Three-Dimensional Visualization of a Human Chromosome Using Coherent X-Ray Diffraction

Nishino, Yoshinori; Takahashi, Yukio; Imamoto, Naoko; Ishikawa, Tetsuya; Maeshima, Kazuhiro

doi:10.1103/physrevlett.102.018101

Cited by 292 publications

(191 citation statements)

References 31 publications

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“…CXDI has been demonstrated on biological unstained specimens by using soft (12,13) and hard x-rays (14,15). In its original form (9), CXDI imposes considerable limitations and preconditions to the experimental setup or the sample, excluding in particular extended samples and assuming an idealized plane wave illumination function.…”

mentioning

confidence: 99%

Quantitative biological imaging by ptychographic x-ray diffraction microscopy

Giewekemeyer

Thibault²,

Kalbfleisch³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

248

206

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Recent advances in coherent x-ray diffractive imaging have paved the way to reliable and quantitative imaging of noncompact specimens at the nanometer scale. Introduced a year ago, an advanced implementation of ptychographic coherent diffractive imaging has removed much of the previous limitations regarding sample preparation and illumination conditions. Here, we apply this recent approach toward structure determination at the nanoscale to biological microscopy. We show that the projected electron density of unstained and unsliced freeze-dried cells of the bacterium Deinococcus radiodurans can be derived from the reconstructed phase in a straightforward and reproducible way, with quantified and small errors. Thus, the approach may contribute in the future to the understanding of the highly disputed nucleoid structure of bacterial cells. In the present study, the estimated resolution for the cells was 85 nm (half-period length), whereas 50-nm resolution was demonstrated for lithographic test structures. With respect to the diameter of the pinhole used to illuminate the samples, a superresolution of about 15 was achieved for the cells and 30 for the test structures, respectively. These values should be assessed in view of the low dose applied on the order of ≃1.3 · 10 5 Gy, and were shown to scale with photon fluence.bacterial nucleoid | cellular imaging | coherent x-ray diffractive imaging | x-ray microscopy

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mentioning

confidence: 99%

Quantitative biological imaging by ptychographic x-ray diffraction microscopy

Giewekemeyer

Thibault²,

Kalbfleisch³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

248

206

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“…From many projected two-dimensional images thus obtained, a three-dimensional real-space structure can be constructed by applying the method of tomography. Such a three-dimensional human chromosome structure as revealed by coherent 2.5 Å X-rays from synchrotron radiation has been reported (Nishino et al, 2009).…”

Section: Introductionmentioning

confidence: 86%

Classifying and assembling two-dimensional X-ray laser diffraction patterns of a single particle to reconstruct the three-dimensional diffraction intensity function: resolution limit due to the quantum noise

Tokuhisa¹,

Taka

Kono

et al. 2012

Acta Cryst Sect A

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A new two-step algorithm is developed for reconstructing the three-dimensional diffraction intensity of a globular biological macromolecule from many experimentally measured quantum-noise-limited two-dimensional X-ray laser diffraction patterns, each for an unknown orientation. The first step is classification of the two-dimensional patterns into groups according to the similarity of direction of the incident X-rays with respect to the molecule and an averaging within each group to reduce the noise. The second step is detection of common intersecting circles between the signal-enhanced two-dimensional patterns to identify their mutual location in the three-dimensional wavenumber space. The newly developed algorithm enables one to detect a signal for classification in noisy experimental photon-count data with as low as $0.1 photons per effective pixel. The wavenumber of such a limiting pixel determines the attainable structural resolution. From this fact, the resolution limit due to the quantum noise attainable by this new method of analysis as well as two important experimental parameters, the number of two-dimensional patterns to be measured (the load for the detector) and the number of pairs of two-dimensional patterns to be analysed (the load for the computer), are derived as a function of the incident X-ray intensity and quantities characterizing the target molecule.

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“…Although DNA, chromatin and chromosomes have been studied in vitro by smallangle neutron or X-ray scattering [198][199][200], diffraction [201] or coherent diffractive imaging [202] (see section 1.3.2). Here we report results from an in situ analysis of the nucleus content of 3T3 fibroblast cells [203].…”

Section: Introductionmentioning

confidence: 99%

Investigating Cellular Nanoscale with X-rays

Hémonnot¹

2016

Göttingen Series in X-Ray Physics

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Three-Dimensional Visualization of a Human Chromosome Using Coherent X-Ray Diffraction

Cited by 292 publications

References 31 publications

Quantitative biological imaging by ptychographic x-ray diffraction microscopy

Quantitative biological imaging by ptychographic x-ray diffraction microscopy

Classifying and assembling two-dimensional X-ray laser diffraction patterns of a single particle to reconstruct the three-dimensional diffraction intensity function: resolution limit due to the quantum noise

Investigating Cellular Nanoscale with X-rays

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