Gold-FISH: In Situ Hybridization of Microbial Cells for Combined Fluorescence and Scanning Electron Microscopy

2016 ◽  
pp. 545-557
Author(s):  
Hannes Schmidt ◽  
Thilo Eickhorst
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
In Situ Hybridization ◽  
Microbial Cells ◽  
Gold Fish ◽  
Scanning Electron

scholarly journals In situ hybridization by scanning electron microscopy for painting, centromeric, and YAC localization

2005 ◽  
Vol 68 (2) ◽  
pp. 115-120
Author(s):  
M. Reguzzoni ◽  
M. Protasoni ◽  
M. Maserati ◽  
B. Pressato ◽  
A. Manelli ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
In Situ Hybridization ◽  
Scanning Electron

Methanosaeta fibers in anaerobic migrating blanket reactors

2000 ◽  
Vol 41 (4-5) ◽  
pp. 35-39 ◽  
Author(s):  
L.T. Angenent ◽  
D. Zheng ◽  
S. Sung ◽  
L. Raskin
Keyword(s):  
Electron Microscopy ◽  
Fatty Acids ◽  
Scanning Electron Microscopy ◽  
In Situ Hybridization ◽  
Light Microscopy ◽  
Volatile Fatty Acids ◽  
Dense Structure ◽  
Scanning Electron ◽  
Granular Blanket

An anaerobic migrating blanket reactor (AMBR) was seeded with flocculent biomass from a digester and fed a substrate consisting of volatile fatty acids and sucrose to study granulation. After three months of operation, a mature granular blanket developed in the reactor. Moreover, fibers of approximately 1 cm long had become prevalent in the AMBR. Scanning electron microscopy (SEM) and light microscopy revealed a very dense structure consisting of bundles of filaments resembling Methanosaeta cells. Further studies with fluorescence in-situ hybridization (FISH), showed that Methanosaeta concilii was the predominant microorganism in these fibers.

Preparing plant chromosomes for scanning electron microscopy

Genome ◽  
1990 ◽  
Vol 33 (3) ◽  
pp. 333-339 ◽  
Author(s):  
John E. Dillé ◽  
Douglas C. Bittel ◽  
Kathleen Ross ◽  
J. Perry Gustafson
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
In Situ Hybridization ◽  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
Light Microscopy ◽  
Plant Chromosomes ◽  
Cellular Debris ◽  
Scanning Electron

The scanning electron microscope may be useful in the analysis of plant chromosomes treated with in situ hybridization, especially when the probes and (or) chromosomes are near or beyond the resolution of the light microscope. Usual methods of plant chromosome preparation are unsuitable for scanning electron microscope observation as a result of cellular debris, which also interferes with probe hybridization. A method is described whereby protoplasts are obtained from fixed root tips by enzymatic digestion and applied to slides in a manner that produces little or no cellular debris overlying the chromosomes. The slides were examined by scanning electron microscopy and light microscopy after C-banding and in situ hybridization with a rye nucleolus organizer region spacer probe. This technique, which allows for scanning electron microscope visualization of bands and probes not easily identified with light microscopy, should prove useful in the physical mapping of low copy number or unique DNA sequences.Key words: protoplasts, rice, wheat, rye, physical maps, in situ hybridization.

scholarly journals The unique disarticulation layer formed in the rachis of Aegilops longissima probably results from the spatial co-expression of Btr1 and Btr2

2020 ◽  
Author(s):  
Xiaoxue Zeng ◽  
Gang Chen ◽  
Lei Wang ◽  
Akemi Tagiri ◽  
Shinji Kikuchi ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
In Situ Hybridization ◽  
Brittle Rachis ◽  
Aegilops Longissima ◽  
Triticum Species ◽  
Rna In Situ Hybridization ◽  
Rachis Node ◽  
Scanning Electron

Abstract Background and Aims The brittle rachis trait is a feature of many wild grasses, particularly within the tribe Triticeae. Wild Hordeum and Triticum species form a disarticulation layer above the rachis node, resulting in the production of wedge-type dispersal units. In Aegilops longissima, only one or two of the nodes in the central portion of its rachis are brittle. In Triticeae species, the formation of a disarticulation layer above the rachis node requires the co-transcription of the two dominant and complementary genes Btr1 and Btr2. This study aims to establish whether homologues of Btr1 and/or Btr2 underlie the unusual brittle rachis phenotype observed in Ae. longissima. Methods Scanning electron microscopy was used to examine the disarticulation surfaces. Quantitative RT-PCR and RNA in situ hybridization experiments were used to identify gene expression in the immature inflorescence. Key Results Analysis based on scanning electron microscopy was able to demonstrate that the disarticulation surfaces formed in the Ae. longissima rachis are morphologically indistinguishable from those formed in the rachises of wild Hordeum and Triticum species. RNA in situ hybridization showed that in the immature Ae. longissima inflorescence, the intensity of Btr1 transcription varied from high at the rachis base to low at its apex, while that of Btr2 was limited to the nodes in the central to distal portion of the rachis. Conclusions The disarticulation pattern shown by Ae. longissima results from the limitation of Btr1 and Btr2 co-expression to nodes lying in the centre of the rachis.

scholarly journals Ultrastructural Visualization of 3D Chromatin Folding Using Serial Block-Face Scanning Electron Microscopy and In Situ Hybridization (3D-EMISH)

2020 ◽  
Author(s):  
Paweł Trzaskoma ◽  
Błażej Ruszczycki ◽  
Byoungkoo Lee ◽  
Katarzyna K. Pels ◽  
Katarzyna Krawczyk ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
In Situ Hybridization ◽  
3 Dimensional ◽  
Face Scanning ◽  
Chromatin Folding ◽  
Block Face ◽  
High Level ◽  
Scanning Electron

AbstractThe human genome is extensively folded into 3-dimensional organization, yet the detailed 3D chromatin folding structures have not been fully visualized due to the lack of robust and ultra- resolution imaging capability. Here, we report the development of a novel electron microscopy method that combines serial block-face scanning electron microscopy with in situ hybridization (3D-EMISH) to visualize 3D chromatin folding at targeted genomic regions with ultra-resolution (5×5×30 nm in xyz dimensions, respectively). We applied 3D-EMISH to human lymphoblastoid cells at a 1.7 Mb segment of the genome and visualized a large number of distinctive 3D chromatin folding structures in high ultra-resolution. We further quantitatively characterized the reconstituted chromatin folding structures by identifying sub-domains, and uncovered a high level of heterogeneity in chromatin folding ultrastructures, suggestive of extensive dynamic fluidity in 3D chromatin states.

scholarly journals Cellular Identification of a Novel Uncultured Marine Stramenopile (MAST-12 Clade) Small-Subunit rRNA Gene Sequence from a Norwegian Estuary by Use of Fluorescence In Situ Hybridization-Scanning Electron Microscopy

2007 ◽  
Vol 73 (8) ◽  
pp. 2718-2726 ◽  
Author(s):  
Karolina Kolodziej ◽  
Thorsten Stoeck
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Rrna Gene ◽  
Target Sequence ◽  
Scanning Electron

ABSTRACT Revealing the cellular identity of organisms behind environmental eukaryote rRNA gene sequences is a major objective in microbial diversity research. We sampled an estuarine oxygen-depleted microbial mat in southwestern Norway and retrieved an 18S rRNA gene signature that branches in the MAST-12 clade, an environmental marine stramenopile clade. Detailed phylogenetic analyses revealed that MAST-12 branches among the heterotrophic stramenopiles as a sister of the free-living Bicosoecida and the parasitic genus Blastocystis. Specific sequence signatures confirmed a relationship to these two groups while excluding direct assignment. We designed a specific oligonucleotide probe for the target sequence and detected the corresponding organism in incubation samples using fluorescence in situ hybridization (FISH). Using the combined FISH-scanning electron microscopy approach (T. Stoeck, W. H. Fowle, and S. S. Epstein, Appl. Environ. Microbiol. 69:6856-6863, 2003), we determined the morphotype of the target organism among the very diverse possible morphologies of the heterotrophic stramenopiles. The unpigmented cell is spherical and about 5 μm in diameter and possesses a short flagellum and a long flagellum, both emanating anteriorly. The long flagellum bears mastigonemes in a characteristic arrangement, and its length (30 μm) distinguishes the target organism from other recognized heterotrophic stramenopiles. The short flagellum is naked and often directed posteriorly. The organism possesses neither a lorica nor a stalk. The morphological characteristics that we discovered should help isolate a representative of a novel stramenopile group, possibly at a high taxonomic level, in order to study its ultrastructure, physiological capabilities, and ecological role in the environment.

High-Resolution Resistance Mapping in SEM

2018 ◽  
Author(s):  
Grigore Moldovan ◽  
Wolfgang Joachimi ◽  
Guillaume Boetsch ◽  
Jörg Jatzkowski ◽  
Frank Altman
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
High Resolution ◽  
Reference Structure ◽  
Total Resistance ◽  
Embedded Electronics ◽  
Improved Performance ◽  
Mapping Techniques ◽  
Scanning Electron

Abstract This work presents advanced resistance mapping techniques based on Scanning Electron Microscopy (SEM) with nanoprobing systems and the related embedded electronics. Focus is placed on recent advances to reduce noise and increase speed, such as integration of dedicated in situ electronics into the nanoprobing platform, as well as an important transition from current-sensitive to voltagesensitive amplification. We show that it is now possible to record resistance maps with a resistance sensitivity in the 10W range, even when the total resistance of the mapped structures is in the range of 100W. A reference structure is used to illustrate the improved performance, and a lowresistance failure case is presented as an example of analysis made possible by these developments.

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