Evaluation of gel filtration resins for the removal of PCR-inhibitory substances from soils and sediments

Miller, Daniel N.

doi:10.1016/s0167-7012(00)00228-1

Cited by 96 publications

(68 citation statements)

References 16 publications

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“…The most commonly used physical disruption methods are freezing-thawing or freezing-boiling [12,43,71] and bead-mill homogenization [37,41,42,63]. When testing a "bead beating" method, Bürgmann et al [7] established that DNA yields increased with longer beating times, higher speed and reduced extraction buffer volumes but at the cost of DNA shearing.…”

Section: Cell Lysismentioning

confidence: 99%

See 1 more Smart Citation

Extraction of DNA from soil

Robe¹,

Nalin²,

Capellano³

et al. 2003

European Journal of Soil Biology

253

164

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Section: Cell Lysismentioning

confidence: 99%

“…2. Gel filtration resins including sephadex G200 [30] and G150, Sepharose 2B, 4B and 6B, Biogel P100 and P200 have been evaluated in comparative studies [26,37,41]. Sepharose resins demonstrated a better separation of DNA from humic acids.…”

Section: Nucleic Acid Extraction and Purificationmentioning

confidence: 99%

Extraction of DNA from soil

Robe¹,

Nalin²,

Capellano³

et al. 2003

European Journal of Soil Biology

253

164

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“…After precipitation with icecold isopropanol overnight at -20°C, the DNA was washed in cold 70% ethanol, dried, redissolved in 30 µl of Milli-Q water and stored at -80°C. Four replicate tubes were used per sediment type and the extracted DNA was then pooled.DNA was further purified using a Sepharose 4B column (Miller 2001). Briefly, Sepharose 4B was packed by gravity in a 2.5 ml syringe to a final volume of 2 ml.…”

mentioning

confidence: 99%

Sediment properties and bacterial community in burrows of the ghost shrimp Pestarella tyrrhena (Decapoda: Thalassinidea)

Papaspyrou¹,

Gregersen²,

Cox³

et al. 2005

Aquat. Microb. Ecol.

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Chemical properties of burrow wall sediment from burrows of the thalassinidean shrimp Pestarella (=Callianassa) tyrrhena located at Vravrona Bay (Aegean Sea, Greece) were studied and found to be very different from the sediment surface and ambient anoxic sediment. P. tyrrhena burrow walls had significantly higher amounts of silt and clay, while total organic carbon (TOC) was up to 6 times higher than in surrounding sediment. Chlorophyll a (chl a) accounted for a small fraction of TOC and showed similar values in burrow walls and surface sediment, whereas the low chl a: chl a + phaeopigment ratio indicated the presence of more fresh material in the latter. Biopolymers (carbohydrates, proteins and lipids) were 4 to 11 times higher in burrow walls than in the surrounding sediment, accounting for 47% of TOC. The low protein:carbohydrate ratio indicated that the high TOC in the burrow walls was caused by the presence of aged detritus of low nutritional quality, such as seagrass detritus. The distinct conditions along the burrow wall also affected the bacterial community and resulted in a 10-fold increase of bacterial abundance. Molecular fingerprints of the bacterial communities showed that the bacterial composition of the burrow wall was more similar to the ambient anoxic sediment and showed less seasonal change than the sediment surface. These results suggest that burrow walls have distinct properties and should not be considered merely as a simple extension of the sediment surface. KEY WORDS: Bioturbation · Organic matter · Seagrass detritus · Bacteria · PCR-DGGE · Pestarella tyrrhena Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 38: [181][182][183][184][185][186][187][188][189][190] 2005 ditions in the burrows (Kristensen 1988, Ziebis et al. 1996, Furukawa 2001. The availability of labile organic matter combined with steep chemical gradients and narrow redox zonation has a significant impact on the chemical and biological composition of the burrow environment. Bacterial abundances have been shown to be higher along burrow walls compared to either surface or ambient sediment (Aller & Aller 1986, Branch & Pringle 1987, Dworschak 2001. In addition, burrow walls show increased heterotrophic activity by both aerobic and anaerobic bacteria, resulting in increased rates of organic matter decomposition (Aller & Aller 1986, Reichardt 1988, Gribsholt et al. 2003.Thalassinidean ghost shrimps have been recognised in recent years as one of the most effective bioturbating groups of macrofaunal organisms, with significant impacts on the benthic environment (Griffis & Suchanek 1991, Reise 2002. Pestarella tyrrhena is an important bioturbator, commonly found in muddy and fine sandy intertidal and shallow subtidal coastal sediments, where it often creates dense monospecific populations. It is a selective deposit feeder that constructs deep and complex burrows, constantly digging new branches or filling up existing ones (Dworschak 1987). P. tyrrhena increases the organi...

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“…Basically, substances such as polysaccharides, phenolic and humic compounds in soil and plant must be removed (Tsai & Olson 1991). The inhibitory substances can be removed using different columns and resins such as gel filtration (also known as size exclusion) resins, agarose gel electrophoresis, template dilution (Miller 2001), and commercial kits. Several practical DNA extraction methods such as isopropanol, silica-columns, magnetic beads, lyophilisation, freeze-grind and heat treatment have been used for extraction of high-quality DNA from microorganisms such as fungi and bacteria in order to minimise the influence of the extraction in the quantification of a low copy number of target (Cullen & Hirsch 1998;Reeleder et al 2003;Ippolito et al 2004;Weller et al 2007;Garrido et al 2009;Williams et al 2009;Bilodeau et al 2012).…”

Section: Real-time Pcr Considerationsmentioning

confidence: 99%

Real-time PCR applied to study on plant pathogens: potential applications in diagnosis - a review

Mirmajlessi¹,

Loit²,

Mänd³

et al. 2015

Plant Prot. Sci.

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Mirmajlessi S.M., Loit E., Mänd M., Mansouripour S.M. (2015): Real-time PCR applied to study on plant pathogens: potential applications in diagnosis -a review. Plant Protect Sci., 51: 177-190.Quantitative real-time PCR (qPCR) technique incorporates traditional polymerase chain reaction (PCR) efficiency with the production of a specific fluorescent signal, measuring the kinetics of the reaction in the early PCR phases and providing quantification of specific targets in various environmental samples. There are an increasing number of chemistries to detect PCR products, which are widely used in plant pathology as they cluster into the amplicon sequence non-specific and sequence-specific techniques. In this review, we illustrate a general description of major chemistries and discuss some considerations for assay development as it applies for a wide range of applications in epidemiological studies. The technique has become the gold standard for early detection of pathogens and a fundamental tool in the research laboratory.

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Evaluation of gel filtration resins for the removal of PCR-inhibitory substances from soils and sediments

Cited by 96 publications

References 16 publications

Extraction of DNA from soil

Extraction of DNA from soil

Sediment properties and bacterial community in burrows of the ghost shrimp Pestarella tyrrhena (Decapoda: Thalassinidea)

Real-time PCR applied to study on plant pathogens: potential applications in diagnosis - a review

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