Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT

We previously described X-ray histotomography, a high-resolution, non-destructive form of X-ray microtomography (micro-CT) imaging customized for three-dimensional (3D), digital histology, allowing quantitative, volumetric tissue and organismal phenotyping (Ding et al., 2019). Here, we have combined micro-CT with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. The resulting images enabled whole-body, computational analyses of regional melanin content and morphology. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy, and further allowed direct quantitative comparisons of melanin content across wild-type and mutant samples, including subtle phenotypes not previously noticed. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, 3D computational phenomic analysis of a specific cell type at cellular resolution, with potential applications in other model organisms and melanocytic neoplasms. Advances such as this in whole-organism, high-resolution phenotyping provide superior context for studying the phenotypic effects of genetic, disease, and environmental variables.

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Whole-organism 3D Quantitative Characterization of Zebrafish Melanin by Silver Deposition Micro-CT

10.1101/2021.03.11.434673 ◽

2021 ◽

Author(s):

Spencer R. Katz ◽

Maksim A. Yakovlev ◽

Daniel J. Vanselow ◽

Yifu Ding ◽

Alex Y. Lin ◽

...

Keyword(s):

Silver Staining ◽

Skin Color ◽

Large Scale ◽

Imaging Modality ◽

Three Dimensional ◽

Whole Body ◽

Model Organisms ◽

Micro Ct ◽

Melanin Content ◽

Silver Deposition

AbstractMelanin-rich zebrafish melanophores are used to study pigment development, human skin color, and as a large-scale screening phenotype. To facilitate more detailed whole-body, computational analyses of melanin content and morphology, we have combined X-ray microtomography (micro-CT), a non-destructive, full-volume imaging modality, with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy, and allowed direct quantitative comparisons of melanin content across wild-type and mutant samples, for both dramatic and subtle phenotypes not previously described. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, three-dimensional computational phenomic analysis of a particular cell type at cellular resolution, with potential applications in other model organisms and human melanoma biopsies. Whole-organism, high-resolution phenotyping is a challenging ideal, but provides superior context for functional studies of mutations, diseases, and environmental influences.

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Simple low dose radiography allows precise lung volume assessment in mice

Scientific Reports ◽

10.1038/s41598-021-83319-5 ◽

2021 ◽

Vol 11 (1) ◽

Cited By ~ 1

Author(s):

Amara Khan ◽

Andrea Markus ◽

Thomas Rittmann ◽

Jonas Albers ◽

Frauke Alves ◽

...

Keyword(s):

Lung Function ◽

Whole Body ◽

Acquisition Time ◽

Micro Ct ◽

Lung Volumes ◽

X Ray ◽

Promising Tool ◽

Volume Assessment ◽

Set Up ◽

Time Required

AbstractX-ray based lung function (XLF) as a planar method uses dramatically less X-ray dose than computed tomography (CT) but so far lacked the ability to relate its parameters to pulmonary air volume. The purpose of this study was to calibrate the functional constituents of XLF that are biomedically decipherable and directly comparable to that of micro-CT and whole-body plethysmography (WBP). Here, we developed a unique set-up for simultaneous assessment of lung function and volume using XLF, micro-CT and WBP on healthy mice. Our results reveal a strong correlation of lung volumes obtained from radiographic XLF and micro-CT and demonstrate that XLF is superior to WBP in sensitivity and precision to assess lung volumes. Importantly, XLF measurement uses only a fraction of the radiation dose and acquisition time required for CT. Therefore, the redefined XLF approach is a promising tool for preclinical longitudinal studies with a substantial potential of clinical translation.

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Three-dimensional crystallization of membrane proteins

Quarterly Reviews of Biophysics ◽

10.1017/s0033583500004625 ◽

1988 ◽

Vol 21 (4) ◽

pp. 429-477 ◽

Cited By ~ 156

Author(s):

W. Kühlbrandt

Keyword(s):

High Resolution ◽

Membrane Proteins ◽

Membrane Protein ◽

Protein Complexes ◽

Three Dimensional ◽

Biological Macromolecules ◽

X Ray ◽

X Ray Crystallography ◽

Membrane Protein Complexes ◽

Essential Prerequisite

As recently as 10 years ago, the prospect of solving the structure of any membrane protein by X-ray crystallography seemed remote. Since then, the threedimensional (3-D) structures of two membrane protein complexes, the bacterial photosynthetic reaction centres of Rhodopseudomonas viridis (Deisenhofer et al. 1984, 1985) and of Rhodobacter sphaeroides (Allen et al. 1986, 1987 a, 6; Chang et al. 1986) have been determined at high resolution. This astonishing progress would not have been possible without the pioneering work of Michel and Garavito who first succeeded in growing 3-D crystals of the membrane proteins bacteriorhodopsin (Michel & Oesterhelt, 1980) and matrix porin (Garavito & Rosenbusch, 1980). X-ray crystallography is still the only routine method for determining the 3-D structures of biological macromolecules at high resolution and well-ordered 3-D crystals of sufficient size are the essential prerequisite.

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Three-dimensional analysis of plant structure using high-resolution X-ray computed tomography

Trends in Plant Science ◽

10.1016/s1360-1385(02)00004-3 ◽

2003 ◽

Vol 8 (1) ◽

pp. 2-6 ◽

Cited By ~ 100

Author(s):

Wolfgang H Stuppy ◽

Jessica A Maisano ◽

Matthew W Colbert ◽

Paula J Rudall ◽

Timothy B Rowe

Keyword(s):

Computed Tomography ◽

High Resolution ◽

Dimensional Analysis ◽

Three Dimensional ◽

Plant Structure ◽

X Ray ◽

X Ray Computed

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Three dimensional characterization of laser ablation craters using high resolution X-ray computed tomography

Spectrochimica Acta Part B Atomic Spectroscopy ◽

10.1016/j.sab.2017.11.011 ◽

2018 ◽

Vol 139 ◽

pp. 75-82 ◽

Cited By ~ 4

Author(s):

A.H. Galmed ◽

A. du Plessis ◽

S.G. le Roux ◽

E. Hartnick ◽

H. Von Bergmann ◽

...

Keyword(s):

Computed Tomography ◽

Laser Ablation ◽

High Resolution ◽

Three Dimensional ◽

X Ray ◽

X Ray Computed

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Qualitative and quantitative investigation of soils and porous rocks by using very high resolution X-ray micro-CT imaging

Unsaturated Soils: Research & Applications ◽

10.1201/b17034-98 ◽

2014 ◽

pp. 699-702

Author(s):

G Zacher ◽

T Paul ◽

M Halisch ◽

P Westenberger

Keyword(s):

High Resolution ◽

Ct Imaging ◽

Micro Ct ◽

Porous Rocks ◽

Quantitative Investigation ◽

X Ray ◽

Qualitative And Quantitative ◽

Very High

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Three Dimensional X-Ray Computed Tomography in Materials Science

MRS Bulletin ◽

10.1557/s0883769400066525 ◽

1988 ◽

Vol 13 (1) ◽

pp. 13-18 ◽

Cited By ~ 27

Author(s):

J.H. Kinney ◽

Q.C. Johnson ◽

U. Bonse ◽

M.C. Nichols ◽

R.A. Saroyan ◽

...

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

Sample Preparation ◽

Visible Light ◽

Three Dimensional ◽

Materials Characterization ◽

Imaging Technology ◽

X Ray ◽

X Ray Imaging ◽

Visible Light Imaging

Imaging is the cornerstone of materials characterization. Until the middle of the present century, visible light imaging provided much of the information about materials. Though visible light imaging still plays an extremely important role in characterization, relatively low spatial resolution and lack of chemical sensitivity and specificity limit its usefulness.The discovery of x-rays and electrons led to a major advance in imaging technology. X-ray diffraction and electron microscopy allowed us to characterize the atomic structure of materials. Many materials vital to our high technology economy and defense owe their existence to the understanding of materials structure brought about with these high-resolution methods.Electron microscopy is an essential tool for materials characterization. Unfortunately, electron imaging is always destructive due to the sample preparation that must be done prior to imaging. Furthermore, electron microscopy only provides information about the surface of a sample. Three dimensional information, of great interest in characterizing many new materials, can be obtained only by time consuming sectioning of an object.The development of intense synchrotron light sources in addition to the improvements in solid state imaging technology is revolutionizing materials characterization. High resolution x-ray imaging is a potentially valuable tool for materials characterization. The large depth of x-ray penetration, as well as the sensitivity of absorption crosssections to atomic chemistry, allows x-ray imaging to characterize the chemistry of internal structures in macroscopic objects with little sample preparation. X-ray imaging complements other imaging modalities, such as electron microscopy, in that it can be performed nondestructively on metals and insulators alike.

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