scholarly journals Friends with Benefits: An Inside Look of Periodontal Microbes’ Interactions Using Fluorescence In Situ Hybridization—Scoping Review

2021 ◽  
Vol 9 (7) ◽  
pp. 1504
Author(s):  
Guilherme Melo Esteves ◽  
José António Pereira ◽  
Nuno Filipe Azevedo ◽  
Andreia Sofia Azevedo ◽  
Luzia Mendes
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Scoping Review ◽  
Large Scale ◽  
Spatial Organization ◽  
Ex Vivo ◽  
Microbial Composition ◽  
Friends With Benefits ◽  
Anaerobic Microorganisms

Fluorescence in situ hybridization (FISH) has proven to be particularly useful to describe the microbial composition and spatial organization of mixed microbial infections, as it happens in periodontitis. This scoping review aims to identify and map all the documented interactions between microbes in periodontal pockets by the FISH technique. Three electronic sources of evidence were consulted in search of suitable articles up to 7 November 2020: MEDLINE (via PubMed), Scopus (Elsevier: Amsterdam, The Netherlands), and Web of Science (Clarivate Analytics: Philadelphia, PA, USA) online databases. Studies that showed ex vivo and in situ interactions between, at least, two microorganisms were found eligible. Ten papers were included. Layered or radially ordered multiple-taxon structures are the most common form of consortium. Strict or facultative anaerobic microorganisms are mostly found in the interior and the deepest portions of the structures, while aerobic microorganisms are mostly found on the periphery. We present a model of the microbial spatial organization in sub- and supragingival biofilms, as well as how the documented interactions can shape the biofilm formation. Despite the already acquired knowledge, available evidence regarding the structural composition and interactions of microorganisms within dental biofilms is incomplete and large-scale studies are needed.

scholarly journals Development of a single-cell array for large-scale DNA fluorescence in situ hybridization

Lab on a Chip ◽  
2013 ◽  
Vol 13 (7) ◽  
pp. 1316 ◽  
Author(s):  
Yingru Liu ◽  
Brett Kirkland ◽  
James Shirley ◽  
Zhibin Wang ◽  
Peipei Zhang ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Single Cell ◽  
Large Scale ◽  
Cell Array

scholarly journals Comparative Fluorescence in Situ Hybridization Mapping of a 431-kb Arabidopsis thaliana Bacterial Artificial Chromosome Contig Reveals the Role of Chromosomal Duplications in the Expansion of the Brassica rapa Genome

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 833-838 ◽  
Author(s):  
Scott A Jackson ◽  
Zhukuan Cheng ◽  
Ming Li Wang ◽  
Howard M Goodman ◽  
Jiming Jiang
Keyword(s):  
Arabidopsis Thaliana ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Brassica Rapa ◽  
Physical Mapping ◽  
Large Scale ◽  
Repetitive Sequences ◽  
Comparative Genome ◽  
Artificial Chromosomes

Abstract Comparative genome studies are important contributors to our understanding of genome evolution. Most comparative genome studies in plants have been based on genetic mapping of homologous DNA loci in different genomes. Large-scale comparative physical mapping has been hindered by the lack of efficient and affordable techniques. We report here the adaptation of fluorescence in situ hybridization (FISH) techniques for comparative physical mapping between Arabidopsis thaliana and Brassica rapa. A set of six bacterial artificial chromosomes (BACs) representing a 431-kb contiguous region of chromosome 2 of A. thaliana was mapped on both chromosomes and DNA fibers of B. rapa. This DNA fragment has a single location in the A. thaliana genome, but hybridized to four to six B. rapa chromosomes, indicating multiple duplications in the B. rapa genome. The sizes of the fiber-FISH signals from the same BACs were not longer in B. rapa than those in A. thaliana, suggesting that this genomic region is duplicated but not expanded in the B. rapa genome. The comparative fiber-FISH mapping results support that chromosomal duplications, rather than regional expansion due to accumulation of repetitive sequences in the intergenic regions, played the major role in the evolution of the B. rapa genome.

scholarly journals Large-Scale Species-Specific Microbial Identification by Fluorescence In Situ Hybridization

2020 ◽  
Vol 118 (3) ◽  
pp. 464a
Author(s):  
Sungho Kim ◽  
Jae-Kyeong Im ◽  
Seungmin Yun ◽  
Hwasooo Koh ◽  
Donghoon Kang ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Large Scale ◽  
Microbial Identification ◽  
Species Specific

scholarly journals Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation

2021 ◽  
Vol 22 (13) ◽  
pp. 7124
Author(s):  
Guanqing Liu ◽  
Tao Zhang
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Large Scale ◽  
Three Dimensional ◽  
Single Copy ◽  
Probe Design ◽  
Design Tools ◽  
Hybridization Probe ◽  
Research Areas

Oligonucleotides fluorescence in situ hybridization (Oligo-FISH) is an emerging technology and is an important tool in research areas such as detection of chromosome variation, identification of allopolyploid, and deciphering of three-dimensional (3D) genome structures. Based on the demand for highly efficient oligo probes for oligo-FISH experiments, increasing numbers of tools have been developed for probe design in recent years. Obsolete oligonucleotide design tools have been adapted for oligo-FISH probe design because of their similar considerations. With the development of DNA sequencing and large-scale synthesis, novel tools have been designed to increase the specificity of designed oligo probes and enable genome-scale oligo probe design, which has greatly improved the application of single copy oligo-FISH. Despite this, few studies have introduced the development of the oligo-FISH probe design tools and their application in FISH experiments systematically. Besides, a comprehensive comparison and evaluation is lacking for the available tools. In this review, we provide an overview of the oligo-FISH probe design process, summarize the development and application of the available tools, evaluate several state-of-art tools, and eventually provide guidance for single copy oligo-FISH probe design.

Large-scale isolation of human 1p36-specific P1 clones and their use for fluorescence in situ hybridization

1994 ◽  
Vol 11 (5-6) ◽  
pp. 140-147 ◽  
Author(s):  
Christoph Lengauer ◽  
Traudl Henn ◽  
Patrick Onyango ◽  
Fiona Francis ◽  
Hans Lehrach ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Large Scale
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