Analysis of community structures in anaerobic processes using a quantitative real-time PCR method

2005 ◽  
Vol 52 (1-2) ◽  
pp. 85-91 ◽  
Author(s):  
Y. Yu ◽  
C. Lee ◽  
S. Hwang
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Rrna Gene ◽  
Quantitative Real Time Pcr ◽  
Community Structures ◽  
Specific Primer ◽  
Anaerobic Processes ◽  
Promising Tool ◽  
Pcr Method ◽  
Group Specific Primer

The methanogenic community structures of four different anaerobic processes were characterized using a quantitative real-time PCR with group-specific primer and probe sets targeting the 16S rRNA gene (rDNA). The group specific primer and probe sets were developed and used to detect the orders Methanosarcinales, and the families Methanosarcinaceae and Methanosaetaceae. Two separate sets targeting the domains Archaea and Bacteria were also used. Each microbial population in different anaerobic processes was determined and the relative abundance in the system was compared with each other. Dominant methanogenic populations and the community structures in the processes were varied by hydraulic retention time and acetate concentration. This indicates that the real-time PCR method with the primer and probe sets is a promising tool to analyze community structures in anaerobic processes.

scholarly journals Real-Time PCR Assay for Detection and Enumeration of Dekkera bruxellensis in Wine

2003 ◽  
Vol 69 (12) ◽  
pp. 7430-7434 ◽  
Author(s):  
Trevor G. Phister ◽  
David A. Mills
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Pcr Primers ◽  
Rrna Gene ◽  
Dekkera Bruxellensis ◽  
Pcr Assay ◽  
Specific Pcr ◽  
Spoilage Yeast ◽  
Pcr Method ◽  
26S Rrna

ABSTRACT Traditional methods to detect the spoilage yeast Dekkera bruxellensis from wine involve lengthy enrichments. To overcome this difficulty, we developed a quantitative real-time PCR method to directly detect and enumerate D. bruxellensis in wine. Specific PCR primers to D. bruxellensis were designed to the 26S rRNA gene, and nontarget yeast and bacteria common to the winery environment were not amplified. The assay was linear over a range of cell concentrations (6 log units) and could detect as little as 1 cell per ml in wine. The addition of large amounts of nontarget yeasts did not impact the efficiency of the assay. This method will be helpful to identify possible routes of D. bruxellensis infection in winery environments. Moreover, the time involved in performing the assay (3 h) should enable winemakers to more quickly make wine processing decisions in order to reduce the threat of spoilage by D. bruxellensis.

scholarly journals GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

Database ◽  
2011 ◽  
Vol 2011 ◽  
Author(s):  
Carine Gubelmann ◽  
Alexandre Gattiker ◽  
Andreas Massouras ◽  
Korneel Hens ◽  
Fabrice David ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Quantitative Real Time Pcr ◽  
Specific Primer

Collaborative Validation of an Event-Specific Quantitative Real-Time PCR Method for Genetically Modified Rice Event TT51-1 Detection

2013 ◽  
Vol 61 (25) ◽  
pp. 5953-5960 ◽  
Author(s):  
Yuhua Wu ◽  
Litao Yang ◽  
Yinglong Cao ◽  
Guiwen Song ◽  
Ping Shen ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Genetically Modified ◽  
Quantitative Real Time Pcr ◽  
Genetically Modified Rice ◽  
Pcr Method

A Quantitative Real-Time PCR Method Using an X-Linked Gene for Sex Typing in Pigs

2012 ◽  
Vol 54 (2) ◽  
pp. 493-496 ◽  
Author(s):  
Maria Ballester ◽  
Anna Castelló ◽  
Yuliaxis Ramayo-Caldas ◽  
Josep M. Folch
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Quantitative Real Time Pcr ◽  
Sex Typing ◽  
Linked Gene ◽  
Pcr Method

Quantitative Detection of Campylobacter jejuni on Fresh Chicken Carcasses by Real-Time PCR

2007 ◽  
Vol 70 (6) ◽  
pp. 1373-1378 ◽  
Author(s):  
ANNA-CLARA RÖNNER ◽  
HANS LINDMARK
Keyword(s):  
Detection Limit ◽  
Real Time ◽  
Dna Extraction ◽  
Campylobacter Jejuni ◽  
Real Time Pcr ◽  
Close Correlation ◽  
Quantitative Detection ◽  
Quantitative Real Time Pcr ◽  
Direct Plating ◽  
Pcr Method

Campylobacter jejuni infection is a significant cause of foodborne gastroenteritis worldwide. Consumption and handling of poultry products is believed to be the primary risk factor for campylobacteriosis. Risk assessments require quantitative data, and C. jejuni is enumerated usually by direct plating, which sometimes allows growth of non-Campylobacter bacteria. The objective of the present study was to develop a quantitative real-time PCR method (q-PCR) for enumerating C. jejuni in chicken rinse without a culturing step. The procedure to obtain the template for the PCR assay involved (i) filtration of 10 ml of chicken rinse, (ii) centrifugation of the sample, and (iii) total DNA extraction from the pellet obtained using a commercial DNA extraction kit. The detection limit of the method was comparable to that for plating 100 μl of chicken rinse on modified charcoal cefoperazone deoxycholate agar, and the detection limit could be further improved 10-fold by concentrating the DNA eluate by ethanol precipitation. A close correlation for spiked chicken rinse was obtained for the results of the quantitative real-time PCR method and direct plating (r = 0.99). The coefficient of correlation for the methods was 0.87 when samples from chicken carcasses on the slaughter line were analyzed, whereas a lower correlation (r = 0.76) was obtained when samples from retail carcasses were analyzed. Greater variation in the proportion of dead and/or viable but not culturable Campylobacter types in the retail samples may explain the decreased correlation between the methods. Overall, the new method is simple and fast and the results obtained are closely correlated with those for direct plating for samples containing a low proportion of dead Campylobacter cells.

scholarly journals Genotyping of Acantamoeba spp. from rhisophere in Hungary

2020 ◽  
Vol 67 (3) ◽  
pp. 171-175
Author(s):  
Erika Orosz ◽  
Katalin Posta
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Human Pathogens ◽  
Quantitative Real Time Pcr ◽  
Potential Health ◽  
Granulomatous Amoebic Encephalitis ◽  
Related Genotype ◽  
Biological Methods

The protista Acanthamoeba is a free-living amoeba existing in various environments. A number of species among protista are recognized as human pathogens, potentially causing Acanthamoeba keratitis (AK), granulomatous amoebic encephalitis (GAE), and chronic granulomatous lesions. In this study, 10 rhizosphere samples were collected from maize and alfalfa plants in experimental station at Institute of Genetics, Microbiology and Biotechnology, Szent István University. We detected Acanthamoeba based on the quantitative real-time PCR assay and sequence analysis of the 18S rRNA gene. All studied molecular biological methods are suitable for the detection of Acanthamoeba infection in humans. The quantitative real-time PCR-based methods are more sensitive, simple, and easy to perform; moreover, these are opening avenue to detect the effect of number of parasites on human disease. Acanthamoeba species were detected in five (5/10; 50%) samples. All Acanthamoeba strains belonged to T4 genotype, the main AK-related genotype worldwide. Our result confirmed Acanthamoeba strains in rhizosphere that should be considered as a potential health risk associated with human activities in the environment.

scholarly journals A quantitative real-time PCR method for absolute telomere length

BioTechniques ◽  
2008 ◽  
Vol 44 (6) ◽  
pp. 807-809 ◽  
Author(s):  
Nathan J. O'Callaghan ◽  
Varinderpal S. Dhillon ◽  
Philip Thomas ◽  
Michael Fenech
Keyword(s):  
Telomere Length ◽  
Real Time ◽  
Real Time Pcr ◽  
Quantitative Real Time Pcr ◽  
Pcr Method

scholarly journals A human fecal contamination score for ranking recreational sites using the HF183/BacR287 quantitative real-time PCR method

2018 ◽  
Vol 128 ◽  
pp. 148-156 ◽  
Author(s):  
Yiping Cao ◽  
Mano Sivaganesan ◽  
Catherine A. Kelty ◽  
Dan Wang ◽  
Alexandria B. Boehm ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Fecal Contamination ◽  
Quantitative Real Time Pcr ◽  
Pcr Method
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