scholarly journals Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure–function studies

2021 ◽  
Vol 77 (3) ◽  
pp. 173-185
Author(s):  
John R. Helliwell
Keyword(s):  
Structure Function ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Protein Crystal ◽  
X Rays ◽  
Time Resolved ◽  
X Ray ◽  
Precision And Accuracy ◽  
Electron Microscopes

The distinctive features of the physics-based probes used in understanding the structure of matter focusing on biological sciences, but not exclusively, are described in the modern context. This is set in a wider scope of holistic biology and the scepticism about `reductionism', what is called the `molecular level', and how to respond constructively. These topics will be set alongside the principles of accuracy and precision, and their boundaries. The combination of probes and their application together is the usual way of realizing accuracy. The distinction between precision and accuracy can be blurred by the predictive force of a precise structure, thereby lending confidence in its potential accuracy. These descriptions will be applied to the comparison of cryo and room-temperature protein crystal structures as well as the solid state of a crystal and the same molecules studied by small-angle X-ray scattering in solution and by electron microscopy on a sample grid. Examples will include: time-resolved X-ray Laue crystallography of an enzyme Michaelis complex formed directly in a crystal equivalent to in vivo; a new iodoplatin for radiation therapy predicted from studies of platin crystal structures; and the field of colouration of carotenoids, as an effective assay of function, i.e. their colouration, when unbound and bound to a protein. The complementarity of probes, as well as their combinatory use, is then at the foundation of real (biologically relevant), probe-artefacts-free, structure–function studies. The foundations of our methodologies are being transformed by colossal improvements in technologies of X-ray and neutron sources and their beamline instruments, as well as improved electron microscopes and NMR spectrometers. The success of protein structure prediction from gene sequence recently reported by CASP14 also opens new doors to change and extend the foundations of the structural sciences.

Transmission electron microscope studies in special ceramics

1978 ◽  
Vol 36 (1) ◽  
pp. 268-269
Author(s):  
A. Zangvil ◽  
L.J. Gauckler ◽  
G. Schneider ◽  
M. Rühle
Keyword(s):  
Phase Diagrams ◽  
Crystal Structures ◽  
Thin Foil ◽  
Limited Extent ◽  
Complex Materials ◽  
X Ray Diffraction ◽  
X Ray ◽  
Transmission Electron ◽  
Electron Microscopes ◽  
Lattice Resolution

The use of high temperature special ceramics which are usually complex materials based on oxides, nitrides, carbides and borides of silicon and aluminum, is critically dependent on their thermomechanical and other physical properties. The investigations of the phase diagrams, crystal structures and microstructural features are essential for better understanding of the macro-properties. Phase diagrams and crystal structures have been studied mainly by X-ray diffraction (XRD). Transmission electron microscopy (TEM) has contributed to this field to a very limited extent; it has been used more extensively in the study of microstructure, phase transformations and lattice defects. Often only TEM can give solutions to numerous problems in the above fields, since the various phases exist in extremely fine grains and subgrain structures; single crystals of appreciable size are often not available. Examples with some of our experimental results from two multicomponent systems are presented here. The standard ion thinning technique was used for the preparation of thin foil samples, which were then investigated with JEOL 200A and Siemens ELMISKOP 102 (for the lattice resolution work) electron microscopes.

X-ray Gabor holography

1995 ◽  
Vol 53 ◽  
pp. 612-613
Author(s):  
Steve Lindaas ◽  
Chris Jacobsen ◽  
Alex Kalinovsky ◽  
Malcolm Howells
Keyword(s):  
Surface Relief ◽  
Biological Imaging ◽  
Specimen Preparation ◽  
X Rays ◽  
X Ray ◽  
Water Window ◽  
Biological Objects ◽  
Transmission Imaging ◽  
Atomic Force ◽  
Electron Microscopes

Soft x-ray microscopy offers an approach to transmission imaging of wet, micron-thick biological objects at a resolution superior to that of optical microscopes and with less specimen preparation/manipulation than electron microscopes. Gabor holography has unique characteristics which make it particularly well suited for certain investigations: it requires no prefocussing, it is compatible with flash x-ray sources, and it is able to use the whole footprint of multimode sources. Our method serves to refine this technique in anticipation of the development of suitable flash sources (such as x-ray lasers) and to develop cryo capabilities with which to reduce specimen damage. Our primary emphasis has been on biological imaging so we use x-rays in the water window (between the Oxygen-K and Carbon-K absorption edges) with which we record holograms in vacuum or in air.The hologram is recorded on a high resolution recording medium; our work employs the photoresist poly(methylmethacrylate) (PMMA). Following resist “development” (solvent etching), a surface relief pattern is produced which an atomic force microscope is aptly suited to image.

scholarly journals Optimization of X-ray Investigations in Dentistry Using Optical Coherence Tomography

Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4554
Author(s):  
Ralph-Alexandru Erdelyi ◽  
Virgil-Florin Duma ◽  
Cosmin Sinescu ◽  
George Mihai Dobre ◽  
Adrian Bradu ◽  
...  
Keyword(s):  
Optical Coherence Tomography ◽  
Radiation Dose ◽  
Imaging Techniques ◽  
Image Resolution ◽  
Optical Coherence ◽  
X Rays ◽  
High Quality ◽  
X Ray

The most common imaging technique for dental diagnoses and treatment monitoring is X-ray imaging, which evolved from the first intraoral radiographs to high-quality three-dimensional (3D) Cone Beam Computed Tomography (CBCT). Other imaging techniques have shown potential, such as Optical Coherence Tomography (OCT). We have recently reported on the boundaries of these two types of techniques, regarding. the dental fields where each one is more appropriate or where they should be both used. The aim of the present study is to explore the unique capabilities of the OCT technique to optimize X-ray units imaging (i.e., in terms of image resolution, radiation dose, or contrast). Two types of commercially available and widely used X-ray units are considered. To adjust their parameters, a protocol is developed to employ OCT images of dental conditions that are documented on high (i.e., less than 10 μm) resolution OCT images (both B-scans/cross sections and 3D reconstructions) but are hardly identified on the 200 to 75 μm resolution panoramic or CBCT radiographs. The optimized calibration of the X-ray unit includes choosing appropriate values for the anode voltage and current intensity of the X-ray tube, as well as the patient’s positioning, in order to reach the highest possible X-rays resolution at a radiation dose that is safe for the patient. The optimization protocol is developed in vitro on OCT images of extracted teeth and is further applied in vivo for each type of dental investigation. Optimized radiographic results are compared with un-optimized previously performed radiographs. Also, we show that OCT can permit a rigorous comparison between two (types of) X-ray units. In conclusion, high-quality dental images are possible using low radiation doses if an optimized protocol, developed using OCT, is applied for each type of dental investigation. Also, there are situations when the X-ray technology has drawbacks for dental diagnosis or treatment assessment. In such situations, OCT proves capable to provide qualitative images.

scholarly journals Semi-automated protein crystal mounting device for the sulfur single-wavelength anomalous diffraction method

2010 ◽  
Vol 43 (2) ◽  
pp. 341-346 ◽  
Author(s):  
Yu Kitago ◽  
Nobuhisa Watanabe ◽  
Isao Tanaka
Keyword(s):  
Diffraction Method ◽  
Systematic Errors ◽  
Protein Crystal ◽  
X Rays ◽  
Anomalous Diffraction ◽  
X Ray ◽  
Frozen Solution ◽  
Custom Made ◽  
Protein Molecules ◽  
X Ray Absorption

Use of longer-wavelength X-rays has advantages for the detection of small anomalous signals from light atoms, such as sulfur, in protein molecules. However, the accuracy of the measured diffraction data decreases at longer wavelengths because of the greater X-ray absorption. The capillary-top mounting method (formerly the loopless mounting method) makes it possible to eliminate frozen solution around the protein crystal and reduces systematic errors in the evaluation of small anomalous differences. However, use of this method requires custom-made tools and a large amount of skill. Here, the development of a device that can freeze the protein crystal semi-automatically using the capillary-top mounting method is described. This device can pick up the protein crystal from the crystallization drop using a micro-manipulator, and further procedures, such as withdrawal of the solution around the crystal by suction and subsequent flash freezing of the protein crystal, are carried out automatically. This device makes it easy for structural biologists to use the capillary-top mounting method for sulfur single-wavelength anomalous diffraction phasing using longer-wavelength X-rays.

scholarly journals THE EFFECTS OF ROENTGEN RAYS ON CELL-VIRUS ASSOCIATIONS

1943 ◽  
Vol 78 (4) ◽  
pp. 285-304 ◽  
Author(s):  
William F. Friedewald ◽  
Rubert S. Anderson
Keyword(s):  
X Rays ◽  
Pathological Changes ◽  
Cellular Division ◽  
Papilloma Virus ◽  
X Ray ◽  
Crude Extracts ◽  
Domestic Rabbits ◽  
Roentgen Rays

The virus-induced papillomas of cottontail as well as domestic rabbits regress completely within a few weeks when exposed to 5,000 r of x-ray irradiation. The x-rays do not immediately kill the papilloma cells, but lead to death by inhibiting cellular division and producing pathological changes in the cells which then continue to differentiate. The virus associated with the growths, however, not only persists in undiminished amount during regression, but often an increased yield of it can be obtained on extraction. The fibroma virus in crude extracts or in vivo is inactivated by far less irradiation than the papilloma virus. 10,000 r destroys 90 per cent or more of the infectivity of the fibroma virus, whereas at least 100,000 r is required to inactivate 50 per cent of the papilloma virus in extracts containing about the same amount of protein. No variant of the papilloma virus or fibroma virus has been encountered as a result of the irradiation.

Structural dynamics of PZT thin films at the nanoscale

2005 ◽  
Vol 902 ◽  
Author(s):  
Alexei Grigoriev ◽  
Dal-Hyun Do ◽  
Dong Min Kim ◽  
Chang-Beom Eom ◽  
Bernhard Adams ◽  
...  
Keyword(s):  
Crystal Lattice ◽  
Lattice Distortion ◽  
Piezoelectric Effect ◽  
Polarization Switching ◽  
X Rays ◽  
Time Resolved ◽  
X Ray ◽  
Converse Piezoelectric Effect ◽  
Ferroelectric Capacitors ◽  
Crystal Lattice Distortion

AbstractWhen an electric field is applied to a ferroelectric the crystal lattice spacing changes as a result of the converse piezoelectric effect. Although the piezoelectric effect and polarization switching have been investigated for decades there has been no direct nanosecond-scale visualization of these phenomena in solid crystalline ferroelectrics. Synchrotron x-rays allow the polarization switching and the crystal lattice distortion to be visualized in space and time on scales of hundreds of nanometers and hundreds of picoseconds using ultrafast x-ray microdiffraction. Here we report the polarization switching visualization and polarization domain wall velocities for Pb(Zr0.45Ti0.55)O3 thin film ferroelectric capacitors studied by time-resolved x-ray microdiffraction.

scholarly journals A hydroxyapatite phantom material for the calibration of in vivo x-ray fluorescence systems of bone strontium and lead quantification

2021 ◽  
Author(s):  
Eric Da Silva
Keyword(s):  
Monte Carlo ◽  
Soft Tissue ◽  
Monte Carlo Simulations ◽  
Calibration Procedure ◽  
X Rays ◽  
X Ray ◽  
Total Phosphate Concentration ◽  
High Concentrations ◽  
Phantom Material

A hydroxyaptite [HAp; Ca5(PO4)3OH] phantom material was developed with the goal of improving the calibration protocol of the 125I-induced in vivo X-ray fluorescence (IVXRF) system of bone strontium quantification with further application to other IVXRF bone metal quantification systems, particulary those associated with bone lead quantification. It was found that calcium can be prepared pure of inherent contamination from strontium (and other elements) through a hydroxide precipitation producing pure Ca(OH)2, thereby, allowing for the production of a blank phantom which has not been available previously. The pure Ca(OH)2 can then be used for the preparation of pure CaHPO4 ⋅ 2H2O. A solid state pure HAp phantom can then be prepared by reaction of Ca(OH)2 and CaHPO4 ⋅ 2H2O mixed as to produce a Ca/P mole ratio of 1.67, that in HAp and the mineral phase of bone, in the presence of a setting solution prepared as to raise the total phosphate concentration of the solution by increasing the solubility CaHPO4 ⋅ 2H2O and thereby precipitating HAp. The procedure can only be used to prepare phantoms in which doping with the analyte does not disturb the Ca/P ratio substantially. In cases in which phantoms are to be prepared with high concentrations of strontium, the cement mixture can be modified as to introduce strontium in the form of Sr(OH)2 ⋅ 8H2O as to maintain a (Ca + Sr)/P ratio of 1.67. It was found by both X-ray diffraction spectrometry and Raman spectroscopy studies that strontium substitutes for calcium as in bone when preparing phantoms by this route. The necessity for the blank bone phantoms was assessed through the first blank bone phantom measurement and Monte Carlo simulations. It was found that for the 125I-induced IVXRF system of bone strontium quantification, the source, 125I brachytherapy seeds may be contributing coherently and incoherently scattered zirconium X-rays to the measured spectra, thereby requiring the use of the blank bone phantom as a means of improving the overall quantification methodology. Monte Carlo simulations were employed to evaluate any improvement by the introduction of HAp phantoms into the coherent normalization-based calibration procedure. It was found that HAp phantoms remove the need for a coherent conversion factor (CCF) thereby potentially increasing accuracy of the quantification. Further, it was found that in order for soft tissue attenuation corrections to be possible using spectroscopic information alone, HAp along with a suitable soft tissue surrogate material need to be employed. The HAp phantom material was used for the evaluations of portable X-ray analyzer systems for their potential for IVXRF quantification of lead and strontium with a focus on a comparison between tungsten, silver and rhodium target systems. Silver and rhodium target X-ray tube systems were found to be comparable for this quantification.

The Limits of Resolution in X-Ray Microscopy

1997 ◽  
Vol 3 (S2) ◽  
pp. 1185-1186
Author(s):  
J. Maser ◽  
C. Jacobsen ◽  
S. Spector
Keyword(s):  
Near Field ◽  
High Spectral Resolution ◽  
X Rays ◽  
Thin Specimen ◽  
Selective Labeling ◽  
X Ray ◽  
Luminescent Probes ◽  
Electron Microscopes ◽  
Good Signal ◽  
Do So

In far-field microscopes, the spatial resolution is ultimately limited by the wavelength of the radiation used. While near-field and related microscopes can improve upon this, they can only do so with thin specimen regions. Thin specimens can also be studied at atomic resolution using electron microscopes. To achieve improved resolution on micrometer-thick specimens, another alternative is to use significantly shorter photon wavelengths. We discuss here the use of soft x-rays for microscopy and their resolution limits.Image formation requires resolution and contrast. by using soft x-rays with a photon energy between the K absorption edges of carbon and oxygen, one is able to image hydrated biological specimens with high contrast. The contrast is such that no addi-tional staining is required, while efforts are also underway to utilize gold and luminescent probes for selective labeling. In addition, x-ray sources have high spectral resolution and good signal-to-background relative to electron microscopes which allows for elemental and chemical state mapping of major constituents.

scholarly journals Structure–function studies of Rgg binding to pheromones and target promoters reveal a model of transcription factor interplay

2020 ◽  
Vol 117 (39) ◽  
pp. 24494-24502
Author(s):  
Glenn C. Capodagli ◽  
Kaitlyn M. Tylor ◽  
Jason T. Kaelber ◽  
Vasileios I. Petrou ◽  
Michael J. Federle ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Structure Function ◽  
Transcriptional Activation ◽  
Molecular Basis ◽  
Streptococcus Thermophilus ◽  
X Ray ◽  
Target Dna ◽  
Dna Promoters

Regulator gene of glucosyltransferase (Rgg) family proteins, such as Rgg2 and Rgg3, have emerged as primary quorum-sensing regulated transcription factors in Streptococcus species, controlling virulence, antimicrobial resistance, and biofilm formation. Rgg2 and Rgg3 function is regulated by their interaction with oligopeptide quorum-sensing signals called short hydrophobic peptides (SHPs). The molecular basis of Rgg–SHP and Rgg–target DNA promoter specificity was unknown. To close this gap, we determined the cryoelectron microscopy (cryo-EM) structure of Streptococcus thermophilus Rgg3 bound to its quorum-sensing signal, SHP3, and the X-ray crystal structure of Rgg3 alone. Comparison of these structures with that of an Rgg in complex with cyclosporin A (CsA), an inhibitor of SHP-induced Rgg activity, reveals the molecular basis of CsA function. Furthermore, to determine how Rgg proteins recognize DNA promoters, we determined X-ray crystal structures of both Streptococcus dysgalactiae Rgg2 and S. thermophilus Rgg3 in complex with their target DNA promoters. The physiological importance of observed Rgg–DNA interactions was dissected using in vivo genetic experiments and in vitro biochemical assays. Based on these structure–function studies, we present a revised unifying model of Rgg regulatory interplay. In contrast to existing models, where Rgg2 proteins are transcriptional activators and Rgg3 proteins are transcriptional repressors, we propose that both are capable of transcriptional activation. However, when Rgg proteins with different activation requirements compete for the same DNA promoters, those with more stringent activation requirements function as repressors by blocking promoter access of SHP-bound conformationally active Rgg proteins. While a similar gene expression regulatory scenario has not been previously described, in all likelihood it is not unique to streptococci.

scholarly journals Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources

2019 ◽  
Vol 20 (6) ◽  
pp. 1401 ◽  
Author(s):  
Marius Schmidt
Keyword(s):  
Structural Biology ◽  
Free Electron ◽  
Reaction Dynamics ◽  
X Rays ◽  
Free Electron Lasers ◽  
Macromolecular Crystallography ◽  
Time Resolved ◽  
X Ray ◽  
Methodological Aspects

The focus of structural biology is shifting from the determination of static structures to the investigation of dynamical aspects of macromolecular function. With time-resolved macromolecular crystallography (TRX), intermediates that form and decay during the macromolecular reaction can be investigated, as well as their reaction dynamics. Time-resolved crystallographic methods were initially developed at synchrotrons. However, about a decade ago, extremely brilliant, femtosecond-pulsed X-ray sources, the free electron lasers for hard X-rays, became available to a wider community. TRX is now possible with femtosecond temporal resolution. This review provides an overview of methodological aspects of TRX, and at the same time, aims to outline the frontiers of this method at modern pulsed X-ray sources.

Sign in / Sign up

Export Citation Format

Share Document