scholarly journals Assaying three-dimensional cellular architecture using X-ray tomographic and correlated imaging approaches

2020 ◽  
Vol 295 (46) ◽  
pp. 15782-15793 ◽  
Author(s):  
Peter O. Bayguinov ◽  
Max R. Fisher ◽  
James A. J. Fitzpatrick
Keyword(s):  
Spatial Organization ◽  
Three Dimensional ◽  
Specific Protein ◽  
Multidimensional Data ◽  
Data Sets ◽  
X Rays ◽  
Correlative Microscopy ◽  
Protein Targets ◽  
X Ray ◽  
Cellular Architecture

Much of our understanding of the spatial organization of and interactions between cellular organelles and macromolecular complexes has been the result of imaging studies utilizing either light- or electron-based microscopic analyses. These classical approaches, while insightful, are nonetheless limited either by restrictions in resolution or by the sheer complexity of generating multidimensional data. Recent advances in the use and application of X-rays to acquire micro- and nanotomographic data sets offer an alternative methodology to visualize cellular architecture at the nanoscale. These new approaches allow for the subcellular analyses of unstained vitrified cells and three-dimensional localization of specific protein targets and have served as an essential tool in bridging light and electron correlative microscopy experiments. Here, we review the theory, instrumentation details, acquisition principles, and applications of both soft X-ray tomography and X-ray microscopy and how the use of these techniques offers a succinct means of analyzing three-dimensional cellular architecture. We discuss some of the recent work that has taken advantage of these approaches and detail how they have become integral in correlative microscopy workflows.

scholarly journals Determination of crystallographic intensities from sparse data

IUCrJ ◽  
2015 ◽  
Vol 2 (1) ◽  
pp. 29-34 ◽  
Author(s):  
Kartik Ayyer ◽  
Hugh T. Philipp ◽  
Mark W. Tate ◽  
Jennifer L. Wierman ◽  
Veit Elser ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Crystal Size ◽  
Three Dimensional ◽  
Sparse Data ◽  
Data Sets ◽  
X Rays ◽  
Diffraction Intensity ◽  
X Ray ◽  
Proof Of Principle

X-ray serial microcrystallography involves the collection and merging of frames of diffraction data from randomly oriented protein microcrystals. The number of diffracted X-rays in each frame is limited by radiation damage, and this number decreases with crystal size. The data in the frame are said to be sparse if too few X-rays are collected to determine the orientation of the microcrystal. It is commonly assumed that sparse crystal diffraction frames cannot be merged, thereby setting a lower limit to the size of microcrystals that may be merged with a given source fluence. TheEMCalgorithm [Loh & Elser (2009),Phys. Rev. E,80, 026705] has previously been applied to reconstruct structures from sparse noncrystalline data of objects with unknown orientations [Philippet al.(2012),Opt. Express,20, 13129–13137; Ayyeret al.(2014),Opt. Express,22, 2403–2413]. Here, it is shown that sparse data which cannot be oriented on a per-frame basis can be used effectively as crystallographic data. As a proof-of-principle, reconstruction of the three-dimensional diffraction intensity using sparse data frames from a 1.35 kDa molecule crystal is demonstrated. The results suggest that serial microcrystallography is, in principle, not limited by the fluence of the X-ray source, and collection of complete data sets should be feasible at, for instance, storage-ring X-ray sources.

scholarly journals Is Micro X-ray Computer Tomography a Suitable Non-Destructive Method for the Characterisation of Dental Materials?

Polymers ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1271
Author(s):  
Andreas Koenig ◽  
Leonie Schmohl ◽  
Johannes Scheffler ◽  
Florian Fuchs ◽  
Michaela Schulz-Siegmund ◽  
...  
Keyword(s):  
Flexural Strength ◽  
Computer Tomography ◽  
Mechanical Performance ◽  
Dental Materials ◽  
Three Dimensional ◽  
X Rays ◽  
Scanning Calorimetry ◽  
X Ray ◽  
Multiple Measurements ◽  
High Doses

The aim of the study was to investigate the effect of X-rays used in micro X-ray computer tomography (µXCT) on the mechanical performance and microstructure of a variety of dental materials. Standardised bending beams (2 × 2 × 25 mm3) were forwarded to irradiation with an industrial tomograph. Using three-dimensional datasets, the porosity of the materials was quantified and flexural strength was investigated prior to and after irradiation. The thermal properties of irradiated and unirradiated materials were analysed and compared by means of differential scanning calorimetry (DSC). Single µXCT measurements led to a significant decrease in flexural strength of polycarbonate with acrylnitril-butadien-styrol (PC-ABS). No significant influence in flexural strength was identified for resin-based composites (RBCs), poly(methyl methacrylate) (PMMA), and zinc phosphate cement (HAR) after a single irradiation by measurement. However, DSC results suggest that changes in the microstructure of PMMA are possible with increasing radiation doses (multiple measurements, longer measurements, higher output power from the X-ray tube). In summary, it must be assumed that X-ray radiation during µXCT measurement at high doses can lead to changes in the structure and properties of certain polymers.

Visualizing Fluid Flows With X-Rays

2007 ◽  
Author(s):  
Theodore J. Heindel ◽  
Terrence C. Jensen ◽  
Joseph N. Gray
Keyword(s):  
Computed Tomography ◽  
Flow Visualization ◽  
Three Dimensional ◽  
Fluid Flows ◽  
X Rays ◽  
Radiographic Images ◽  
Optical Access ◽  
X Ray ◽  
X Ray Computed ◽  
Density Map

There are several methods available to visualize fluid flows when one has optical access. However, when optical access is limited to near the boundaries or not available at all, alternative visualization methods are required. This paper will describe flow visualization using an X-ray system that is capable of digital X-ray radiography, digital X-ray stereography, and digital X-ray computed tomography (CT). The unique X-ray flow visualization facility will be briefly described, and then flow visualization of various systems will be shown. Radiographs provide a two-dimensional density map of a three dimensional process or object. Radiographic images of various multiphase flows will be presented. When two X-ray sources and detectors simultaneously acquire images of the same process or object from different orientations, stereographic imaging can be completed; this type of imaging will be demonstrated by trickling water through packed columns and by absorbing water in a porous medium. Finally, local time-averaged phase distributions can be determined from X-ray computed tomography (CT) imaging, and this will be shown by comparing CT images from two different gas-liquid sparged columns.

Recent Developments In Monochromatic Microprobe X-Ray Fluorescence (MMXRF)

1998 ◽  
Vol 4 (S2) ◽  
pp. 378-379
Author(s):  
Z. W. Chen ◽  
D. B. Wittry
Keyword(s):  
Materials Science ◽  
High Vacuum ◽  
Three Dimensional ◽  
High Sensitivity ◽  
X Rays ◽  
Fluorescence Excitation ◽  
X Ray ◽  
Quantitative Microanalysis ◽  
Recent Developments ◽  
Fifth Order

A monochromatic x-ray microprobe based on a laboratory source has recently been developed in our laboratory and used for fluorescence excitation. This technique provides high sensitivity (ppm to ppb), nondestructive, quantitative microanalysis with minimum sample preparation and does not require a high vacuum specimen chamber. It is expected that this technique (MMXRF) will have important applications in materials science, geological sciences and biological science.Three-dimensional focusing of x-rays can be obtained by using diffraction from doubly curved crystals. In our MMXRF setup, a small x-ray source was produced by the bombardment of a selected target with a focused electron beam and a toroidal mica diffractor with Johann pointfocusing geometry was used to focus characteristic x-rays from the source. In the previous work ∼ 108 photons/s were obtained in a Cu Kα probe of 75 μm × 43 μm in the specimen plane using the fifth order reflection of the (002) planes of mica.

scholarly journals Lower resolution Laue neutron data yield correct nanocluster formulations

2014 ◽  
Vol 70 (a1) ◽  
pp. C187-C187
Author(s):  
Alison Edwards
Keyword(s):  
Neutron Diffraction ◽  
Single Crystal ◽  
Diffraction Pattern ◽  
Precise Determination ◽  
Data Sets ◽  
X Rays ◽  
Low Resolution ◽  
Neutron Data ◽  
X Ray ◽  
Product Formulation

"The renaissance in Laue studies - at neutron sources - provides us with access to single crystal neutron diffraction data for synthetic compounds without requiring synthesis of prohibitively large amounts of compound or improbably large crystals. Such neutron diffraction studies provide vital data where proof of the presence or absence of hydrogen in particular locations is required and which cannot validly be proved by X-ray studies. Since the commissioning of KOALA at OPAL in 2009[1] we have obtained numerous data sets which demonstrate the vital importance of measuring data even where the extent of the diffraction pattern is at relatively low resolution - especially when compared to that obtainable for the same compound with X-rays. In the Laue experiment performed with a fixed radius detector, data reduction is only feasible for crystals in the ""goldilocks"" zone – where the unit cell is relatively large for the detector, a correspondingly low resolution diffraction pattern in which adjacent spots are less affected by overlap will yield more data against which a structure can be refined than a pattern of higher resolution – one where neighbouring spots overlap rendering both unusable (in our current methodology). Analogous application of powder neutron diffraction in such determinations is also considered. Single crystal neutron diffraction studies of several important compounds (up to 5KDa see figure below)[2] in which precise determination of hydride content by neutron diffraction was pivotal to the final formulation will be presented. The neutron data sets typically possess 20% or fewer unique data at substantially "lower resolution" than the corresponding X-ray data sets. Careful refinement clearly reveals chemical detail which is typically unexplored in related X-ray diffraction studies reporting high profile chemistry despite the synthetic route being one which hydride ought to be considered/excluded in product formulation."

Structural study of the X-ray-induced enzymatic reaction of octahaem cytochromecnitrite reductase

2015 ◽  
Vol 71 (5) ◽  
pp. 1087-1094 ◽  
Author(s):  
A. A. Trofimov ◽  
K. M. Polyakov ◽  
V. A. Lazarenko ◽  
A. N. Popov ◽  
T. V. Tikhonova ◽  
...  
Keyword(s):  
Nitrite Reductase ◽  
Catalytic Reaction ◽  
Active Sites ◽  
Enzymatic Reaction ◽  
Absorbed Dose ◽  
Free Form ◽  
Data Sets ◽  
X Rays ◽  
X Ray ◽  
Site Water

Octahaem cytochromecnitrite reductase from the bacteriumThioalkalivibrio nitratireducenscatalyzes the reduction of nitrite to ammonium and of sulfite to sulfide. The reducing properties of X-ray radiation and the high quality of the enzyme crystals allow study of the catalytic reaction of cytochromecnitrite reductase directly in a crystal of the enzyme, with the reaction being induced by X-rays. Series of diffraction data sets with increasing absorbed dose were collected from crystals of the free form of the enzyme and its complexes with nitrite and sulfite. The corresponding structures revealed gradual changes associated with the reduction of the catalytic haems by X-rays. In the case of the nitrite complex the conversion of the nitrite ions bound in the active sites to NO species was observed, which is the beginning of the catalytic reaction. For the free form, an increase in the distance between the oxygen ligand bound to the catalytic haem and the iron ion of the haem took place. In the case of the sulfite complex no enzymatic reaction was detected, but there were changes in the arrangement of the active-site water molecules that were presumably associated with a change in the protonation state of the sulfite ions.

scholarly journals Hard X-ray polarizer to enable simultaneous three-dimensional nanoscale imaging of magnetic structure and lattice strain

2016 ◽  
Vol 23 (5) ◽  
pp. 1210-1215 ◽  
Author(s):  
Jonathan Logan ◽  
Ross Harder ◽  
Luxi Li ◽  
Daniel Haskel ◽  
Pice Chen ◽  
...  
Keyword(s):  
Magnetic Circular Dichroism ◽  
Three Dimensional ◽  
Control Sample ◽  
Magnetic Ordering ◽  
X Rays ◽  
Diffractive Imaging ◽  
X Ray ◽  
Coherent Diffractive Imaging ◽  
Diffraction Patterns ◽  
A New Technique

Recent progress in the development of dichroic Bragg coherent diffractive imaging, a new technique for simultaneous three-dimensional imaging of strain and magnetization at the nanoscale, is reported. This progress includes the installation of a diamond X-ray phase retarder at beamline 34-ID-C of the Advanced Photon Source. The performance of the phase retarder for tuning X-ray polarization is demonstrated with temperature-dependent X-ray magnetic circular dichroism measurements on a gadolinium foil in transmission and on a Gd5Si2Ge2crystal in diffraction geometry with a partially coherent, focused X-ray beam. Feasibility tests for dichroic Bragg coherent diffractive imaging are presented. These tests include (1) using conventional Bragg coherent diffractive imaging to determine whether the phase retarder introduces aberrations using a nonmagnetic gold nanocrystal as a control sample, and (2) collecting coherent diffraction patterns of a magnetic Gd5Si2Ge2nanocrystal with left- and right-circularly polarized X-rays. Future applications of dichroic Bragg coherent diffractive imaging for the correlation of strain and lattice defects with magnetic ordering and inhomogeneities are considered.

scholarly journals Synchrotron radiation X-ray tomographic microscopy (SRXTM) of brachiopod shell interiors for taxonomy: Preliminary report

2010 ◽  
pp. 109-117 ◽  
Author(s):  
Neda Motchurova-Dekova ◽  
David Harper
Keyword(s):  
Synchrotron Radiation ◽  
Three Dimensional ◽  
X Rays ◽  
X Ray ◽  
Fine Grained ◽  
Internal Structures ◽  
Efficient Alternative ◽  
Micro Tomography ◽  
Light Beams ◽  
Non Destructive

Synchrotron radiation X-ray tomographic microscopy (SRXTM) is a non-destructive technique for the investigation and visualization of the internal features of solid opaque objects, which allows reconstruction of a complete three-dimensional image of internal structures by recording of the differences in the effects on the passage of waves of energy reacting with those structures. Contrary to X-rays, produced in a conventional X-ray tube, the intense synchrotron light beams are sharply focused like a laser beam. We report encouraging results from the use of SRXTM for purely taxonomic purposes in brachiopods: an attempt to find a non-destructive and more efficient alternative to serial sectioning and several other methods of dissection together with the non-destructive method of X-ray computerised micro-tomography. Two brachiopod samples were investigated using SRXTM. In ?Rhynchonella? flustracea it was possible to visualise the 3D shape of the crura and dental plates. In Terebratulina imbricata it was possible to reveal the form of the brachidium. It is encouraging that we have obtained such promising results using SRXTM with our very first two fortuitous samples, which had respectively fine-grained limestone and marl as infilling sediment, in contrast to the discouraging results communicated to us by some colleagues who have tested specimens with such infillings using X-ray micro-tomography. In future the holotypes, rare museum specimens or delicate Recent material may be preferentially subjected to this mode of analysis.

Diffraction

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Red Light ◽  
Three Dimensional ◽  
Three Dimensions ◽  
X Rays ◽  
X Ray ◽  
Original Direction ◽  
Computational Procedures ◽  
Scattering Material ◽  
Opaque Object ◽  
Diffraction Effects

Diffraction refers to the effects observed when light is scattered into directions other than the original direction of the light, without change of wavelength. An X-ray photon may interact with an electron and set the electron oscillating with the X-ray frequency. The oscillating electron may radiate an X-ray photon of the same wavelength, in a random direction, when it returns to its unexcited state. Other processes may also occur, akin to fluorescence, which emit X-rays of longer wavelengths, but these processes do not give diffraction effects. Just as we see a red card because red light is scattered off the card into our eyes, objects are observed with X-rays because an illuminating X-ray beam is scattered into the X-ray detector. Our eye can analyse details of the card because its lens forms an image on the retina. Since no X-ray lens is available, the scattered X-ray beam cannot be converted directly into an image. Indirect computational procedures have to be used instead. X-rays are penetrating radiation, and can be scattered from electrons throughout the whole scattering object, while light only shows the external shape of an opaque object like a red card. This allows X-rays to provide a truly three-dimensional image. When X-rays pass near an atom, only a tiny fraction of them is scattered: most of the X-rays pass further into the object, and usually most of them come straight out the other side of the whole object. In forming an image, these ‘straight through’ X-rays tell us nothing about the structure, and they are usually captured by a beam stop and ignored. This chapter begins by explaining that the diffraction of light or X-rays can provide a precise physical realization of Fourier’s method of analysing a regularly repeating function. This method may be used to study regularly repeating distributions of scattering material. Beginning in one dimension, examples will be used to bring out some fundamental features of diffraction analysis. Graphic examples of two-dimensional diffraction provide further demonstrations. Although the analysis in three dimensions depends on exactly the same principles, diffraction by a three-dimensional crystal raises additional complications.

Radiological anatomy of the oral cavity

2013 ◽  
Author(s):  
Martin E. Atkinson
Keyword(s):  
Soft Tissues ◽  
Three Dimensional ◽  
Compact Bone ◽  
X Rays ◽  
Radiological Anatomy ◽  
X Ray ◽  
Periodontal Tissues ◽  
Sensitive Film ◽  
Mineralized Tissues ◽  
Pass Through

The radiographs most frequently taken in general dental practice are of the teeth and their immidiate supporting tissues for detection of dental caries or assessment of bone loss in periodontal disease. Intraoral radiographs are taken by placing the X-ray-sensitive film or receptor in the mouth close to the teeth being investigated. Extraoral radiographs use larger films or receptors positioned externally and produce a view of the entire dentition and its supporting structures on a single film; they are used to ascertain the state of development of the dentitions prior to orthodontic treatment, for example. Dental panoramic tomographs (DPTs) are the most frequent extraoral radiographs. A radiograph is a negative photographic record. Dense structures such as bone are designated as radio-opaque; they absorb some X-rays and appear white on radiographs. More X-rays pass through less dense radiolucent structures such as air-filled cavities which show up as black areas. The contrast between different tissues of the structures which the X-ray beam passes through is determined by their radiodensity which, in turn, is largely due to their content of metallic elements. Calcium and iron are the prevalent heavy metals in the body. Calcium is combined with phosphate to form hydroxyapatite crystals in bones and mineralized tissues in teeth. Iron is present in haemoglobin in blood, but only large concentrations of blood, such as those found within the heart chambers, show up on X-rays. In sequence from densest to most lucent, the radiodensity of the dental and periodontal tissues are: enamel, dentine, cementum, compact bone, cancellous bone, demineralized carious enamel and dentine, dental soft tissues such as pulp and periodontal ligament, and air; gold and silver–mercury amalgam metallic restorative materials are even denser than enamel. A radiograph is a two-dimensional representation of a three-dimensional situation. The orientation of anatomical structures relative to the X-ray beam is a major factor determining their appearance on the film. For example, a beam travelling through the long axis of a radiodense structure will produce a whiter image on the film than one passing through its shorter axis because more X-rays are absorbed; the structure will also have a different shape.

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