scholarly journals A sequence from Drosophila melanogaster 18S rRNA bearing the conserved hypermodified nucleoside amψ: analysis by reverse transcription and high-performance liquid chromatography

1981 ◽  
Vol 9 (7) ◽  
pp. 1723-1742 ◽  
Author(s):  
Douglas C. Youvan ◽  
John E. Hearst
Keyword(s):  
High Performance Liquid Chromatography ◽  
Drosophila Melanogaster ◽  
Liquid Chromatography ◽  
Reverse Transcription ◽  
High Performance ◽  
18S Rrna

scholarly journals Development of a Denaturing High-Performance Liquid Chromatography Method for Detection of Protist Parasites of Metazoans

2008 ◽  
Vol 74 (14) ◽  
pp. 4336-4345 ◽  
Author(s):  
Christofer Troedsson ◽  
Richard F. Lee ◽  
Vivica Stokes ◽  
Tina L. Walters ◽  
Paolo Simonelli ◽  
...  
Keyword(s):  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
High Performance ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Chromatography Method ◽  
Factors Affecting ◽  
Triethylammonium Acetate

ABSTRACT Increasingly, diseases of marine organisms are recognized as significant biotic factors affecting ecosystem health. However, the responsible disease agents are often unknown and the discovery and description of novel parasites most often rely on morphological descriptions made by highly trained specialists. Here, we describe a new approach for parasite discovery, utilizing denaturing high-performance liquid chromatography (DHPLC) reverse-phase ion-paring technology. Systematic investigations of major DHPLC variables, including temperature, gradient conditions, and target amplicon characteristics were conducted to develop a mechanistic understanding of DNA fragment separation by DHPLC. As a model system, 18S rRNA genes from the blue crab (Callinectes sapidus) and a parasitic dinoflagellate Hematodinium sp. were used. Binding of 18S rRNA gene PCR amplicons to the DNA separation column in the presence of triethylammonium acetate (TEAA) was inversely correlated with temperature and could be predicted based on the estimated DNA helicity of the PCR amplicon. Amplicons of up to 498 bp were resolved as single chromatographic peaks if they had high (>95%) DNA helicity. Amplicons that differed by as few as 2 bp could be resolved. Separation of 18S rRNA gene PCR amplicons was optimized by simultaneous manipulation of both temperature and solvent gradients. The optimal conditions included targeting regions of high DNA helicity (>95%), temperatures in the range of 57 to 63°C, and a linear acetonitrile gradient from 13.75 to 17.5% acetonitrile in 0.1 M TEAA (55 to 70% buffer B) over a 9-min period. Under these conditions, amplicons from a variety of parasites and their hosts can be separated and detected by DHPLC.

scholarly journals Detection and Discovery of Crustacean Parasites in Blue Crabs (Callinectes sapidus) by Using 18S rRNA Gene-Targeted Denaturing High-Performance Liquid Chromatography

2008 ◽  
Vol 74 (14) ◽  
pp. 4346-4353 ◽  
Author(s):  
Christofer Troedsson ◽  
Richard F. Lee ◽  
Tina Walters ◽  
Vivica Stokes ◽  
Karrie Brinkley ◽  
...  
Keyword(s):  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
High Performance ◽  
18S Rrna ◽  
Callinectes Sapidus ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Sequence Information ◽  
Blue Crabs ◽  
Crustacean Parasites

ABSTRACT Recently, we described a novel denaturing high-performance liquid chromatography (DHPLC) approach useful for initial detection and identification of crustacean parasites. Because this approach utilizes general primers targeted to conserved regions of the 18S rRNA gene, a priori genetic sequence information on eukaryotic parasites is not required. This distinction provides a significant advantage over specifically targeted PCR assays that do not allow for the detection of unknown or unsuspected parasites. However, initial field evaluations of the DHPLC assay suggested that because of PCR-biased amplification of dominant host genes it was not possible to detect relatively rare parasite genes in infected crab tissue. Here, we describe the use of a peptide nucleic acid (PNA) PCR hybridization blocking probe in association with DHPLC (PNA-PCR DHPLC) to overcome inherent PCR bias associated with amplification of rare target genes by use of generic primers. This approach was utilized to detect infection of blue crabs (Callinectes sapidus) by the parasitic dinoflagellate Hematodinium sp. Evaluation of 76 crabs caught in Wassaw Sound, GA, indicated a 97% correspondence between detection of the parasite by use of a specific PCR diagnostic assay and that by use of PNA-PCR DHPLC. During these studies, we discovered one crab with an association with a previously undescribed protist symbiont. Phylogenetic analysis of the amplified symbiont 18S rRNA gene indicated that it is most closely related to the free-living kinetoplastid parasite Procryptobia sorokini. To our knowledge, this is the first report of this parasite group in a decapod crab and of this organism exhibiting a presumably parasitic life history.

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