Corrigendum: Identification and application of AFLP-derived genetic markers for quantitative PCR-based tracking of Bacillus and Paenibacillus spp. released in soil

2010 ◽  
Vol 56 (1) ◽  
pp. 87-87
Author(s):  
Miguel A. Providenti ◽  
Melissa Begin ◽  
Samielle Hynes ◽  
Christine Lamarche ◽  
David Chitty ◽  
...  
Keyword(s):  
Quantitative Pcr ◽  
Genetic Markers

scholarly journals Quantitative PCR for Genetic Markers of Human Fecal Pollution

2009 ◽  
Vol 75 (17) ◽  
pp. 5507-5513 ◽  
Author(s):  
Orin C. Shanks ◽  
Catherine A. Kelty ◽  
Mano Sivaganesan ◽  
Manju Varma ◽  
Richard A. Haugland
Keyword(s):  
Quantitative Pcr ◽  
Genetic Markers ◽  
Quantitative Methods ◽  
Animal Species ◽  
Fecal Pollution ◽  
Rrna Gene ◽  
Target Dna ◽  
Pcr Assays ◽  
Wastewater Samples ◽  
Human Specific

ABSTRACT Assessment of health risk and fecal bacterial loads associated with human fecal pollution requires reliable host-specific analytical methods and a rapid quantification approach. We report the development of quantitative PCR assays for quantification of two recently described human-specific genetic markers targeting Bacteroidales-like cell surface-associated genes. Each assay exhibited a range of quantification from 10 to 1 � 106 copies of target DNA. For each assay, internal amplification controls were developed to detect the presence or absence of amplification inhibitors. The assays predominantly detected human fecal specimens and exhibited specificity levels greater than 97% when tested against 265 fecal DNA extracts from 22 different animal species. The abundance of each human-specific genetic marker in primary effluent wastewater samples collected from 20 geographically distinct locations was measured and compared to quantities estimated by real-time PCR assays specific for rRNA gene sequences from total Bacteroidales and enterococcal fecal microorganisms. Assay performances combined with the prevalence of DNA targets in sewage samples provide experimental evidence supporting the potential application of these quantitative methods for monitoring fecal pollution in ambient environmental waters.

Factors affecting the presence of human-associated and fecal indicator real-time quantitative PCR genetic markers in urban-impacted recreational beaches

2014 ◽  
Vol 64 ◽  
pp. 196-208 ◽  
Author(s):  
Marirosa Molina ◽  
Shayla Hunter ◽  
Mike Cyterski ◽  
Lindsay A. Peed ◽  
Catherine A. Kelty ◽  
...  
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Genetic Markers ◽  
Fecal Indicator ◽  
Factors Affecting ◽  
Real Time Quantitative Pcr ◽  
Recreational Beaches

scholarly journals Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution

2007 ◽  
Vol 74 (3) ◽  
pp. 745-752 ◽  
Author(s):  
Orin C. Shanks ◽  
Emina Atikovic ◽  
A. Denene Blackwood ◽  
Jingrang Lu ◽  
Rachel T. Noble ◽  
...  
Keyword(s):  
Genetic Marker ◽  
Quantitative Pcr ◽  
Genetic Markers ◽  
Animal Species ◽  
Fecal Pollution ◽  
Rrna Gene ◽  
Broad Distribution ◽  
Assay Performance ◽  
Target Dna ◽  
Bovine Feces

ABSTRACTAccurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described bovine feces-specific genetic markers and a method for the enumeration of these markers using a Markov chain Monte Carlo approach. Both assays exhibited a range of quantification from 25 to 2 × 106copies of target DNA, with a coefficient of variation of <2.1%. One of these assays can be multiplexed with an internal amplification control to simultaneously detect the bovine-specific genetic target and presence of amplification inhibitors. The assays detected only cattle fecal specimens when tested against 204 fecal DNA extracts from 16 different animal species and also demonstrated a broad distribution among individual bovine samples (98 to 100%) collected from five geographically distinct locations. The abundance of each bovine-specific genetic marker was measured in 48 individual samples and compared to quantitative PCR-enumerated quantities of rRNA gene sequences representing totalBacteroidetes,Bacteroides thetaiotaomicron, and enterococci in the same specimens. Acceptable assay performance combined with the prevalence of DNA targets across different cattle populations provides experimental evidence that these quantitative assays will be useful in monitoring bovine fecal pollution in ambient waters.

Validation and application of quantitative PCR assays using host-specific Bacteroidales genetic markers for swine fecal pollution tracking

2017 ◽  
Vol 231 ◽  
pp. 1569-1577 ◽  
Author(s):  
Lihua Fan ◽  
Jiangbing Shuai ◽  
Ruoxue Zeng ◽  
Hongfei Mo ◽  
Suhua Wang ◽  
...  
Keyword(s):  
Quantitative Pcr ◽  
Genetic Markers ◽  
Fecal Pollution ◽  
Pcr Assays

Identification and application of AFLP-derived genetic markers for quantitative PCR-based tracking of Bacillus and Paenibacillus spp. released in soil

2009 ◽  
Vol 55 (10) ◽  
pp. 1166-1175 ◽  
Author(s):  
Miguel A. Providenti ◽  
Melissa Begin ◽  
Samielle Hynes ◽  
Christine Lamarche ◽  
David Chitty ◽  
...  
Keyword(s):  
Detection Limit ◽  
Quantitative Pcr ◽  
Genetic Markers ◽  
Paenibacillus Polymyxa ◽  
Soil Core ◽  
Environmental Persistence ◽  
Natural Systems ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Different Strains

In this study, we show that noncoding sequences from amplified fragment length polymorphisms (AFLPs) can provide robust and sensitive genetic markers suitable for PCR-based discrimination of closely related strains of Bacillus and Paenibacillus , and quantitative PCR (qPCR)-based tracking of the strains in complex natural systems like soil. Quantitative PCR was accurate in the ~1 × 109 to ~1 × 104 colony forming units (CFU)/g soil range. The detection limit was improved to ~1 × 102 CFU/g when amplicons were analyzed by gel electrophoresis. Studies with laboratory-contained intact soil-core microcosms indicated that environmental persistence trends vary among different strains. For example, Bacillus circulans ATCC 9500, Bacillus amyloliquefaciens DSL 13563-0, Bacillus licheniformis ATCC 12713, Paenibacillus polymyxa NRRL B-4317, and 3 Bacillus subtilis strains (ATCC 6051A, ATCC 55405, and NRRL B-941) died down to below the 1 × 102 CFU/g detection limit by days 28–105. In contrast, over a 105-day period, B. licheniformis ATCC 55406, Bacillus megaterium NRRL B-14308, and P. polymyxa strains ATCC 55407 and DSL 13540-4 died down but persisted at levels just above the detection limit, whereas Bacillus thuringiensis ATCC 13367 experienced a less than 10-fold decrease in cell numbers.

Evaluation of Faecalibacterium 16S rDNA genetic markers for accurate identification of swine faecal waste by quantitative PCR

2016 ◽  
Vol 181 ◽  
pp. 193-200 ◽  
Author(s):  
Chuanren Duan ◽  
Yamin Cui ◽  
Yi Zhao ◽  
Jun Zhai ◽  
Baoyun Zhang ◽  
...  
Keyword(s):  
16S Rdna ◽  
Quantitative Pcr ◽  
Genetic Markers ◽  
Accurate Identification

530: Termining Risk for Prostate Cancer at Prostate Biopsy using Genetic Markers

2005 ◽  
Vol 173 (4S) ◽  
pp. 144-145
Author(s):  
Robert K. Nam ◽  
William Zhang ◽  
John Trachtenberg ◽  
Michael A.S. Jewett ◽  
Steven Narod
Keyword(s):  
Prostate Cancer ◽  
Genetic Markers ◽  
Prostate Biopsy

Memory Processes, Aging, Cognitive Decline, and Neurodegenerative Diseases

2006 ◽  
Vol 11 (4) ◽  
pp. 304-311 ◽  
Author(s):  
Lars-Göran Nilsson
Keyword(s):  
Cognitive Impairment ◽  
Cognitive Decline ◽  
Neurodegenerative Disease ◽  
Genetic Markers ◽  
Brain Activity ◽  
Memory Performance ◽  
Modeling And Simulations ◽  
Aging And Health ◽  
Explained Variance ◽  
Different Levels

This paper presents four domains of markers that have been found to predict later cognitive impairment and neurodegenerative disease. These four domains are (1) data patterns of memory performance, (2) cardiovascular factors, (3) genetic markers, and (4) brain activity. The critical features of each domain are illustrated with data from the longitudinal Betula Study on memory, aging, and health ( Nilsson et al., 1997 ; Nilsson et al., 2004 ). Up to now, early signs regarding these domains have been examined one by one and it has been found that they are associated with later cognitive impairment and neurodegenerative disease. However, it was also found that each marker accounts for only a very small part of the total variance, implying that single markers should not be used as predictors for cognitive decline or neurodegenerative disease. It is discussed whether modeling and simulations should be used as tools to combine markers at different levels to increase the amount of explained variance.

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