• Asian Pacific Journal of Cancer Prevention
• /
• v.17 no.10
• /
• pp.4741-4745
• /
• 2016

Background and Objective: Any role of human papillomavirus (HPV) in the development of breast cancer is conjectural. The aim of this study was to investigate possible links between HPV and breast cancer in women, Sanandaj, Iran. Methods: In this case-control study, 70 formalin fixed and paraffin embedded blocks of breast malignant tumors as a case group and 70 blocks of lesions without malignancy were selected as controls. Sections about $10{\mu}m$ thick were prepared. After removing the paraffin, DNA was extracted. Samples were tested by PCR using general and high-risk specific HPV primers. Results: All 70 malignant breast tumors (cases) were invasive ductal carcinomas, and of the 70 controls, 17 (24.3%) were fibrocystic tumors and 53 (75.7%) fibroadenomas. The age range of women in the case group was 25-72 years old and in the control group It was13-66 years. Using HPV general primers two samples were positive in the case group, confirmed to be HPV-18 using high-risk specific primers. Conclusion: No statistically significant association was found between breast cancer and HPV. It is necessary to confirm this result by further investigations in other populations.

• The Plant Pathology Journal
• /
• v.18 no.1
• /
• pp.12-17
• /
• 2002

For the molecular detection of Sweet potaio feathery mottle virus (SPFMV) from diseased sweet potato plants, reverse transcription and polymerase chain reaction (RT-PCR) was performed with the use of a set of virus-specific primers to amplify an 816 bp product. The viral coat protein gene was selected for the design of the primers. No PCR product was amplified when Turnip mosaic virus, Potato vims Y or Cucumber mosaic virus were used as template in RT-PCR with the SPFMV-specific primers. The lowest concentration of template viral RNA required for detection was 10 fg. The vim was rapidly detected from total nucleic acids of leaves and roots from the virus-infected sweet potato plants as well as from the purified viral RNA by the RT-PCR. Twenty-four sweet potato samples were selected and analyzed by RT-PCR and restriction fragment length polymorphism (RFLP). RFLP analysis of the PCR products showed three restriction patterns, which resulted in some point mutations suggesting the existence of quasi-species for the vims in the infected sweet potato plants.

• BMB Reports
• /
• v.38 no.3
• /
• pp.350-353
• /
• 2005

Alanine at residue 73 (Ala-73) and aspartate at residue 9 (Asp-9) are characteristic to both Cw6 and Cw7 alleles of HLA-C gene and have been suggested as possible markers for psoriasis vulgaris (PsV). However, the results from various ethnic groups/populations are contradictory and inconclusive. In this study, an attempt has been made to examine the association between HLA-C (Ala-73 and Asp-9) and susceptibility to PsV among Saudi patients. Genomic DNA was extracted from 25 Saudi PsV patients and 75 control subjects. Polymerase chain reaction (PCR) was performed to amplify HLA-C sequences using earlier reported primers, C133P and C243PR. Sequence-specific primers were used to specifically detect nucleotide coding for Ala-73 and Asp-9 in all the subjects. The results showed significantly higher frequency of Asp-9 (84.0% versus 61.3%) in PsV patients as compared to controls (p < 0.05, 2-tailed Fisher's exact test). The frequencies of Ala-73 among PsV patients (92%) and controls (88%) did not differ significantly.

• Journal of Microbiology
• /
• v.38 no.2
• /
• pp.105-108
• /
• 2000

Oligonucleotide primers amplifying a 344 bp fragment on the integrin-like protein alpha-INT1p gene (${\alpha}$INT1) of Candida albicans were synthesized for screenign of C. albicans from clinicalsamples by the polymerase chain reaction (PCR). The PCR specifically amplified DNA from C. albicans and none from any other Candida, fungal, or human DNA in standard used here. The PCR assay showed that the primers (LH1 and LH2) were specific for 26 isolates of C. albicans from clinical smaples, whereas the positive fragment, 344 bp, was not amplified from 15 clinical isolates including 14 other medically important Candida species and an isolate of Saccharomyces cerevisiae. PCR was conducted on the urine samples of 20 patients and 4 samples were C. albicans positive. The detection limit of the PCR assay for C. albicans was shown to be approximately 10 cells/ml saline. The PCR system using 344 bp ${\alpha}$INT1 as a target is more specific and rapid than the conventional culture method, and the sensitive detection method is applicable to clinical diagnosis of C. albicans infections.

• Food Science and Preservation
• /
• v.30 no.3
• /
• pp.383-394
• /
• 2023

The ultra-fast quantitative real-time polymerase chain reaction (qPCR) assay was developed and validated to differentiate the morphologically similar ones, Oncorhynchus keta and Oncorhynchus mykiss. Species-specific primers were designed for the COI genes of mtDNA. The species-specific primers designed for O. keta and O. mykiss were selectively amplified by O. keta and O. mykiss DNA, respectively. The sensitivity of O. keta and O. mykiss primers was 1 ng/μL. Quantitative testing showed that the results met the 'Guidelines on Standard Procedures for Preparing Analysis Method such as Food' proposed by the Ministry of Food and Drug Safety. The qPCR method developed and validated in this study for identifying O. keta and O. mykiss has advantages such as speed and field applicability. Therefore, this method is expected to help control forgery and alteration of raw materials in the seafood industry.

• Journal of Microbiology
• /
• v.42 no.3
• /
• pp.216-222
• /
• 2004

In a previous paper, the ogdH gene that encodes 2-oxoglutarat dehydrogenase was isolated from Salmonella typhimurium. The catalytic N-terminal region in the enzyme was found to be very specific for the Salmonella species. Therefore, the aim of the present study was to detect S. typhimurium in food sources using primers designed for OGDH-l and OGDH-2 which were based on the salmonella-specific region of the ogdH gene. A simple polymerase chain reaction (PCR) detection method was developed to detect low numbers of S. typhimurium in a chicken meat microbial consortium. Using the ogdH-specific primers under stringent amplification conditions and for gene probe analysis, fewer than 100 colony-forming units (CFUs) were detectable when pure cultures were employed. When the PCR assay was run on S. typhimurium-contaminated meat contents, only the positive meat samples containing as few as 200 CFUs reacted to the assay. The method employed for sample processing is simple and it was determined to provide a sensitive means of detecting trace amounts of S. typhimurium-specific sequences in the presence of mixed meat microbial populations. When compared with six representative intestinal gram-negative bacterial strains in foods, including Vibrio parahaemolyticus, V. vulnificus, Enterobacter cloacae, E. coli O157:H7, Pseudomonas aeruginosa, and Proteus sp., S. typhimurium had a unique and distinct PCR product (796 bp). In conclusion, the two OGDH primers were found to be rapid and sensitive detectors of Salmonella spp for the PCR method.

• Advances in Traditional Medicine
• /
• v.7 no.1
• /
• pp.26-33
• /
• 2007

Genetic polymorphism and molecular authentication were investigated with the commercial medicinal herb, Peony (Paeonia spp.), using random amplified polymorphic DNA (RAPD) markers. To identify the polymorphism of the RAPD patterns among plant origins, 20 different random primers were applied to the genomic DNA extracted from Paeonia spp. plants such as Paeonia (P.) lactiflora, P. officinale and P. japonica. Ten primers out of 20 primers could be used to discriminate the plant species in the same genus and 72 out of 81 scored DNA fragments (88.9%) generated with these primers were polymorphic. Especially, four primers, such as OPA1, OPA3, OP9, and OPA13, were useful to discriminate the plant origins among the species of Peony. In the results of cluster analysis using RAPD data obtained from the 10 primers, Peony (Paeonia spp.) plants used in this study were grouped into the two distinctive clusters, genetically. Herb medicine, especially P. lactiflora, were easily identified, when species-specific primers were applied to the investigation for discriminating herb medicine currently traded in domestic herb market, Kyungdongmart. Consequently, RAPD analysis was useful method to discriminate plant origins and the commercial medicinal herbs, Paeonia spp..

• Journal of Microbiology and Biotechnology
• /
• v.18 no.9
• /
• pp.1492-1495
• /
• 2008

Successful control of Xanthomonas oryzae pv. oryzicola, the causal agent of bacterial leaf streak, requires a specific and reliable diagnostic tool. A pathovar-specific PCR assay was developed for the rapid and accurate detection ofthe plant pathogenic bacterium Xanthomonas oryzae pv. oryzicola in diseased plant. Based on differences in a membrane fusion protein gene of Xanthomonas oryzae pv. oryzicola and other microorganisms, which was generated from NCBI (http://www.ncbi.nlm.nih.gov/) and CMR (http://cmr.tigr.org/) BLAST searches, one pair of pathovar-specific primers, XOCMF/XOCMR, was synthesized. Primers XOCMF and XOCMR from a membrane fusion protein gene were used to amplity a 488-bp DNA fragment. The PCR product was only produced from 4 isolates of Xanthomonas oryzae pv. oryzicola among 37 isolates of other pathovars and species of Xanthomonas, Pectobacterium, Pseudomonas, Burkholderia, Escherichia coli, and Fusarium oxysporum f.sp. dianthi. The results suggested that the assay detected the pathogen more rapidly and accurately than standard isolation methods.

• Journal of Microbiology and Biotechnology
• /
• v.14 no.4
• /
• pp.737-744
• /
• 2004

A multiplex polymerase chain reaction (PCR) was developed for the simultaneous detection and differentiation among Vairimorpha spp. and Nosema spp. and identification of Vairimorpha necatrix from Lepidoptera insects. Three sets of primers were selected from different genomic sequences to specifically amplify an 831 bp amplicon within the SSU rRNA gene, specific for both Vairimorpha spp. and Nosema spp. (MSSR primer); a 542 bp amplicon within the SSU rRNA gene, specific for Vairimorpha spp. (VSSU primer); and a 476 bp amplicon within the actin gene, specific for Vairimorpha necatrix (VNAG primer). Using the primers in conjunction with multiplex PCR, it was possible to detect Vairimorpha spp. and Nosema spp. and to differentiate between them. The sensitivity of this PCR assay was approximately 10 spores per milliliter. It is proposed that the multiplex PCR is a sensitive, specific, and rapid tool that can serve as a useful differential diagnostic tool for detecting Vairimorpha spp. and Nosema spp. in Lepidoptera insect.

• Research in Plant Disease
• /
• v.21 no.3
• /
• pp.180-185
• /
• 2015

In the present work, a pair of primers specific to Tomato yellow leaf curl virus (TYLCV) was designed to allow specific amplification of DNA fragments from any TYLCV isolates using an extensive alignment of the complete genome sequences of TYLCV isolates deposited in the GenBank database. A pair of primers which allows the specific amplification of tomato ${\beta}$-tubulin gene was also analyzed as an internal PCR control. A duplex PCR method with the developed primer sets showed that TYLCV could be directly detected from the leaf crude sap of infected tomato plants. In addition, our developed duplex PCR method could determine PCR errors for TYLCV diagnosis, suggesting that this duplex PCR method with the primer sets is a good tool for specific and sensitive TYLCV diagnosis. The developed duplex PCR method was further verified from tomato samples collected from some farms in Korea, suggesting that this developed PCR method is a simple and reliable tool for rapid and large-scale TYLCV detections in tomato plants.