scholarly journals Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations

2013 ◽  
Vol 29 (13) ◽  
pp. i189-i198 ◽  
Author(s):  
Salim Akhter Chowdhury ◽  
Stanley E. Shackney ◽  
Kerstin Heselmeyer-Haddad ◽  
Thomas Ried ◽  
Alejandro A. Schäffer ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
In Situ Hybridization ◽  
Tumor Cell ◽  
Fluorescence In Situ Hybridization ◽  
Cell Populations ◽  
Hybridization Data

Combination of Cytology, Fluorescence In Situ Hybridization for Aneuploidy, and Reverse-Transcriptase Polymerase Chain Reaction for Human Mammaglobin/Mammaglobin B Expression Improves Diagnosis of Malignant Effusions

2004 ◽  
Vol 22 (3) ◽  
pp. 474-483 ◽  
Author(s):  
Michael Fiegl ◽  
Margot Haun ◽  
Anita Massoner ◽  
Jens Krugmann ◽  
Elisabeth Müller-Holzner ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
In Situ Hybridization ◽  
Tumor Cell ◽  
Fluorescence In Situ Hybridization ◽  
Cell Detection ◽  
Malignant Cells ◽  
Chain Reaction ◽  
Tumor Cell Detection ◽  
Polymerase Chain

Purpose The identification of malignant cells in effusions by conventional cytology is hampered by its limited sensitivity. The aim of this study was to improve tumor cell detection in effusions by molecular approaches. Materials and Methods A total of 157 effusions from patients with tumors and 72 effusions from patients without a history or evidence of malignancy were included in this study. All effusion specimens were evaluated in parallel by cytology, fluorescence in situ hybridization (FISH) for aneuploidy, and reverse-transcriptase polymerase chain reaction (RT-PCR) for expression of human mammaglobin (hMAM) and mammaglobin B (hMAM-B). Results In effusions from patients with tumors, the sensitivities of tumor cell detection by cytology, FISH, and hMAM and hMAM-B detection were 46.2%, 53.3%, 36.4%, and 57.7%, respectively. The corresponding specificities were 94.4%, 97.0%, 87.1%, and 88.6%. Notably, a high percentage of effusions containing malignant cells were in fact transudates, indicating the necessity for molecular diagnostic work-up of transudates collected from patients with tumors. Dependent on the tumor type, the use of appropriate marker combinations improved tumor cell detection in effusions significantly. By combining all four diagnostic tests, a positive test result indicating the presence of malignancy was achieved in 81.1%, with a fairly good specificity of 70.1%. Conclusion Molecular techniques are definitely useful to detect malignancy in cytologically negative effusions. Tumor cell detection in effusions can be significantly improved by FISH and PCR techniques applying appropriate molecular markers. This finding should help to improve tumor staging, prognostic assessment, and treatment monitoring.

scholarly journals Natural Communities of Novel Archaea and Bacteria with a String-of-Pearls-Like Morphology: Molecular Analysis of the Bacterial Partners

2002 ◽  
Vol 68 (2) ◽  
pp. 933-937 ◽  
Author(s):  
Christine Moissl ◽  
Christian Rudolph ◽  
Robert Huber
Keyword(s):  
Phylogenetic Analysis ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Major Constituent ◽  
Filamentous Bacteria ◽  
In Series ◽  
Taxonomic Affiliation ◽  
String Of Pearls ◽  
Natural Communities

ABSTRACT A recently discovered bacterial/archaeal association, growing in a string-of-pearls-like structure, thrives in the cold (∼10�C) sulfidic marsh water of the Sippenauer Moor near Regensburg, Bavaria, Germany. It forms characteristic, macroscopically visible globules, the pearls, containing microcolonies of novel euryarchaeota, which are surrounded by mainly filamentous bacteria (C. Rudolph, G. Wanner, and R. Huber, Appl. Environ. Microbiol. 67:2336-2344, 2001). Single pearls in series are connected by white threads. Here we report the first detailed molecular investigations of the taxonomic affiliation of the bacteria contributing to the strings of pearls. Phylogenetic analysis showed the dominance of a single phylotype (clone sipK4) within single pearls most closely related to Thiothrix unzii. The presence of Thiothrix sipK4 as a major constituent of single pearls and of the pearl-connecting white threads was verified by fluorescence in situ hybridization.

scholarly journals Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data

2018 ◽  
Vol 36 (12) ◽  
pp. 1183-1190 ◽  
Author(s):  
Qian Zhu ◽  
Sheel Shah ◽  
Ruben Dries ◽  
Long Cai ◽  
Guo-Cheng Yuan
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Hybridization Data

scholarly journals α-Proteobacterial Symbionts of Marine Bryozoans in the Genus Watersipora

2006 ◽  
Vol 73 (1) ◽  
pp. 303-311 ◽  
Author(s):  
Christine M. Anderson ◽  
Margo G. Haygood
Keyword(s):  
Phylogenetic Analysis ◽  
In Situ Hybridization ◽  
16S Rrna ◽  
Fluorescence In Situ Hybridization ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Symbionts ◽  
California Coast ◽  
Specific Fluorescence

ABSTRACT Bacterial symbionts that resembled mollicutes were discovered in the marine bryozoan Watersipora arcuata in the 1980s. In this study, we used PCR and sequencing of 16S rRNA genes, specific fluorescence in situ hybridization, and phylogenetic analysis to determine that the bacterial symbionts of “W. subtorquata” and “W. arcuata” from several locations along the California coast are actually closely related α-Proteobacteria, not mollicutes. We propose the names “Candidatus Endowatersipora palomitas” and “Candidatus Endowatersipora rubus” for the symbionts of “W. subtorquata” and “W. arcuata,” respectively.

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