DNA extracted Articles
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Evaluation of DNA extraction methods and dilution treatment for detection and quantification of Acanthamoeba in water and biofilm by real-time PCR
Acanthamoeba, human pathogens and natural hosts of pathogenic bacteria, may be accurately detected and quantified by real-time PCR if Acanthamoeba DNA are properly extracted and PCR inhibitors are effectively eliminated. However, the optimization of DNA extraction methods has not been reported for Acanthamoeba. This study compared the effectiveness of two DNA extraction/purification methods ...
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Evaluation of DNA extraction methods and dilution treatment for detection and quantification of
Acanthamoeba in water and biofilm by real-time PCRAcanthamoeba, human pathogens and natural hosts of pathogenic bacteria, may be accurately detected and quantified by real-time PCR if Acanthamoeba DNA are properly extracted and PCR inhibitors are effectively eliminated. However, the optimization of DNA extraction methods has not been reported for Acanthamoeba. This study compared the effectiveness of two DNA extraction/purification methods ...
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A simple, efficient method for the separation of humic substances and DNA from environmental samples
Three different gels (Sepharose 4B, Sephadex G-200, and Sephadex G-50) were evaluated as a means of removing humic contaminants from DNA extracts of environmental samples. Sepharose 4B gave superior separation of DNA from humics, and DNA purified in this way showed consistently greater amplification than DNA purified by the other ...
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Effective DNA extraction method for molecular diagnostics on wood-decay fungi
1. INTRODUCTION Strategically eliminating damage caused by fungus requires precise identification of the fungal species present (using either conventional or molecular diagnostic techniques). The first step in performing molecular diagnostics on wood-decay fungi is to obtain analyzable fungal DNA. Five commercially available kits and one CTAB method were tested and analyzed in order to ...
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PCR amplification and DNA sequence of
mcy A gene: The distribution profile of a toxigenicMicrocystis aeruginosa in the Hartbeespoort Dam, South AfricaUsing new polymerase chain reaction (PCR) primers, a once known to be under-transcribed microcystin synthetase A (mcyA) gene from the only known toxigenic cyanobacterium Microcystis aeruginosa dominating the Hartbeespoort Dam was consistently amplified from genomic DNA extracted from a set of algal and cell free water samples collected across this dam. In addition to this, five more mcy genes ...
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qPCR detection versus microscopy observations for assessing presence–absence of Didymosphenia geminata in Quebec rivers (Canada)
Microscopic versus qPCR (quantitative polymerase chain reaction) analyses were compared for the detection of Didymosphenia geminata in biofilms and water filtrates from seven Gaspésie rivers (Canada). For the qPCR approach, two DNA extraction kits (QIAamp DNA Micro Kit, Qiagen and PowerSoil DNA Isolation Kit, Mo Bio Laboratories) and two pairs of primers were considered. The pair of primers ...
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Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples
We compared and statistically evaluated the effectiveness of nine DNA extraction procedures by using frozen and dried samples of two silt loam soils and a silt loam wetland sediment with different organic matter contents. The effects of different chemical extractants (sodium dodecyl sulfate [SDS], chloroform, phenol, Chelex 100, and guanadinium isothiocyanate), different physical disruption ...
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Evaluation and optimization of dna extraction and purification procedures for soil and sediment samples
We compared and statistically evaluated the effectiveness of nine DNA extraction procedures by using frozen and dried samples of two silt loam soils and a silt loam wetland sediment with different organic matter contents. The effects of different chemical extractants (sodium dodecyl sulfate [SDS], chloroform, phenol, Chelex 100, and guanadinium isothiocyanate), different physical disruption ...
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A new immunomagnetic bead separation–surfactant extraction treatment protocol for rapid and sensitive quantitative PCR detection of Cryptosporidium parvum DNA
The Cryptosporidium oocyst is encased in a robust wall that is extremely resistant to detrimental environmental factors such as chlorine used to disinfect potable water. Therefore, extracting oocyst DNA is not a trivial undertaking. Standard procedures used to extract DNA from oocysts, such as freeze–thaw (F/T) methods and DNA purification kits, are time-consuming and expensive and are ...
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Development of a rapid screening method for the detection of pathogenic
Escherichia coli using a combination of Colilert® Quanti-Trays/2000 and PCRThe use of culture based methods for the detection of Escherichia coli (E. coli) only gives information on the occurrence of E. coli and not pathogenicity of the organisms detected. To detect the both indicator and diarrhoeagenic E. coli (DEC) a method was developed using the Colilert® Quanti-Tray/2000 system and polymerase chain reaction (PCR). A total of 619 samples were collected from springs ...
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Induction of thymine dimers by solar radiation in natural freshwater phytoplankton assemblages in Patagonia, Argentina
Natural phytoplankton assemblages from a freshwater lake in Trelew (Province of Chubut, Patagonia, Argentina) were exposed to natural solar radiation at different depths in a water basin filled with fresh water rich in humic substances. Samples were taken at regular intervals for DNA extraction and subsequent analysis of DNA damage by determining the formation of thymine dimers using an ...
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High frequency of
Helicobacter pylori DNA in drinking water in Kermanshah, Iran, during June–November 2012To gain a better understanding of transmission and selecting appropriate measures for preventing the spread of Helicobacter pylori, the aim of this study was to investigate the prevalence of H. pylori in drinking water samples in Kermanshah, Iran. Drinking water samples were collected from around Kermanshah and filtered through 0.45 μm nitrocellulose filters. The bacterial sediment was ...
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A novel genetic marker for the rapid detection of
Bacteroides fragilis in recreational water as a human-specific faecal indicatorBacteroides spp. has gained substantial interest among the suggested potential candidates for alternative faecal indicators for untreated recreational waters by the US EPA. Interest in Bacteroides as a faecal indicator is based upon the relative abundance of selected members of the Bacteroides genus in the human colon and human faeces. In this study, we developed a real-time PCR detection system ...
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Evaluation of alternative DNA extraction processes and real-time PCR for detecting Cryptosporidium parvum in drinking water
USEPA Method 1623 is the standard method in the United States for the detection of Cryptosporidium in water samples, but quantitative real-time polymerase chain reaction (qPCR) is an alternative technique that has been successfully used to detect Cryptosporidium in aqueous matrices. This study examined various modifications to a commercial nucleic acid extraction procedure in order to enhance ...
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Characterization of nitrifying bacteria communities of soils from different ecological regions of China by molecular and conventional methods
Soil nitrification rate is very different among soil types, as a result of differences in physical and chemical properties. Little is known about the composition of the nitrifying bacteria community. In this investigation, three soils (fluvo-aquic soil, permeable paddy soil and red earth) from different geo-ecological regions in China were characterized for their nitrification activities and ...
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In xenopus egg extracts, dna replication initiates preferentially at or near asymmetric at sequences
Previous observations led to the conclusion that in Xenopus eggs and during early development, DNA replication initiates at regular intervals but with no apparent sequence specificity. Conversely, here, we present evidence for site-specific DNA replication origins in Xenopus egg extracts. Using DNA, we show that DNA replication origins are activated in clusters in regions that contain closely ...
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Metagenomes obtained by ‘deep sequencing’ – what do they tell about the enhanced biological phosphorus removal communities?
Metagenomics enables studies of the genomic potential of complex microbial communities by sequencing bulk genomic DNA directly from the environment. Knowledge of the genetic potential of a community can be used to formulate and test ecological hypotheses about stability and performance. In this study deep metagenomics and fluorescence in situ hybridization (FISH) were used to study a full-scale ...
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Radioprotection by Acorus calamus: studies on in vivo DNA damage and repair
Whole-body exposure of mice to 4 Gy γ-irradiation resulted in considerable damage in the genomic DNA of peripheral blood leucocytes, bone marrow cells and splenocytes. An alkaline comet assay revealed that the nuclear DNA comet parameters of these cells, such as %DNA in tail, tail length, tail moment and Olive tail moment, had increased following whole-body γ-irradiation. Administration of Acorus ...
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Pilot scale evaluation of SANI® process for sludge minimization and greenhouse gas reduction in saline sewage treatment
This study reports on a pilot trial of the SANI® process (Sulfate reduction, Autotrophic denitrification and Nitrification Integrated process) in Hong Kong. A pilot-scale SANI plant treating saline sewage at 10 m3/day was scaled-up from a lab-scale system treating synthetic saline sewage. The plant consisted of a sulfate reduction up-flow sludge bed (SRUSB), an anoxic bioreactor (BAR1) for ...
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Rapid, specific and quantitative polymerase chain reaction (PCR) detection of pathogenic protozoa
Entamoeba histolytica for drinking water supplyIn this study, a quantitative species-specific polymerase chain reaction (PCR) method to rapidly detect E. histolytica in water is developed. First, the specificity of E. histolytica PCR detection was verified by using species-specific primers of 16S-like rRNA genes to clearly differentiate it from the closely related amoebae species E. dispar and E. moshkovskii. The sensitivity of this method ...
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