DNA amplification using PCR with abutting primers

Molecular Biology - DNA analysis of ñîmplex biological objects (wastewater, soil, archaeological and forensic samples, etc.) is currently of great interest. DNA of these objects is...     

Involvement of phytohormones in the development of interaction between wheat seedlings and endophytic <Emphasis Type="Italic">Bacillus subtilis</Emphasis> strain 11BM

Wheat (Triticum aestivum L., cv. Kazakhstanskaya 10) seedling growth activation by the endophytic 11BM strain of the bacterium Bacillus subtilis Cohn and the involvement of phytohormones in this process were studied. At the concentration used, bacteria enhanced wheat root and shoot growth as compared to control. Biotests demonstrated auxin-, cytokinin-, and gibberellin-like activities of the endophyte, but the result depended on the way of experiment performing. When wheat seeds were treated with the spores of B. subtilis 11BM strain, the concentrations of IAA and ABA increased transiently in the roots and shoots of the seedlings. The involvement of IAA oxidase in the plant response to inoculation with bacteria was shown; it was accompanied by a decrease in enzyme activity, which occurred later than auxin accumulation. It was concluded that observed changes in the hormonal status of wheat plants under the influence of the endophytic bacterial strain may be one of the mechanisms for seedling growth stimulation.     

Synthesis of circular DNA templates with T4 RNA ligase for rolling circle amplification

Molecular Biology - Currently, isothermal methods of nucleic acid amplification have been well established; in particular, rolling circle amplification is of great interest. In this approach,...     

The influence of CpG (5′-d(CpG)-3′ dinucleotides) methylation on ultrasonic DNA fragmentation

Abstract

DNA methylation is an important way of gene regulation. The variety of methods for DNA methylation analysis based on chemical modification or enzyme digestion has been proposed. However, DNA is able to undergo transformations under physical power. Here, we report that the cytosine methylation in CpG dinucleotides determines the difference in fragmentation rate of methylated and unmethylated DNA under sonication. We found that at the beginning of sonication, methylated DNAs are degraded faster than unmethylated one, and the difference in fragmentation degree can be evaluated with high reliability by quantitative polymerase chain reaction (qPCR). The optimal parameters that provide the greatest difference in amount of amplifiable DNA targets corresponding to fragmentation degree are the following: moderate amplicon size (about 150–250?bp), medium CpG sparseness (one CpG dinucleotide per ～12–14 nucleotides of the chain), and short sonication time (less than 5?min). Along with CpG, the CpA and CpT contents of amplified regions should be taken into account for proper DNA fragmentation by ultrasound as well. The obtained data could be used for elaboration of a method for comparative methylation testing, when there is no need to detect methylation of certain CpG dinucleotides. This method will be simple (can be used by any technician familiar with PCR), low cost (no need to use an expensive reagents), and fast (only brief DNA sonication and conventional qPCR are carried out).

Communicated by Ramaswamy H. Sarma     

The Effect of Salicylic Acid on Peroxidase Activity in Wheat Calli Cocultured with the Bunt Pathogen Tilletia caries

The effect of salicylic acid (SA) on peroxidase activity in wheat (Triticum aestivum L.) calli cocultured with the bunt pathogen Tilletia caries was studied. Fungal infection was shown to activate cytoplasmic peroxidase. SA suppressed total peroxidase activity but did not inhibit the peroxidase with pI 9.8. A novel chitin-specific peroxidase with pI 3.5 appeared after the SA treatment. The infection of SA-treated cells with Tilletia caries activated the isoenzymes with pI 3.5, 4.8, and 7.5 and stimulated their secretion into the culture medium. The ability of SA to control wheat peroxidase activity during pathogenesis is discussed. The important role of this control in plant defense responses to the bunt pathogen is emphasized.     

Structure of the <Emphasis Type="Italic">TADHN</Emphasis> gene for dehydrin-like protein of soft wheat and activation of its expression by ABA and 24-epibrassinolide

The structure of the cloned fragment of wheat (Triticum aestivum L.) TADHN gene encoding dehydrin-like protein was examined. A comparative analysis of nucleotide and deduced amino acid sequences revealed a high homology of this fragment with sequences of the barley dhn8 gene and wheat wcor gene family. In deduced amino acid sequence of the TADHN fragment, a 15-residue region EKKGFLEKIKEKLPG was found, which corresponded to a highly conserved K-segment of dehydrins. Wheat seedling treatment with 3.7 μM ABA and 0.4 μM 24-epibrassinolide exerted similar stimulatory effects on expression of the TADHN gene, which indicates the involvement of dehydrins in the protective action of these phytohormones in wheat plants.     

Changes in the Phytohormone Levels in Wheat Calli as Affected by Salicylic Acid and Infection with Tilletia caries,a Bunt Pathogenic Agent

The role of salicylic acid (SA) in growth regulation and the change in the levels of phytohormones (IAA, ABA, and cytokinins) were studied in the wheat calli co-cultured with bunt pathogen Tilletia caries. Calli infection with T. caries resulted in the hypertrophied callus growth and simultaneous increase in phytohormone level. The addition of SA to the nutrient media decreased the callus growth induced by the pathogen, whereas the level of investigated phytohormones was not affected. In the SA-treated infected calli, the formation of necrotic lesions was observed in the zones of contact of the fungal mycelium with callus cells that limited pathogen growth. The authors suggest that the stabilization of the hormonal balance of plant cells at pathogenesis is one of the possible mechanisms of the SA protective action in vitro and in vivo. Hence, co-culturing wheat calli and T. caries fungus appeared to be a convenient model for assessing SA protective action.     

Effect of Salicylic Acid on the Activity of Antioxidant Enzymes in Wheat under Conditions of Salination

The effect of pretreatment with 0.05 mM salicylic acid (SA) on the activity of superoxide dismutase (SOD) and peroxidase in the roots of four-day-old seedlings of wheat (Triticum aestivum L.) was studied under conditions of salination. The level of the stress-induced accumulation of active oxygen species and, therefore, activities of SOD and peroxidase in seedlings pretreated with SA were significantly lower than in untreated seedlings, which indicates that these enzymes contribute to the protective effect of SA on plants under conditions of salination.     

PCR-based evaluation of sequence specificity of DNA fragmentation by ultrasound

Ultrasonic fragmentation, which is a simple and convenient method for the mechanical degradation of DNA, is widely used in modern genome studies as one of the sample preparation steps. It has been recently found that the DNA breaks occur more often in the regions containing 5'-CG-3' dinucleotides. We studied the influence of the 5'-CG-3' dinucleotides on the efficiency of the 28S rRNA gene amplification during PCR with sonicated DNA of Mantis religiosa. It was shown that the amplification rate depends on the template length and the number of 5'-CG-3' dinucleotides. Amplification of the DNA regions with a higher 5'-CG-3' density is less efficient because of their higher sensitivity to ultrasound. The amount of the amplified DNA templates is inversely proportional to the 5'-CG-3'number.     

Effect of salicylic acid on the activity of antioxidant enzymes in wheat under conditions of salination

The effect of pretreatment with 0.05 mM salicylic acid (SA) on the activity of superoxide dismutase (SOD) and peroxidase in the roots of four-day-old seedlings of wheat (Triticum aestivum L.) was studied under conditions of salination. The level of the stress-induced accumulation of active oxygen species and, therefore, activities of SOD and peroxidase in seedlings pretreated with SA were significantly lower than in untreated seedlings, which indicates that these enzymes contribute to the protective effect of SA on plants under conditions of salination.