81 research outputs found
3D Imaging of a Phase Object from a Single Sample Orientation Using an Optical Laser
Ankylography is a new 3D imaging technique, which, under certain
circumstances, enables reconstruction of a 3D object from a single sample
orientation. Here, we provide a matrix rank analysis to explain the principle
of ankylography. We then present an ankylography experiment on a microscale
phase object using an optical laser. Coherent diffraction patterns are acquired
from the phase object using a planar CCD detector and are projected onto a
spherical shell. The 3D structure of the object is directly reconstructed from
the spherical diffraction pattern. This work may potentially open the door to a
new method for 3D imaging of phase objects in the visible light region.
Finally, the extension of ankylography to more complicated and larger objects
is suggested.Comment: 22 pages 5 figure
Quantitative Imaging of Single, Unstained Viruses with Coherent X-rays
Since Perutz, Kendrew and colleagues unveiled the structure of hemoglobin and
myoglobin based on X-ray diffraction analysis in the 1950s, X-ray
crystallography has become the primary methodology used to determine the 3D
structure of macromolecules. However, biological specimens such as cells,
organelles, viruses and many important macromolecules are difficult or
impossible to crystallize, and hence their structures are not accessible by
crystallography. Here we report, for the first time, the recording and
reconstruction of X-ray diffraction patterns from single, unstained viruses.
The structure of the viral capsid inside a virion was visualized. This work
opens the door for quantitative X-ray imaging of a broad range of specimens
from protein machineries, viruses and organelles to whole cells. Moreover, our
experiment is directly transferable to the use of X-ray free electron lasers,
and represents a major experimental milestone towards the X-ray imaging of
single macromolecules.Comment: 16 pages, 5 figure
Noninvasive 3D Structural Analysis of Arthropod by Synchrotron X-Ray Phase Contrast Tomography
X-ray imaging techniques significantly advanced our understanding of materials and biology, among which phase contrast X-ray microscopy has obvious advantages in imaging biological specimens which have low contrast by conventional absorption contrast microscopy. In this paper, three-dimensional microstructure of arthropod with high contrast has been demonstrated by synchrotron X-ray in-line phase contrast tomography. The external morphology and internal structures of an earthworm were analyzed based upon tomographic reconstructions with and without phase retrieval. We also identified and characterized various fine structural details such as the musculature system, the digestive system, the nervous system, and the circulatory system. This work exhibited the high efficiency, high precision, and wide potential applications of synchrotron X-ray phase contrast tomography in nondestructive investigation of low-density materials and biology
Coherent diffraction microscopy at SPring-8: instrumentation, data acquisition and data analysis
An instrumentation and data analysis review of coherent diffraction microscopy at SPring-8 is given. This work will be of interest to those who want to apply coherent diffraction imaging to studies of materials science and biological samples
Identification of the C-Reactive Protein Interaction Network Using a Bioinformatics Approach Provides Insights into the Molecular Pathogenesis of Hepatocellular Carcinoma
Background/Aims: C reactive protein (CRP) levels are elevated in many diseases, including malignant tumors and cardiovascular disorders. In this study, the protein interaction network for CRP was evaluated to determine the importance of CRP and its interacting proteins in the molecular pathogenesis of hepatocellular carcinoma (HCC). Methods: Isobaric tags for relative and absolute quantitation (iTRAQ) and mass spectrometry were used to identify CRP interacting proteins in SMMC7721 cells. Moreover, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to evaluate enriched genes and pathways for differentially expressed genes using DAVID and WebGestalt. Co-immunoprecipitation and western blot analyses were employed to assess interactions between CRP and KRT8, ANXA2, ENO2, and HSP90B1. Results: In total, 52 proteins that interact with CRP were identified. A GO analysis suggested that most of the interacting proteins were involved in CRP complexes and regulated metabolic processes. A KEGG pathway analysis suggested that most CRP-interacting proteins contribute to the TRAIL signaling pathway, Class I PI3K/Akt signaling pathway, plasma membrane estrogen receptor signaling, Nectin adhesion pathway, and S1P1 pathway. Immunoprecipitation and western blot analyses revealed interactions between CRP and KRT8, ANXA2, ENO2, and HSP90B1. Conclusions: iTRAQ based proteomic profiling revealed the network of CRP interacting proteins. This network may activate the PI3K/Akt signaling pathway, thereby contributing to the pathogenesis of HCC
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Single-shot 3D coherent diffractive imaging of core-shell nanoparticles with elemental specificity.
We report 3D coherent diffractive imaging (CDI) of Au/Pd core-shell nanoparticles with 6.1 nm spatial resolution with elemental specificity. We measured single-shot diffraction patterns of the nanoparticles using intense x-ray free electron laser pulses. By exploiting the curvature of the Ewald sphere and the symmetry of the nanoparticle, we reconstructed the 3D electron density of 34 core-shell structures from these diffraction patterns. To extract 3D structural information beyond the diffraction signal, we implemented a super-resolution technique by taking advantage of CDI's quantitative reconstruction capabilities. We used high-resolution model fitting to determine the Au core size and the Pd shell thickness to be 65.0 ± 1.0 nm and 4.0 ± 0.5 nm, respectively. We also identified the 3D elemental distribution inside the nanoparticles with an accuracy of 3%. To further examine the model fitting procedure, we simulated noisy diffraction patterns from a Au/Pd core-shell model and a solid Au model and confirmed the validity of the method. We anticipate this super-resolution CDI method can be generally used for quantitative 3D imaging of symmetrical nanostructures with elemental specificity
Three-dimensional structure determination from a single view
The ability to determine the structure of matter in three dimensions has
profoundly advanced our understanding of nature. Traditionally, the most widely
used schemes for 3D structure determination of an object are implemented by
acquiring multiple measurements over various sample orientations, as in the
case of crystallography and tomography (1,2), or by scanning a series of thin
sections through the sample, as in confocal microscopy (3). Here we present a
3D imaging modality, termed ankylography (derived from the Greek words ankylos
meaning 'curved' and graphein meaning 'writing'), which enables complete 3D
structure determination from a single exposure using a monochromatic incident
beam. We demonstrate that when the diffraction pattern of a finite object is
sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of
the object is determined by the 2D spherical pattern. We confirm the
theoretical analysis by performing 3D numerical reconstructions of a sodium
silicate glass structure at 2 Angstrom resolution and a single poliovirus at 2
- 3 nm resolution from 2D spherical diffraction patterns alone. Using
diffraction data from a soft X-ray laser, we demonstrate that ankylography is
experimentally feasible by obtaining a 3D image of a test object from a single
2D diffraction pattern. This approach of obtaining complete 3D structure
information from a single view is anticipated to find broad applications in the
physical and life sciences. As X-ray free electron lasers (X-FEL) and other
coherent X-ray sources are under rapid development worldwide, ankylography
potentially opens a door to determining the 3D structure of a biological
specimen in a single pulse and allowing for time-resolved 3D structure
determination of disordered materials.Comment: 30 page
Single-shot 3D coherent diffractive imaging of core-shell nanoparticles with elemental specificity
We report 3D coherent diffractive imaging (CDI) of Au/Pd core-shell nanoparticles with 6.1 nm spatial resolution with elemental specificity. We measured single-shot diffraction patterns of the nanoparticles using intense x-ray free electron laser pulses. By exploiting the curvature of the Ewald sphere and the symmetry of the nanoparticle, we reconstructed the 3D electron density of 34 core-shell structures from these diffraction patterns. To extract 3D structural information beyond the diffraction signal, we implemented a super-resolution technique by taking advantage of CDI's quantitative reconstruction capabilities. We used high-resolution model fitting to determine the Au core size and the Pd shell thickness to be 65.0 +/- 1.0 nm and 4.0 +/- 0.5 nm, respectively. We also identified the 3D elemental distribution inside the nanoparticles with an accuracy of 3%. To further examine the model fitting procedure, we simulated noisy diffraction patterns from a Au/Pd core-shell model and a solid Au model and confirmed the validity of the method. We anticipate this super-resolution CDI method can be generally used for quantitative 3D imaging of symmetrical nanostructures with elemental specificity.111Ysciescopu
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