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Advanced Synchrotron Radiation as a Quantum Tool for Exploring Deep...
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Advanced Synchrotron Radiation as a Quantum Tool for Exploring Deep Life Sciences

A special issue of Quantum Beam Science (ISSN 2412-382X).

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 16123

Special Issue Editor

Dr. Akinari Yokoya

E-Mail Website
Guest Editor
National Institutes for Quantum and Radiological Science and Technology, Tokai Quantum Beam Science Center, Tokai, Ibaraki, Japan
Interests: radiation biophysics; DNA damage and repair; electron paramagnetic resonance; microbeam; live cell imaging

Special Issue Information

Dear Colleagues,

Synchrotron radiation from accelerators has been widely used in various biological fields as a quantum tool with an energy region from UV to X-rays. In addition to numerous protein crystallography studies, which have been performed from early on in the development of the technique, recent advances in low-emittance third-generation storage rings can now provide a high-quality photon beam for experiments revealing the properties of biological materials. The energetically monochromatized photon beam allows particular electronic states of biological molecules to be targeted. In particular, spectroscopic techniques with high-energy resolution have been used to accumulate evidence of the physicochemical processes involved in radiation damage to DNA in order to understand the mechanism of mutation and cancer induction. The use of spatially focused X-ray microbeams can target not only particular cells in organs but also specific organelles in living cells. This could be used as a new method to manipulate cell functions or to observe cellular responses to radiation stress. Combined with a photoelastic modulator, the high-frequency switching of circular polarizations is used in the vacuum UV region. This technique has been used to obtain circular dichroism (CD) measurements over a wide wavelength range from vacuum UV to visible light and could be applied to reveal the secondary structures of non-crystallized biomolecules in solution or under biomimetic conditions. The structural changes caused by epigenetic modification, such as phosphorylation of proteins, are also potential CD targets. Furthermore, the coherence of the X-rays obtained in the third-generation facilities and in X-ray free-electron laser facilities is expected to elucidate inhomogeneous structures and their dynamics in living cells. Preliminary studies are in progress. This Special Issue reports the frontiers of biological research using synchrotron radiation.

Dr. Akinari Yokoya
Guest Editor

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Keywords

  • synchrotron radiation
  • biology
  • spectroscopy
  • microbeam
  • circular dichroism
  • coherent X-rays
  • DNA, proteins

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Published Papers (5 papers)

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Research

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13 pages, 1774 KiB  
Article
Enhanced Cell Inactivation and Double-Strand Break Induction in V79 Chinese Hamster Cells by Monochromatic X-Rays at Phosphorus K-Shell Absorption Peak
by Teruaki Konishi, Daichi Yoshihara, Munetoshi Maeda, Daisuke Ohsawa, Noriko Usami and Kotaro Hieda
Quantum Beam Sci. 2020, 4(4), 38; https://doi.org/10.3390/qubs4040038 - 20 Oct 2020
Cited by 1 | Viewed by 3089
Abstract
The cell inactivation and DNA double-strand break (DSB) induction by K-shell ionization of phosphorus atoms and Auger electrons were investigated. Monochromatic X-rays of on and below the phosphorus K-shell absorption peak, 2.153 keV and 2.147 keV were exposed to Chinese hamster lung fibroblast [...] Read more.
The cell inactivation and DNA double-strand break (DSB) induction by K-shell ionization of phosphorus atoms and Auger electrons were investigated. Monochromatic X-rays of on and below the phosphorus K-shell absorption peak, 2.153 keV and 2.147 keV were exposed to Chinese hamster lung fibroblast V79 cells. Survival fractions were plotted against exposure, Ψ [nC/kg] and the linear-quadratic model was adapted to estimate the parameters, α and β, of the survival curves. DSB induction rate [DSB/cell/Ψ] was estimated from the measured fractions of induced DNA fragments below 4.6 Mbp (Find(k < 4.6)), which were determined using pulse field gel electrophoresis. As results, cell inactivation and DSB induction rate of on the peak were significantly higher compared to that of the below. However, when converting Ψ to absorbed dose (Gy) of cell nucleus, the enhanced effect was only observed for parameter α, and not for a survival dose (Gy) of 37%, 10%, and 1% nor for a DSB induction rate. Our findings indicate that enhancement of cell inactivation and DSB induction were due to the additional dose delivered to the DNA and more complex DSB lesions were induced due to the release of phosphorus K-shell photoelectrons and Auger electrons. Full article
(This article belongs to the Special Issue Advanced Synchrotron Radiation as a Quantum Tool for Exploring Deep Life Sciences)
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10 pages, 1865 KiB  
Article
Hydration of Nucleobase as Probed by Electron Emission of Uridine-5′-Mono-Phosphate (UMP) in Aqueous Solution Induced by Nitrogen K-Shell Ionization
by Yasuaki Takeda, Hiroyuki Shimada, Ryosuke Miura, Masatoshi Ukai, Kentaro Fujii, Yoshihiro Fukuda and Yuji Saitoh
Quantum Beam Sci. 2020, 4(1), 10; https://doi.org/10.3390/qubs4010010 - 11 Feb 2020
Cited by 1 | Viewed by 2836
Abstract
To identify the precise early radiation processes of DNA lesions, we measure electron kinetic energy spectra emitted from uridine-5′ monophosphate (UMP) in aqueous solution for the photoionization of the N 1s orbital electron and for the following Auger effect using a monochromatic soft [...] Read more.
To identify the precise early radiation processes of DNA lesions, we measure electron kinetic energy spectra emitted from uridine-5′ monophosphate (UMP) in aqueous solution for the photoionization of the N 1s orbital electron and for the following Auger effect using a monochromatic soft X-ray synchrotron radiation at energies above the nitrogen K-shell ionization threshold. The change of photoelectron spectra for UMP in aqueous solutions at different proton concentrations (pH = 7.5 and 11.3) is ascribed to the chemical shift of the N3 nitrogen atom in uracil moiety of canonical and deprotonated forms. The lowest double ionization potentials for aqueous UMP at different pH obtained from the Auger electron spectra following the N 1s photoionization values show the electrostatic aqueous interaction of uracil moiety of canonical (neutral) and deprotonated (negatively charged) forms with hydrated water molecules. Full article
(This article belongs to the Special Issue Advanced Synchrotron Radiation as a Quantum Tool for Exploring Deep Life Sciences)
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14 pages, 2095 KiB  
Article
Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays
by Marie-Anne Hervé du Penhoat, Anis Hamila, Marie-Pierre Gaigeot, Rodolphe Vuilleumier, Kentaro Fujii, Akinari Yokoya and Marie-Françoise Politis
Quantum Beam Sci. 2019, 3(4), 24; https://doi.org/10.3390/qubs3040024 - 10 Dec 2019
Cited by 4 | Viewed by 2877
Abstract
It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation [...] Read more.
It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR2+ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs. Full article
(This article belongs to the Special Issue Advanced Synchrotron Radiation as a Quantum Tool for Exploring Deep Life Sciences)
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Review

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10 pages, 4387 KiB  
Review
Targeting Specific Sites in Biological Systems with Synchrotron X-Ray Microbeams for Radiobiological Studies at the Photon Factory
by Akinari Yokoya and Noriko Usami
Quantum Beam Sci. 2020, 4(1), 2; https://doi.org/10.3390/qubs4010002 - 9 Jan 2020
Cited by 7 | Viewed by 3458
Abstract
X-ray microbeams have been used to explore radiobiological effects induced by targeting a specific site in living systems. Synchrotron radiation from the Photon Factory, Japan, with high brilliance and highly parallel directionality is a source suitable for delivering a particular beam size or [...] Read more.
X-ray microbeams have been used to explore radiobiological effects induced by targeting a specific site in living systems. Synchrotron radiation from the Photon Factory, Japan, with high brilliance and highly parallel directionality is a source suitable for delivering a particular beam size or shape, which can be changed according to target morphology by using a simple metal slit system (beam size from 5 μm to several millimeters). Studies have examined the non-targeted effects, called bystander cellular responses, which are thought to be fundamental mechanisms of low-dose or low-dose-rate effects in practical radiation risk research. Narrow microbeams several tens of micrometers or less in their size targeted both the cell nucleus and the cytoplasm. Our method combined with live-cell imaging techniques has challenged the traditional radiobiological dogma that DNA damage is the only major cause of radiation-induced genetic alterations and is gradually revealing the role of organelles, such as mitochondria, in these biological effects. Furthermore, three-dimensionally cultured cell systems have been used as microbeam targets to mimic organs. Combining the spatial fractionation of X-ray microbeams and a unique ex vivo testes organ culture technique revealed that the tissue-sparing effect was induced in response to the non-uniform radiation fields. Spatially fractionated X-ray beams may be a promising tool in clinical radiation therapy. Full article
(This article belongs to the Special Issue Advanced Synchrotron Radiation as a Quantum Tool for Exploring Deep Life Sciences)
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11 pages, 1203 KiB  
Review
Structural Alterations of Histone Proteins in DNA-Damaged Cells Revealed by Synchrotron Radiation Circular Dichroism Spectroscopy: A New Piece of the DNA-Damage-Response Puzzle
by Yudai Izumi
Quantum Beam Sci. 2019, 3(4), 23; https://doi.org/10.3390/qubs3040023 - 6 Dec 2019
Cited by 1 | Viewed by 3186
Abstract
Double-strand breaks of DNA may lead to discontinuous DNA and consequent loss of genetic information, which may result in mutations or, ultimately, carcinogenesis. To avoid such potentially serious situations, cells have evolved efficient DNA damage repair systems. It is thought that DNA-repair processes [...] Read more.
Double-strand breaks of DNA may lead to discontinuous DNA and consequent loss of genetic information, which may result in mutations or, ultimately, carcinogenesis. To avoid such potentially serious situations, cells have evolved efficient DNA damage repair systems. It is thought that DNA-repair processes involve drastic alterations of chromatin and histone structures, but detection of these altered structures in DNA-damaged cells remains rare in the literature. Recently, synchrotron radiation circular dichroism (SRCD) spectroscopy, which can provide secondary structural information of proteins in solution, has identified structural alterations of histone proteins induced by DNA damage responses. In this review, these results and experimental procedures are discussed with the aim of facilitating further studies of the chromatin remodeling and DNA damage repair pathways using SRCD spectroscopy. Full article
(This article belongs to the Special Issue Advanced Synchrotron Radiation as a Quantum Tool for Exploring Deep Life Sciences)
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