scholarly journals Detection of Bacteria in Environmental Samples by Direct PCR Without DNA Extraction

BioTechniques ◽  
2001 ◽  
Vol 31 (3) ◽  
pp. 598-607 ◽  
Author(s):  
Kimberly A. Fode-Vaughan ◽  
Charles F. Wimpee ◽  
Charles C. Remsen ◽  
Mary Lynne Perille Collins
Keyword(s):  
Dna Extraction ◽  
Environmental Samples ◽  
Direct Pcr

scholarly journals Direct PCR from whole blood, without DNA extraction

1990 ◽  
Vol 18 (19) ◽  
pp. 5908-5909 ◽  
Author(s):  
B. Mercier ◽  
C. Gaucher ◽  
O. Feugeas ◽  
C. Mazurier
Keyword(s):  
Dna Extraction ◽  
Whole Blood ◽  
Direct Pcr

Extracellular DNA in environmental samples: Occurrence, extraction, quantification, and impact on microbial biodiversity assessment

2021 ◽  
Author(s):  
Sakcham Bairoliya ◽  
Jonas Koh Zhi Xiang ◽  
Bin Cao
Keyword(s):  
Dna Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Environmental Samples ◽  
Environmental Dna ◽  
Extracellular Dna ◽  
Biodiversity Assessment ◽  
Microbial Biodiversity ◽  
Technical Details ◽  
The Impact

Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.

scholarly journals Development of Simple Methods of DNA Extraction from Environmental Samples for Monitoring Microbial Community Based on PCR.

2000 ◽  
Vol 36 (4) ◽  
pp. 193-204 ◽  
Author(s):  
KAZUNARI SEI ◽  
KEN-ICHIRO ASANO ◽  
NAOHIRO TATEISHI ◽  
KAZUHIRO MORI ◽  
MICHIHIKO IKE ◽  
...  
Keyword(s):  
Microbial Community ◽  
Dna Extraction ◽  
Environmental Samples ◽  
Community Based

Direct Diagnosis of Trichomonas vaginalis Infection on Archived Pap Smears Using Nested PCR

2015 ◽  
Vol 59 (1) ◽  
pp. 104-108 ◽  
Author(s):  
Hajar Ziaei Hezarjaribi ◽  
Mahbobeh Taghavi ◽  
Mahdi Fakhar ◽  
Shirzad Gholami
Keyword(s):  
Dna Extraction ◽  
Study Design ◽  
Nested Pcr ◽  
Trichomonas Vaginalis ◽  
Direct Detection ◽  
Urogenital Tract ◽  
Pap Smears ◽  
Direct Pcr ◽  
Parasitic Protozoan ◽  
Archived Samples

Objectives: Little information is available concerning PCR-based direct detection of Trichomonas infections on archived Pap (Papanicolaou)-stained smears. This study investigates DNA extraction and amplification from archived Pap smears. Trichomonas vaginalis is a parasitic protozoan that infects the urogenital tract of women. Study Design: DNA from archived Pap-stained smears was successfully amplified using the nested PCR to investigate if it could be used for accurate detection and retrospective epidemiological investigations. Results: In our study, 98 (75.4%) out of 130 specimens of T. vaginalis Pap-stained smears were found to be positive by the nested PCR. Also, direct PCR on the archived Pap smears for identifying T. vaginalis gave a specificity of 100%. Conclusion: PCR-based Pap smears appear to offer an effective method to detect Trichomonas infection in archived samples, being rapid, highly specific and convenient for sampling, particularly in retrospective investigations.

Simple ‘universal’ DNA extraction procedure compatible with direct PCR amplification

1996 ◽  
Vol 52 (4) ◽  
pp. 295-295 ◽  
Author(s):  
D. Goldenberger ◽  
I. Perschil ◽  
M. Ritzler ◽  
M. Altwegg
Keyword(s):  
Dna Extraction ◽  
Extraction Procedure ◽  
Pcr Amplification ◽  
Direct Pcr

scholarly journals Taxonomic identification of airborne pollen from complex environmental samples by DNA metabarcoding: a methodological study for optimizing protocols

2017 ◽  
Author(s):  
Kleopatra Leontidou ◽  
Cristiano Vernesi ◽  
Johannes De Groeve ◽  
Fabiana Cristofolini ◽  
Despoina Vokou ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Chloroplast Dna ◽  
Dna Extraction ◽  
Environmental Samples ◽  
Airborne Pollen ◽  
Reference Database ◽  
Taxonomic Assignment ◽  
Spore Trap ◽  
Custom Made ◽  
Dna Metabarcoding

AbstractMetabarcoding is a promising DNA-based method for identifying airborne pollen from environmental samples with advantages over microscopic methods. This method requires several preparatory steps of the samples, with the extraction protocol being of fundamental importance to obtain an optimal DNA yield. Currently, there is no consensus in sample preparation and DNA extraction, especially for gravimetric pollen samplers. Therefore, the aim of this study was to develop protocols to process environmental samples for pollen DNA extraction and further metabarcoding analysis, and to assess the efficacy of these protocols for the taxonomic assignment of airborne pollen, collected by gravimetric (Tauber trap) and volumetric samplers (Burkard spore trap). Protocols were tested across an increasing complexity of samples, from single-species pure pollen to environmental samples. A short fragment (about 150 base pair) of chloroplast DNA was amplified by universal primers for plants (trnL). After PCR amplification, amplicons were Sanger-sequenced and taxonomic assignment was accomplished by comparison to a custom-made reference database including chloroplast DNA sequences of 46 plant families, including most of the anemophilous taxa occurring in the study area (Trentino, Italy, Eastern Italian Alps). Using as a benchmark the classical morphological pollen analysis, it emerged that DNA metabarcoding is applicable efficiently across a complexity of samples, provided that sample preparation, DNA extraction and amplification protocols are specifically optimized.

scholarly journals ‘Direct PCR’ optimization yields a rapid, cost-effective, nondestructive and efficient method for obtaining DNA barcodes without DNA extraction

2014 ◽  
Vol 14 (6) ◽  
pp. 1271-1280 ◽  
Author(s):  
Wing Hing Wong ◽  
Ywee Chieh Tay ◽  
Jayanthi Puniamoorthy ◽  
Michael Balke ◽  
Peter S. Cranston ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Efficient Method ◽  
Cost Effective ◽  
Dna Barcodes ◽  
Direct Pcr ◽  
Pcr Optimization
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