scholarly journals Visualization of the spatial arrangement of nuclear organization using three-dimensional fluorescence in situ hybridization in early mouse embryos: A new “EASI-FISH chamber glass” for mammalian embryos

2017 ◽  
Vol 63 (2) ◽  
pp. 167-174
Author(s):  
Masataka NAKAYA ◽  
Hideyuki TANABE ◽  
Shingo TAKAMATSU ◽  
Misaki HOSOKAWA ◽  
Tasuku MITANI
Keyword(s):  
Nuclear Organization ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Mouse Embryos ◽  
Mammalian Embryos ◽  
Early Mouse

scholarly journals Three-dimensional electron microscopy of ribosomal chromatin in two higher plants: a cytochemical, immunocytochemical, and in situ hybridization approach.

1991 ◽  
Vol 39 (11) ◽  
pp. 1495-1506 ◽  
Author(s):  
P M Motte ◽  
R Loppes ◽  
M Menager ◽  
R Deltour
Keyword(s):  
Electron Microscopy ◽  
In Situ Hybridization ◽  
Spatial Organization ◽  
Higher Plants ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Thin Sections ◽  
Cytoplasmic Dna ◽  
Immunocytochemical Techniques

We report the 3-D arrangement of DNA within the nucleolar subcomponents from two evolutionary distant higher plants, Zea mays and Sinapis alba. These species are particularly convenient to study the spatial organization of plant intranucleolar DNA, since their nucleoli have been previously reconstructed in 3-D from serial ultra-thin sections. We used the osmium ammine-B complex (a specific DNA stain) on thick sections of Lowicryl-embedded root fragments. Immunocytochemical techniques using anti-DNA antibodies and rDNA/rDNA in situ hybridization were also applied on ultra-thin sections. We showed on tilted images that the OA-B stains DNA throughout the whole thickness of the section. In addition, very low quantities of cytoplasmic DNA were stained by this complex, which is now the best DNA stain used in electron microscopy. Within the nucleoli the DNA was localized in the fibrillar centers, where large clumps of dense chromatin were also visible. In the two plant species intranucleolar chromatin forms a complex network with strands partially linked to chromosomal nucleolar-organizing regions identified by in situ hybridization. This study describes for the first time the spatial arrangement of the intranucleolar chromatin in nucleoli of higher plants using high-resolution techniques.

scholarly journals High Resolution Mapping of Ribosomal DNA in Early Mouse Embryos by Fluorescence In Situ Hybridization1

2006 ◽  
Vol 74 (5) ◽  
pp. 807-815 ◽  
Author(s):  
Lioudmila Romanova ◽  
Farida Korobova ◽  
Ekaterina Noniashvilli ◽  
Andrei Dyban ◽  
Olga Zatsepina
Keyword(s):  
High Resolution ◽  
Ribosomal Dna ◽  
Mouse Embryos ◽  
High Resolution Mapping ◽  
Resolution Mapping ◽  
Early Mouse

scholarly journals In situ genome sequencing resolves DNA sequence and structure in intact biological samples

Science ◽  
2020 ◽  
Vol 371 (6532) ◽  
pp. eaay3446 ◽  
Author(s):  
Andrew C. Payne ◽  
Zachary D. Chiang ◽  
Paul L. Reginato ◽  
Sarah M. Mangiameli ◽  
Evan M. Murray ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Genome Sequencing ◽  
Biological Samples ◽  
Human Fibroblasts ◽  
Genome Structure ◽  
Three Dimensional ◽  
Base Pairs ◽  
Pair Sequence ◽  
Early Mouse

Understanding genome organization requires integration of DNA sequence and three-dimensional spatial context; however, existing genome-wide methods lack either base pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how IGS can directly connect sequence and structure across length scales from single base pairs to whole organisms.

scholarly journals Inferring cell junction tension and pressure from cell geometry

Development ◽  
2021 ◽  
Vol 148 (18) ◽  
pp. dev192773
Author(s):  
Chloé Roffay ◽  
Chii J. Chan ◽  
Boris Guirao ◽  
Takashi Hiiragi ◽  
François Graner
Keyword(s):  
Three Dimensional ◽  
Cell Junction ◽  
Cell Geometry ◽  
Early Mouse Embryo ◽  
Validity Criteria ◽  
Early Mouse ◽  
Computational Analyses ◽  
Non Destructive

ABSTRACTRecognizing the crucial role of mechanical regulation and forces in tissue development and homeostasis has stirred a demand for in situ measurement of forces and stresses. Among emerging techniques, the use of cell geometry to infer cell junction tensions, cell pressures and tissue stress has gained popularity owing to the development of computational analyses. This approach is non-destructive and fast, and statistically validated based on comparisons with other techniques. However, its qualitative and quantitative limitations, in theory as well as in practice, should be examined with care. In this Primer, we summarize the underlying principles and assumptions behind stress inference, discuss its validity criteria and provide guidance to help beginners make the appropriate choice of its variants. We extend our discussion from two-dimensional stress inference to three dimensional, using the early mouse embryo as an example, and list a few possible extensions. We hope to make stress inference more accessible to the scientific community and trigger a broader interest in using this technique to study mechanics in development.

scholarly journals 3D convolutional neural networks-based segmentation to acquire quantitative criteria of the nucleus during mouse embryogenesis

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Yuta Tokuoka ◽  
Takahiro G. Yamada ◽  
Daisuke Mashiko ◽  
Zenki Ikeda ◽  
Noriko F. Hiroi ◽  
...  
Keyword(s):  
Time Series ◽  
Three Dimensional ◽  
Living Cells ◽  
Mouse Embryos ◽  
Model Species ◽  
3D Space ◽  
Image Processing Algorithms ◽  
Processing Algorithms ◽  
Early Mouse ◽  
Instance Segmentation

Abstract During embryogenesis, cells repeatedly divide and dynamically change their positions in three-dimensional (3D) space. A robust and accurate algorithm to acquire the 3D positions of the cells would help to reveal the mechanisms of embryogenesis. To acquire quantitative criteria of embryogenesis from time-series 3D microscopic images, image processing algorithms such as segmentation have been applied. Because the cells in embryos are considerably crowded, an algorithm to segment individual cells in detail and accurately is needed. To quantify the nuclear region of every cell from a time-series 3D fluorescence microscopic image of living cells, we developed QCANet, a convolutional neural network-based segmentation algorithm for 3D fluorescence bioimages. We demonstrated that QCANet outperformed 3D Mask R-CNN, which is currently considered as the best algorithm of instance segmentation. We showed that QCANet can be applied not only to developing mouse embryos but also to developing embryos of two other model species. Using QCANet, we were able to extract several quantitative criteria of embryogenesis from 11 early mouse embryos. We showed that the extracted criteria could be used to evaluate the differences between individual embryos. This study contributes to the development of fundamental approaches for assessing embryogenesis on the basis of extracted quantitative criteria.

scholarly journals Three-Dimensional Fluorescence In Situ Hybridization in Mouse Embryos Using Repetitive Probe Sequences

2010 ◽  
pp. 401-408 ◽  
Author(s):  
Walid E. Maalouf ◽  
Tiphaine Aguirre-Lavin ◽  
Laetitia Herzog ◽  
Isabelle Bataillon ◽  
Pascale Debey ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Three Dimensional ◽  
Mouse Embryos

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Structural organization of escherichia coli ribosomes as determined by immuno electron microscopy

1978 ◽  
Vol 36 (2) ◽  
pp. 166-167 ◽  
Author(s):  
G. Stöffler ◽  
R.W. Bald ◽  
J. Dieckhoff ◽  
H. Eckhard ◽  
R. Lührmann ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
Ribosomal Proteins ◽  
Structural Organization ◽  
Three Dimensional ◽  
Ribosomal Subunit ◽  
Spatial Arrangement ◽  
Small Subunit ◽  
Antibody Binding ◽  
Immuno Electron Microscopy

A central step towards an understanding of the structure and function of the Escherichia coli ribosome, a large multicomponent assembly, is the elucidation of the spatial arrangement of its 54 proteins and its three rRNA molecules. The structural organization of ribosomal components has been investigated by a number of experimental approaches. Specific antibodies directed against each of the 54 ribosomal proteins of Escherichia coli have been performed to examine antibody-subunit complexes by electron microscopy. The position of the bound antibody, specific for a particular protein, can be determined; it indicates the location of the corresponding protein on the ribosomal surface.The three-dimensional distribution of each of the 21 small subunit proteins on the ribosomal surface has been determined by immuno electron microscopy: the 21 proteins have been found exposed with altogether 43 antibody binding sites. Each one of 12 proteins showed antibody binding at remote positions on the subunit surface, indicating highly extended conformations of the proteins concerned within the 30S ribosomal subunit; the remaining proteins are, however, not necessarily globular in shape (Fig. 1).

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