Isolation and Amplification of Genomic DNA from Recalcitrant Dried Berries of Black Pepper (Piper nigrum L.)—A Medicinal Spice

Dhanya, K.; Kizhakkayil, Jaleel; Syamkumar, S.; Sasikumar, B.

doi:10.1007/s12033-007-0044-y

Cited by 20 publications

(10 citation statements)

References 12 publications

(14 reference statements)

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“…We found that the addition of 0.5 M glucose to the extraction buffer improved DNA quality, avoiding contamination and browning by polyphenolics as reported by Permingeati et al (1998). Using ammonium acetate in the extraction procedure could also be of great importance (Dhanya et al 2007). Increasing the extraction buffer volume from the usual 4 ml per gram of tissue to 6 ml resulted in an improved DNA yield.…”

Section: Resultsmentioning

confidence: 99%

An Efficient DNA Extraction Method for Desert Calligonum Species

et al. 2011

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Genetic conservation programs in arid environments rely on molecular methods for diversity assessments. DNA-based molecular profiling will aid in conservation and protection of species from genetic erosion. Obtaining intact genomic DNA from Calligonum species, of sufficiently high-quality that is readily amplifiable using PCR, is challenging because of the presence of the exceptionally large amount of oxidized polyphenolic compounds, polysaccharides, and other secondary metabolites. The present method involves a modification of the available CTAB method employing higher concentrations of NaCl and CTAB, and incorporating PEG 6000 (1%) and glucose. The yield of DNA was 60-670 μg g(-1) of fresh tissue. The protocol has been tested with two species from the arid region. The DNA isolated was successfully amplified by two ITS primer pairs. PCR-RFLP analysis of the ITS1-5.8S-ITS2 region among and within Calligonum species followed by sequencing is under way.

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Section: Resultsmentioning

confidence: 99%

An Efficient DNA Extraction Method for Desert Calligonum Species

et al. 2011

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“…Oaks ( Quercus spp.) have been frequently reported to be some of the most challenging species to obtain high quality and quantity DNA from, as their leaves, shoots, and buds are particularly rich in carbohydrates, phenolic substances and secondary metabolites [ 1 , 2 , 3 ], contaminants that are difficult to remove during standard DNA isolation [ 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

“…Commercial kits are relatively ineffective in extracting DNA from mature leaves of many species of interest [ 10 , 11 , 12 , 13 , 14 , 24 , 25 , 26 , 27 , 30 , 31 ] and require time-consuming and costly pre- and/or post-processing of samples. This may include the digestion of cell walls, isolation of intact protoplasts, enzymatic break down of sugars, isolation of nuclei, mitochondria or chloroplasts, the concentration of the extract, or the separation of DNA from contaminants [ 3 , 5 , 32 , 33 , 34 , 35 ].…”

Section: Introductionmentioning

confidence: 99%

In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes

Barta

Bolander

Bilby

et al. 2017

Plants

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Mature oak (Quercus spp.) leaves, although abundantly available during the plants’ developmental cycle, are rarely exploited as viable sources of genomic DNA. These leaves are rich in metabolites difficult to remove during standard DNA purification, interfering with downstream molecular genetics applications. The current work assessed whether in situ dark adaptation, to deplete sugar reserves and inhibit secondary metabolite synthesis could compensate for the difficulties encountered when isolating DNA from mature leaves rich in secondary metabolites. We optimized a rapid, commercial kit based method to extract genomic DNA from dark- and light-adapted leaves. We demonstrated that in situ dark adaptation increases the yield and quality of genomic DNA obtained from mature oak leaves, yielding templates of sufficiently high quality for direct downstream applications, such as PCR amplification and gene identification. The quality of templates isolated from dark-adapted pin oak leaves particularly improved the amplification of larger fragments in our experiments. From DNA extracts prepared with our optimized method, we identified for the first time partial segments of the genes encoding 18S rRNA and isoprene synthase (IspS) from pin oak (Quercus palustris), whose full genome has not yet been sequenced.

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“…Potassium acetate (PA) has been used to remove proteins during the isolations of DNA and RNA [2,15,24,25], for fixation of animal tissues in biological studies, as a food preservative [13], and to treat diabetic ketoacidosis via its ability to break down into bicarbonate [27]. Moreover, PA can help neutralize the human body from an acidotic state [27].…”

Section: Introductionmentioning

confidence: 99%

Potassium Acetate Blocks Clostridium difficile Toxin A-Induced Microtubule Disassembly by Directly Inhibiting Histone Deacetylase 6, Thereby Ameliorating Inflammatory Responses in the Gut

Kim

Lee

et al. 2016

Journal of Microbiology and Biotechnology

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Clostridium difficile toxin A is known to cause deacetylation of tubulin proteins, which blocks microtubule formation and triggers barrier dysfunction in the gut. Based on our previous finding that the Clostridium difficile toxin A-dependent activation of histone deacetylase 6 (HDAC-6) is responsible for tubulin deacetylation and subsequent microtubule disassembly, we herein examined the possible effect of potassium acetate (PA; whose acetyl group prevents the binding of tubulin to HDAC-6) as a competitive/false substrate. Our results revealed that PA inhibited toxin A-induced deacetylation of tubulin and recovered toxin A-induced microtubule disassembly. In addition, PA treatment significantly decreased the production of IL-6 (a marker of inflamed tissue) in the toxin A-induced mouse enteritis model. An in vitro HDAC assay revealed that PA directly inhibited HDAC-6-mediated tubulin deacetylation, indicating that PA acted as a false substrate for HDAC-6. These results collectively indicate that PA treatment inhibits HDAC-6, thereby reducing the cytotoxicity and inflammatory responses caused by C. difficile toxin A.

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Isolation and Amplification of Genomic DNA from Recalcitrant Dried Berries of Black Pepper (Piper nigrum L.)—A Medicinal Spice

Cited by 20 publications

References 12 publications

An Efficient DNA Extraction Method for Desert Calligonum Species

An Efficient DNA Extraction Method for Desert Calligonum Species

In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes

Potassium Acetate Blocks Clostridium difficile Toxin A-Induced Microtubule Disassembly by Directly Inhibiting Histone Deacetylase 6, Thereby Ameliorating Inflammatory Responses in the Gut

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