Polymerase chain reaction

LAMP-PCR detection of ochratoxigenic Aspergillus species collected from peanut kernel

H. M. Al-Sheikh, LAMP-PCR detection of ochratoxigenic Aspergillus species collected from peanut kernel, vol. 14, pp. 634-644, 2015.

Over the last decade, ochratoxin A (OTA) has been widely described and is ubiquitous in several agricultural products. Ochratoxins represent the second-most important mycotoxin group after aflatoxins. A total of 34 samples were surveyed from 3 locations, including Mecca, Madina, and Riyadh, Saudi Arabia, during 2012. Fungal contamination frequency was determined for surface-sterilized peanut seeds, which were seeded onto malt extract agar media.

Comparison of extraction methods of total microbial DNA from freshwater

P. Li, Yang, S. F., Lv, B. B., Zhao, K., Lin, M. F., Zhou, S., Song, X., and Tang, X. M., Comparison of extraction methods of total microbial DNA from freshwater, vol. 14, pp. 730-738, 2015.

The demand for molecular analysis of aquatic microbial communities in freshwater has highlighted the need for efficient methods of DNA extraction. The centrifugation method and filtration-membrane method are 2 widely used methods for extracting DNA. The objective of this study was to compare the extraction efficiency of 3 methods, including the centrifugation method, filtration-membrane method, and modified filtration-membrane method, by evaluating the quantity and purity of DNA extracts obtained from water.

Distribution of Candida albicans in the oral cavity of children aged 3-5 years of Uygur and Han nationality and their genotype in caries-active groups

N. Wu, Lin, J., Wu, L., and Zhao, J., Distribution of Candida albicans in the oral cavity of children aged 3-5 years of Uygur and Han nationality and their genotype in caries-active groups, vol. 14, pp. 748-757, 2015.

We analyzed the distribution of Candida albicans in the oral cavity of 3-5-year-old children of Uygur and Han nationalities as well as their genotypes in caries-active groups in the Urumqi municipality. CHROMagar Candida was separately cultivated, and we identified 359 Uygur and Han children aged 3-5 years. We randomly selected 20 Han children and 20 Uygur children for this study. We chose a bacterial strain for polymerase chain reaction (PCR) 25S rDNA genotyping and random amplified polymorphic DNA (RAPD) genotyping.

Cut-and-paste-based cloning strategy for large gene site-directed mutagenesis

C. Wang, Wang, T. Y., Zhang, L. Y., Gao, X. J., Wang, X. W., and Jin, C. J., Cut-and-paste-based cloning strategy for large gene site-directed mutagenesis, vol. 14, pp. 5585-5591, 2015.

Site-directed mutagenesis is an essential technique for investigating the mechanisms of gene regulation on a molecular level, as well as for exploring post-translational modifications and functional structure at the protein level. Polymerase chain reaction combining in vitro synthesis of oligonucleotide primers allows for site-directed mutation to be performed with ease. However, site-directed mutagenesis is difficult when larger plasmids are involved.

A simplified genomic DNA extraction protocol for pre-germination genotyping in rice

Y. B. Duan, Zhao, F. L., Chen, H. D., Li, H., Ni, D. H., Wei, P. C., Sheng, W., Teng, J. T., Zhang, A. M., and Xue, J. P., A simplified genomic DNA extraction protocol for pre-germination genotyping in rice, vol. 14, pp. 6369-6375, 2015.

Genotyping is a critical step for molecular marker-assisted selection in rice. Rice genomic DNA samples for genotyping are typically isolated from living tissues such as seedlings. This requires the germination of all candidate seeds and extraction of DNA from the seedlings. Currently, an ideal individual is selected from a very large number of plants, which is time- and labor-consuming, requiring several transplantations of materials and sampling processes. In this study, we developed a simplified genomic DNA extraction protocol in rice by using amylase to treat half-seeds.

Evaluation of five protocols for DNA extraction from leaves of Malus sieversii, Vitis vinifera, and Armeniaca vulgaris

K. Aubakirova, Omasheva, M., Ryabushkina, N., Tazhibaev, T., Kampitova, G., and Galiakparov, N., Evaluation of five protocols for DNA extraction from leaves of Malus sieversii, Vitis vinifera, and Armeniaca vulgaris, vol. 13, pp. 1278-1287, 2014.

Leaves of Malus sieversii, Vitis vinifera, and Armeniaca vulgaris contain substantial amounts of secondary metabolites, which limit the high-quality DNA extraction performance. In this study, five extraction protocols were compared for their ability to produce good quality DNA from fresh and dried (with silica gel) leaves of these species.

Comparison of methods to isolate DNA from Caesalpinia ferrea

C. C. Sousa, Gomes, S. O., Lopes, A. C. A., Gomes, R. L. F., Britto, F. B., Lima, P. S. C., and Valente, S. E. S., Comparison of methods to isolate DNA from Caesalpinia ferrea, vol. 13. pp. 4486-4493, 2014.

Molecular markers are important for characterizing the genetic diversity of plants and can provide the basis for strategies to protect and conserve endangered populations. However, numerous molecular techniques are used, requiring an evaluation of fast and efficient methods to extract DNA. Since molecular studies of Caesalpinia ferrea are rare, it is important to develop and/or adapt a DNA extraction protocol that produces quality DNA samples to enable the design of strategies for the conservation of this threatened species.

Molecular detection of human papillomavirus in Brazilian women with cervical intraepithelial neoplasia in a northeast Brazilian city

J. D. C. Nunes, Vidal, F. C. B., Ferraro, C. T. L., Chein, M. B. C., Brito, L. M. O., and Monteiro, S. C. M., Molecular detection of human papillomavirus in Brazilian women with cervical intraepithelial neoplasia in a northeast Brazilian city, vol. 13, pp. 9077-9085, 2014.

We examined the prevalence of human papillomavirus (HPV) infection in Brazilian women with cervical intraepithelial neoplasia. Our goal was to identify the types of HPV and their association with risk factors. This prospective cross-sectional study included 97 samples collected from women aged 14-79 years at the public health units of gynecological care in São Luís, MA, Brazil. HPV detection was performed by nested polymerase chain reaction and sequence analysis.

Use of simple sequence repeat markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp) cultivars resistant and susceptible to red rot

U. Hameed, Pan, Y. - B., Muhammad, K., Afghan, S., and Iqbal, J., Use of simple sequence repeat markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp) cultivars resistant and susceptible to red rot, vol. 11, pp. 1195-1204, 2012.

Red rod is an economically important disease of sugarcane caused by the fungus Colletotrichum falcatum. We used a simple sequence repeat (SSR)-based marker system to identify and analyze genetic relationships of red rot resistant and susceptible sugarcane cultivars grown in Pakistan. Twenty-one highly polymorphic SSR markers were used for DNA fingerprinting and genetic diversity analysis of 20 sugarcane cultivars. These SSR markers were found to be highly robust; we identified 144 alleles, with 3-11 alleles per marker and a mean of 6.8.

Epstein-Barr virus DNA associated with gastric adenocarcinoma and adjacent non-cancerous mucosa in patients from Manaus, Brazil

P. F. de Aquino, Carvalho, P. C., Fischer, J. Sda Gama, de Souza, A. Q. L., Viana, J. S., Chalub, S. R. S., de Souza, A. D. L., and Carvalho, M. G. C., Epstein-Barr virus DNA associated with gastric adenocarcinoma and adjacent non-cancerous mucosa in patients from Manaus, Brazil, vol. 11, pp. 4442-4446, 2012.

Gastric cancer is one of most frequent causes of death in Brazil. The city of Manaus has one of the highest incidences of this disease in Brazil. The Epstein-Barr virus (EBV) is a ubiquitous herpesvirus that is classified as a group 1 carcinogen by the International Agency for Research on Cancer. We obtained biopsies from 6 control subjects and 10 patients with gastric carcinomas living in Manaus. In the patients, the samples were taken from tumors and from adjacent non-cancerous mucosa.

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