PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 11442808

A microwave-based method for nucleic acid isolation from environmental samples.

M Orsini·V Romano-Spica
View original source ↗Export metadata ↓

Abstract

AIMS: A simple and rapid method was described for DNA isolation directly from activated sludge or other environmental sources, including soil and sediments. METHODS AND RESULTS: The present method is based on microwave thermal shock and provides DNA suitable for further analysis. It is also effective for RNA extraction. CONCLUSION: The protocol is effective, easy, fast and does not require the use of expensive equipment or reagents. SIGNIFICANCE AND IMPACT OF THE STUDY: The described method can be applied to difficult substrates in environmental microbiology studies.

Explore related subjects

DNA, BacterialDNA, FungalEnvironmental MicrobiologyGenes, rRNAGeologic SedimentsMicrowavesRNA, BacterialRNA, Ribosomal, 16SSewageSoil MicrobiologyJournal Article

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

M Orsini, V Romano-Spica. 2001. A microwave-based method for nucleic acid isolation from environmental samples.. https://doi.org/10.1046/j.1472-765x.2001.00938.x

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2026

Embryophyte-wide detection of natural Agrobacterium-mediated horizontal gene transfer reveals an ancient role for mini T-DNAs.

Agrobacterium transfers DNA into plant cells, leading to tumors, hairy roots (HR), and natural genetically modified organisms (nGMOs). Transferred DNAs (T-DNAs) from agrobacteria and T-DNA-derived cellular T-DNAs (cT-DNAs) from nGMOs vary considerably and may carry up to 15 different genes. Among these, opine synthase (ops) genes encode the synthesis of opines used as nutrients by the agrobacteria. Earlier studies predicted large numbers of naturally transformed plant species, but only few have been identified and studied so far. We therefore developed a general method to detect cT-DNAs in all publicly available whole genome sequences (WGS) and Sequence Read Archive (SRA) data from land plants. To avoid false positives, we only retained DNA sequences coding for T-DNA proteins. A total of 2614 nGMO species were identified, most are eudicots. However, cT-DNAs were also found in 82 mosses and 75 ferns, showing that Agrobacterium can also generate natural transformants among the early land plants. Analysis of 149 cT-DNA maps revealed different types of T-DNAs. Most notably, these included small T-DNAs (mini T-DNAs) with a single opine synthase gene. Mini T-DNAs are not expected to induce tumors or HRs. The predominance of mini cT-DNAs in mosses and ferns, and the presence of more complex cT-DNAs in spermatophytes, indicate that mini T-DNAs represent the earliest types of T-DNA. Our study also detected unusual T-DNA integration patterns, with multiple copies spread out over several hundreds of kilobases.

DNA, Bacterial↗
PubMed2003

Ligation mediated PCR performed at low denaturation temperatures--PCR melting profiles.

We show that using low denaturation temperatures (80-88 degrees C) during ligation mediated PCR (LM PCR) of bacterial DNA leads to the amplification of limited sets of the less stable DNA fragments. A set of electrophoretic patterns of such fragments obtained at different denaturation temperatures forms the PCR melting profile (PCR MP). A single pattern obtained for a given temperature and a set of patterns arising after application of several denaturation temperatures (PCR MP) are very specific for the given bacterial genome and may be used for strain characterisation and differentiation. The method may also be used for amplification and isolation of the less stable DNA fragments in a genome.

DNA, Bacterial↗
PubMed2003

Escherichia coli and enterococci at beaches in the Grand Traverse Bay, Lake Michigan: sources, characteristics, and environmental pathways.

This study quantified Escherichia coli (EC) and enterococci (ENT) in beach waters and dominant source materials, correlated these with ambient conditions, and determined selected EC genotypes and ENT phenotypes. Bathing-water ENT criteria were exceeded more frequently than EC criteria, providing conflicting interpretations of water quality. Dominant sources of EC and ENT were bird feces (10(8)/d/bird), storm drains (10(7)/d), and river water (10(11)/d); beach sands, shallow groundwater and detritus were additional sources. Beach-water EC genotypes and ENT phenotypes formed clusters with those from all source types, reflecting diffuse inputs. Some ENT isolates had phenotypes similar to those of human pathogens and/or exhibited high-level resistance to human-use antibiotics. EC and ENT concentrations were influenced by collection time and wind direction. There was a 48-72-h lag between rainfall and elevated EC concentrations at three southern shoreline beaches, but no such lag at western and eastern shoreline beaches, reflecting the influence of beach orientation with respect to cyclic (3-5 d) summer weather patterns. In addition to local contamination sources and processes, conceptual or predictive models of Great Lakes beach water quality should consider regional weather patterns, lake hydrodynamics, and the influence of monitoring method variables (time of day, frequency).

DNA, Bacterial↗