targets for effective mitigation of radiation damage. We identified several key proteins associated with cellular apoptosis using an extensive literature survey. In particular, we focus on the p53 transcription dependent and p53 transcription independent pathways for mitochondrial apoptosis. Our model reproduces known p53 oscillations following radiation damage. The key, experimentally testable hypotheses that we generate are - inhibition of PUMA is an …
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet, investigations over recent decades have found that the diffusion dynamics of DNA-binding proteins are generally complicated and, further, protein-specific. In this review, we collect the experimental and theoretical studies that quantify the diffusion dynamics of DNA-binding proteins and review them from the viewpoint of diffusion processes.
We present the latest advances of the multiscale approach to radiation damage caused by irradiation of a tissue with energetic ions and report the most recent advances in the calculations of complex DNA damage and the effects of thermal spikes on biomolecules. The multiscale approach aims to quantify the most important physical, chemical, and biological phenomena taking place during and following irradiation with ions and provide a better means for clinically-necessary calculations with adequate accuracy. We suggest a way of quantifying the complex clustered damage, one of the most important f…
Formation of amyloid fibrils of various amyloidogenic proteins is dramatically enhanced by ultrasound irradiation. For applying this phenomenon to the study of protein aggregation science and diagnosis of neurodegenerative diseases, a multichannel ultrasound irradiation system with individually adjustable ultrasound-irradiation conditions is necessary. Here, we develop a sonochemical reaction system, where an ultrasonic transducer is placed in each well of a 96-well microplate to perform ultrasonic irradiation of sample solutions under various conditions with high reproducibility, and applied …
Impact of Oxygen on DNA Damage Distribution in 3D Genome and its Correlation to Oxygen Enhancement Ratio after High-LET Irradiation
Department of Engineering Physics, Tsinghua University（清华大学工程物理系）；Key Laboratory of Particle & Radiation Imaging, Tsinghua University, Ministry of Education（教育部粒子与辐射成像重点实验室）；Institute of Fluid Physics, China Academy of Engineering Physics（中国工程物理研究院流体物理研究所）
Some biochemical and metabolic characteristics of bovine sperm cells irradiated with low-level laser were probed and correlated to the irradiation parameters. Bovine spermatozoa were exposed to spatially filtered light from a He-Ne laser (633 nm) with fluences from 150 to 600 mJ/cm2. General biochemical alterations were assessed by vibrational spectroscopy (micro-Fourier-Transform Infrared technique). The mitochondrial membrane potential was assessed by flow cytometry. Lipid peroxidation due to reactive oxygen species (ROS) production was assessed by thiobarbituric acid reactive substances (TB…
Biological effects of proton and light ion irradiations have been studied in detail by analyzing published cell survival data with the help of the probabilistic two-stage radiobiological model. Probabilities of single ion tracks to induce lesions of different severity have been assessed in dependence on their linear energy transfer (LET). The results are presented and their interpretation in terms of $Z_{eff}^2/β^2$ (the effective charge over velocity squared) is discussed.
