scholarly journals X-ray radiation damage to biological samples: recent progress

2019 ◽  
Vol 26 (4) ◽  
pp. 907-911 ◽  
Author(s):  
Elspeth F. Garman ◽  
Martin Weik
Keyword(s):  
Radiation Damage ◽  
Structural Damage ◽  
Low Dose ◽  
Theoretical Calculations ◽  
Relevant Literature ◽  
Radiation Chemistry ◽  
Tissue Samples ◽  
High Quantum Efficiency ◽  
X Ray ◽  
Radiation Induced

With the continuing development of beamlines for macromolecular crystallography (MX) over the last few years providing ever higher X-ray flux densities, it has become even more important to be aware of the effects of radiation damage on the resulting structures. Nine papers in this issue cover a range of aspects related to the physics and chemistry of the manifestations of this damage, as observed in both MX and small-angle X-ray scattering (SAXS) on crystals, solutions and tissue samples. The reports include measurements of the heating caused by X-ray irradiation in ruby microcrystals, low-dose experiments examining damage rates as a function of incident X-ray energy up to 30 keV on a metallo-enzyme using a CdTe detector of high quantum efficiency as well as a theoretical analysis of the gains predicted in diffraction efficiency using these detectors, a SAXS examination of low-dose radiation exposure effects on the dissociation of a protein complex related to human health, theoretical calculations describing radiation chemistry pathways which aim to explain the specific structural damage widely observed in proteins, investigation of radiation-induced damage effects in a DNA crystal, a case study on a metallo-enzyme where structural movements thought to be mechanism related might actually be radiation-damage-induced changes, and finally a review describing what X-ray radiation-induced cysteine modifications can teach us about protein dynamics and catalysis. These papers, along with some other relevant literature published since the last Journal of Synchrotron Radiation Radiation Damage special issue in 2017, are briefly summarized below.

Factors in Photographic Emulsions for Low Dose Electron Crystallography

1980 ◽  
Vol 38 ◽  
pp. 230-231
Author(s):  
T.W. Jeng ◽  
W. Chiu
Keyword(s):  
Radiation Damage ◽  
Low Dose ◽  
Damage Effect ◽  
Photographic Emulsion ◽  
Electron Crystallography ◽  
Electron Microscopic ◽  
X Ray ◽  
Signal Contrast ◽  
Diffraction Patterns ◽  
Photographic Emulsions

With the advances in preparing biological materials in a thin and highly ordered form, and in maintaining them hydrated under vacuum, electron crystallography has become an important tool for biological structure investigation at high resolution (1,2). However, the electron radiation damage would limit the capability of recording reflections with low intensities in an electron diffraction pattern. It has been demonstrated that the use of a low temperature stage can reduce the radiation damage effect and that one can expose the specimen with a higher dose in order to increase the signal contrast (3). A further improvement can be made by selecting a proper photographic emulsion. The primary factors in evaluating the suitability of photographic emulsion for recording low dose diffraction patterns are speed, fog level, electron response at low electron exposure, linearity, and usable range of exposure. We have compared these factors with three photographic emulsions including Kodak electron microscopic plate (EMP), Industrex AA x-ray film (AA x-ray) and Kodak nuclear track film (NTB3).

scholarly journals Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both

2019 ◽  
Vol 26 (4) ◽  
pp. 931-944 ◽  
Author(s):  
Helena Taberman ◽  
Charles S. Bury ◽  
Mark J. van der Woerd ◽  
Edward H. Snell ◽  
Elspeth F. Garman
Keyword(s):  
Reaction Mechanism ◽  
Radiation Damage ◽  
Xylose Isomerase ◽  
Data Sets ◽  
High Resolution Data ◽  
X Ray ◽  
Metal Cofactor ◽  
Acid Environment ◽  
Radiation Induced ◽  
Catalytic Metal

Xylose isomerase (XI) is an industrially important metalloprotein studied for decades. Its reaction mechanism has been postulated to involve movement of the catalytic metal cofactor to several different conformations. Here, a dose-dependent approach was used to investigate the radiation damage effects on XI and their potential influence on the reaction mechanism interpreted from the X-ray derived structures. Radiation damage is still one of the major challenges for X-ray diffraction experiments and causes both global and site-specific damage. In this study, consecutive high-resolution data sets from a single XI crystal from the same wedge were collected at 100 K and the progression of radiation damage was tracked over increasing dose (0.13–3.88 MGy). The catalytic metal and its surrounding amino acid environment experience a build-up of free radicals, and the results show radiation-damage-induced structural perturbations ranging from an absolute metal positional shift to specific residue motions in the active site. The apparent metal movement is an artefact of global damage and the resulting unit-cell expansion, but residue motion appears to be driven by the dose. Understanding and identifying radiation-induced damage is an important factor in accurately interpreting the biological conclusions being drawn.

X-ray radiation-induced amorphization of metal–organic frameworks

2019 ◽  
Vol 21 (23) ◽  
pp. 12389-12395 ◽  
Author(s):  
Remo N. Widmer ◽  
Giulio I. Lampronti ◽  
Nicola Casati ◽  
Stefan Farsang ◽  
Thomas D. Bennett ◽  
...  
Keyword(s):  
Radiation Damage ◽  
Metal Organic Frameworks ◽  
X Rays ◽  
X Ray ◽  
P Accumulation ◽  
Metal Organic ◽  
Radiation Induced ◽  
Crystalline Metal

Accumulation of radiation damage from synchrotron X-rays leads to complete amorphization of the initially crystalline metal–organic frameworks ZIF-4, ZIF-62, and ZIF-zni. The mechanism of this transformation is studied as a function of time and temperature and is shown to be non-isokinetic.

scholarly journals Comprehensive model for X-ray-induced damage in protein crystallography

2019 ◽  
Vol 26 (4) ◽  
pp. 945-957 ◽  
Author(s):  
David M. Close ◽  
William A. Bernhard
Keyword(s):  
Structural Changes ◽  
Theoretical Calculations ◽  
Comprehensive Model ◽  
Additional Insight ◽  
Radiation Physics ◽  
X Ray ◽  
Fundamental Understanding ◽  
Radiation Induced ◽  
The Many ◽  
Significant Effort

Acquisition of X-ray crystallographic data is always accompanied by structural degradation owing to the absorption of energy. The application of high-fluency X-ray sources to large biomolecules has increased the importance of finding ways to curtail the onset of X-ray-induced damage. A significant effort has been under way with the aim of identifying strategies for protecting protein structure. A comprehensive model is presented that has the potential to explain, both qualitatively and quantitatively, the structural changes induced in crystalline protein at ∼100 K. The first step is to consider the qualitative question: what are the radiation-induced intermediates and expected end products? The aim of this paper is to assist in optimizing these strategies through a fundamental understanding of radiation physics and chemistry, with additional insight provided by theoretical calculations performed on the many schemes presented.

scholarly journals Quantitative study of contrast enhancement in soft X-ray micrographs of insect eyes by tissue selective mass loss

2014 ◽  
Vol 21 (5) ◽  
pp. 1153-1159 ◽  
Author(s):  
Andreas Späth ◽  
Benjamin Watts ◽  
Lutz Thilo Wasserthal ◽  
Rainer H. Fink
Keyword(s):  
Mass Loss ◽  
Contrast Enhancement ◽  
Radiation Damage ◽  
Soft Matter ◽  
Absorbed Dose ◽  
Radiochemical Analysis ◽  
X Ray ◽  
Quantitative Studies ◽  
Radiation Induced ◽  
Energy Dependent

Quantitative studies of soft X-ray induced radiation damage in zone-plate-based X-ray microspectroscopy have so far concentrated on investigations of homogeneous specimens. However, more complex materials can show unexpected radiation-induced behaviour. Here a quantitative radiochemical analysis of biological tissue fromXantophan morganii praedictaeyes is presented. Contrast enhancement due to tissue selective mass loss leading to a significant improvement of imaging quality is reported. Since conventional quantitative analysis of the absorbed dose cannot conclusively explain the experimental observations on photon-energy-dependent radiation damage, a significant contribution of photo- and secondary electrons to soft matter damage for photon energies above the investigated absorption edge is proposed.

scholarly journals Low-dose X-ray structure analysis of cytochrome c oxidase utilizing high-energy X-rays

2019 ◽  
Vol 26 (4) ◽  
pp. 912-921 ◽  
Author(s):  
Go Ueno ◽  
Atsuhiro Shimada ◽  
Eiki Yamashita ◽  
Kazuya Hasegawa ◽  
Takashi Kumasaka ◽  
...  
Keyword(s):  
Radiation Damage ◽  
Low Dose ◽  
High Energy ◽  
Array Detector ◽  
X Rays ◽  
Data Set ◽  
X Ray ◽  
Ligand Structure ◽  
Biology I ◽  
On Line

To investigate the effect of high-energy X-rays on site-specific radiation-damage, low-dose diffraction data were collected from radiation-sensitive crystals of the metal enzyme cytochrome c oxidase. Data were collected at the Structural Biology I beamline (BL41XU) at SPring-8, using 30 keV X-rays and a highly sensitive pixel array detector equipped with a cadmium telluride sensor. The experimental setup of continuous sample translation using multiple crystals allowed the average diffraction weighted dose per data set to be reduced to 58 kGy, and the resulting data revealed a ligand structure featuring an identical bond length to that in the damage-free structure determined using an X-ray free-electron laser. However, precise analysis of the residual density around the ligand structure refined with the synchrotron data showed the possibility of a small level of specific damage, which might have resulted from the accumulated dose of 58 kGy per data set. Further investigation of the photon-energy dependence of specific damage, as assessed by variations in UV-vis absorption spectra, was conducted using an on-line spectrometer at various energies ranging from 10 to 30 keV. No evidence was found for specific radiation damage being energy dependent.

Re-examining mechanisms of radiation damage in organic specimens

1990 ◽  
Vol 48 (4) ◽  
pp. 812-813
Author(s):  
David A. Armstrong ◽  
Suichu Luo ◽  
David C. Joy
Keyword(s):  
Mass Loss ◽  
Radiation Damage ◽  
Low Dose ◽  
High Resolution Electron Microscopy ◽  
Limiting Factor ◽  
High Dose ◽  
X Ray ◽  
Resolution Electron ◽  
Significant Mass Loss ◽  
Significant Mass

Radiation damage to organic specimens is the major limiting factor in high resolution electron microscopy studies of biological systems. Electron beam irradiation compromises resolution by altering chemical microstructure, resulting in local mass loss and volume shrinkage in a specimen. All significant mass loss is thought to occur prior to a total incident dose of 50 electrons/ square angstrom If this is the case it is hard to reconcile the observation that images must be recorded at doses of less than 100 el/Å in order to avoid excessive mass loss and shrinkage while microanalytical (EDS and EELS) studies of the same tissue are routinely carried out at doses of 104 - 105el/Å2. Also, since most workers typically use either low dose (for imaging) or high dose (for microapalysis) there are apparently no studies in the literature which attempt to follow the process of radiation damage between these two extremes.We have chosen to investigate mass loss in polymer embedding resins such as are routinely used for TEM imaging as well as for X ray microanalytical applications.

Alpha particle damage in biotite characterized by microfocus X-ray diffraction and Fe K-edge X-ray absorption spectroscopy

2013 ◽  
Vol 77 (6) ◽  
pp. 2867-2882 ◽  
Author(s):  
R. A. D. Pattrick ◽  
J. M. Charnock ◽  
T. Geraki ◽  
J. F. W. Mosselmans ◽  
C. I. Pearce ◽  
...  
Keyword(s):  
Radiation Damage ◽  
Structural Damage ◽  
Xrd Analysis ◽  
Range Order ◽  
Particle Radiation ◽  
Electron Collisions ◽  
Oh Groups ◽  
X Ray ◽  
Xrd Patterns ◽  
Α Particles

AbstractCombined microfocus XAS and XRD analysis of α-particle radiation damage haloes around thorium-containing monazite in Fe-rich biotite reveals changes in both short- and long-range order. The total α-particles flux derived from the Th and U in the monazite over 1.8 Ga was 0.022 α particles per atomic component of the monazite and this caused increasing amounts of structural damage as the monazite emitter is approached. Short-range order disruption revealed by Fe K-edge EXAFS is manifest by a high variability in Fe–Fe bond lengths and a marked decrease in coordination number. XANES examination of the Fe K-edge shows a decrease in energy of the main absorption by up to 1 eV, revealing reduction of the Fe3+ components of the biotite by interaction with the 24He2+, the result of low and thermal energy electrons produced by the cascade of electron collisions. Changes in d spacings in the XRD patterns reveal the development of polycrystallinity and new domains of damaged biotite structure with evidence of displaced atoms due to ionization interactions and nuclear collisions. The damage in biotite is considered to have been facilitated by destruction of OH groups by radiolysis and the development of Frenkel pairs causing an increase in the trioctahedral layer distances and contraction within the trioctahedral layers. The large amount of radiation damage close to the monazite can be explained by examining the electronic stopping flux.

scholarly journals Very Large Amounts of Radiation are Required to Produce Cancer

Dose-Response ◽  
2007 ◽  
Vol 5 (4) ◽  
pp. dose-response.0 ◽  
Author(s):  
Antone L. Brooks ◽  
T. Edmond Hui ◽  
Lezlie A. Couch
Keyword(s):  
Cancer Risk ◽  
Low Dose ◽  
Theoretical Calculations ◽  
Low Doses ◽  
Biological Organization ◽  
The Public ◽  
Increased Risk ◽  
Large Populations ◽  
Radiation Induced Cancer ◽  
Radiation Induced

The public fear of radiation is in part driven by the Linear No Threshold Hypothesis (LNTH), or the concept that each and every ionization increases the risk for cancer. Even if this were true, it is important to recognize that the increased risk is very small at low doses and cannot be detected. This paper demonstrates the large number of assumptions and extrapolations needed when using the LNTH to estimate low-dose cancer risk. The manuscript provides information at every level of biological organization suggesting that many of these linear assumptions do not hold. While the initial damage may be produced linearly with dose, the processing of that damage is very non-linear. Finally, the paper provides the unique prospective on radiation-induced cancer, demonstrating that it takes large amounts (total energy) of radiation delivered to large populations to detect an increase in cancer frequency. These observations are supported by both theoretical calculations and examples based on past human radiation exposure.

scholarly journals Soft X-ray induced radiation damage in thin freeze-dried brain samples studied by FTIR microscopy

2020 ◽  
Vol 27 (5) ◽  
pp. 1218-1226
Author(s):  
Artur D. Surowka ◽  
A. Gianoncelli ◽  
G. Birarda ◽  
S. Sala ◽  
N. Cefarin ◽  
...  
Keyword(s):  
Radiation Damage ◽  
Biological Sample ◽  
Radiation Doses ◽  
Complex Interplay ◽  
Ftir Microscopy ◽  
Tissue Samples ◽  
X Ray ◽  
Freeze Dried ◽  
Resolution Limits ◽  
First Time

In order to push the spatial resolution limits to the nanoscale, synchrotron-based soft X-ray microscopy (XRM) experiments require higher radiation doses to be delivered to materials. Nevertheless, the associated radiation damage impacts on the integrity of delicate biological samples. Herein, the extent of soft X-ray radiation damage in popular thin freeze-dried brain tissue samples mounted onto Si3N4 membranes, as highlighted by Fourier transform infrared microscopy (FTIR), is reported. The freeze-dried tissue samples were found to be affected by general degradation of the vibrational architecture, though these effects were weaker than those observed in paraffin-embedded and hydrated systems reported in the literature. In addition, weak, reversible and specific features of the tissue–Si3N4 interaction could be identified for the first time upon routine soft X-ray exposures, further highlighting the complex interplay between the biological sample, its preparation protocol and X-ray probe.

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