• Korean Journal of Medicinal Crop Science
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• v.23 no.6
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• pp.439-445
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• 2015

Background : Correct identification of Panax species is important to ensure food quality, safety, authenticity and health for consumers. This paper describes a high resolution melting (HRM) analysis based method using internal transcribed spacer (ITS) and 5.8S ribosomal DNA barcoding regions as target (Bar-HRM) to obtain barcoding information for the major Panax species and to identify the origin of ginseng plant. Methods and Results : A PCR-based approach, Bar-HRM was developed to discriminate among Panax species. In this study, the ITS1, ITS2, and 5.8S rDNA genes were targeted for testing, since these have been identified as suitable genes for use in the identification of Panax species. The HRM analysis generated cluster patterns that were specific and sensitive enough to detect small sequence differences among the tested Panax species. Conclusion : The results of this study show that the HRM curve analysis of the ITS regions and 5.8S rDNA sequences is a simple, quick, and reproducible method. It can simultaneously identify three Panax species and screen for variants. Thus, ITS1HRM and 5.8SHRM primer sets can be used to distinguish among Panax species.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.5
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• pp.2063-2068
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• 2012

Aim: Liquid-based cytology is the most often used method for cervical cancer screening, but it is relatively insensitive and frequently gives equivocal results. Used as a complementary procedure, the high-risk human papillomavirus (HPV) DNA test is highly sensitive but not very specific. The human telomerase RNA gene (TERC) is the most often amplified oncogene that is observed in cervical precancerous lesions. We assessed genomic amplification of TERC in liquid-based cytological specimens to explore the optimal strategy of using this for cervical cancer screening. Methods: Six hundred and seventy-one residual cytological specimens were obtained from outpatients aged 25 to 64 years. The specimens were evaluated by the Digene Hybrid Capture 2 (HC2) HPV DNA test and fluorescence in situ hybridization (FISH) with a chromosome probe to TERC (3q26). Colposcopic examination and histological evaluation were performed where indicated. Results: The TERC positive rate was higher in the CIN2+ (CIN2, CIN3 and SCC) group than in the normal and CIN 1 groups (90.0% vs. 10.4%, p < 0.01). In comparison with the HC2 HPV DNA test, the TERC amplification test had lower sensitivity but higher specificity (90.0% vs. 100.0%, 89.6% vs. 44.0%, respectively). TERC amplification test used in conjunction with the HC2 HPV DNA test showed a combination of 90.0% sensitivity and 92.2% specificity. Conclusion: The TERC amplification test can be used to diagnose cervical precancerous lesions. TERC and HPV DNA co-testing shows an optimal combination of sensitivity and specificity for cervical cancer screening.

• Mycobiology
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• v.39 no.2
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• pp.140-142
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• 2011

Soft rot in apple caused by Rhizopus oryzae was found for the first time in Korea. A detailed description of the specimen is given along with its internal transcribed spacer rDNA sequence. The fungus was identified as Rhizopus oryzae based on the mycological characteristics, molecular data, and pathogenicity testing.

• Journal of Genetic Medicine
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• v.4 no.2
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• pp.115-121
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• 2007

Hereditary motor and sensory neuropathy (HMSN; Charcot-Marie-Tooth disease, CMT) was first described by Charcot and Marie in France and, independently, by Tooth in England in 1886. HMSN is the most common form of inherited motor and sensory neuropathy, and is a genetically heterogeneous disorder of the peripheral nervous system. Using positional cloning methods, the chromosomal localization (locus) of more than 40 inherited peripheral neuropathies was found in the last 15 years. However, these genetic analyses also show that many entities do not show linkage to the known loci. This issue deals with a clinical survey of inherited peripheral neuropathies regarding diagnostic approaches based on the molecular findings.

• Journal of Life Science
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• v.11 no.1
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• pp.65-67
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• 2001

In order to develop a rapid and simple method for testing the purity of radish hybrid seeds using a procedure based on the PCR(Polymerase chain reaction), eighty random primers were screened with the genomic DNA extracted from five day old seedlings of inbred parent lines and their F1 hybrids. Two primers, HRM-02 (5'-GAGACCAGAC-3') and HRM-19(5'-TGAGGCGTGT-3'), generate reproducible unique PCR patterns which can identify each parent lines as well as their hybrids. In actual test of randomly selected hybrid seeds using the two marker primers, the purity tested by one primer was exactly same as that of other primer. It suggests that one marker primer selected in this experiment is enough for the purity test of radish hybrid seeds. We demonstrates the use of RAPD(randomly amplified polymorphic DNAs) markers to identify each of inbred parent lines and hybrids by rapid and simple method.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.19
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• pp.8209-8213
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• 2014

Background: Cervical cancer is a common, preventable and manageable disease in women worldwide. Objectives: This study was conducted to determine the cost of follow-up for suspicious precancerous cervical lesions within a screening program using Pap smear or HPV DNA test through the decision tree. Materials and Methods: Patient follow-up processes were determined using standard guidelines and consultation with specialists to design a decision tree model. Costs of treatment in both public and private sectors were identified according to the national tariffs in 2010 and determined based on decision tree and provided services (visits to specialists, colposcopy, and conization) with two modalities: Pap smear and HPV DNA test. The number of patients and the mean cost of treatment in each sector were calculated. The prevalence of lesions and HPV were obtained from literature to estimate the cost of treatment for each woman in the population. Results: Follow-up costs were determined using seven processes for Pap smear and 11 processes for HPV DNA test. The total cost of using Pap smear and HPV DNA process for each woman in the population was 36.1$ and 174$ respectively. Conclusions: The follow-up process for patients with suspicious cervical lesions needs to be included in the existing screening program. HPV DNA test is currently more expensive than Pap smear, it is suggested that we manage precancerous cervical lesions with this latter test.

• Animal Systematics, Evolution and Diversity
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• v.28 no.4
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• pp.269-278
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• 2012

Gobiids are hyperdiverse compared with other teleost groups, with about 2,000 species occurring in marine, freshwater, and blackish habitats, and they show a remarkable variety of morphologies and ecology. Testing the effectiveness of DNA barcodes on species that have emerged as a result of radiation remains a major challenge in evolutionary biology. Here, we used the cytochrome c oxidase subunit 1 (COI) sequences from 144 species of gobies and related species to evaluate the performance of distance-based DNA barcoding and to conduct a phylogenetic analysis. The average intra-genus genetic distance was considerably higher than that obtained in previous studies. Additionally, the interspecific divergence at higher taxonomic levels was not significantly different from that at the intragenus level, suggesting that congeneric gobies possess substantial interspecific sequence divergence in their COI gene. However, levels of intragenus divergence varied greatly among genera, and we do not provide sufficient evidence for using COI for cryptic species delimitation. Significantly more nucleotide changes were observed at the third codon position than that at the first and the second codons, revealing that extensive variation in COI reflects synonymous changes and little protein level variation. Despite clear signatures in several genera, the COI sequences did resolve genealogical relationships in the phylogenetic analysis well. Our results support the validity of COI barcoding for gobiid species identification, but the utilization of more gene regions will assist to offer a more robust gobiid species phylogeny.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.2
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• pp.903-907
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• 2013

Primary screening by HPV DNA testing is an effective method for reducing cervical cancer and has proven more sensitive than cytology. To advance this approach, many molecular methods have been developed. Hybrid capture 2 provides semi-quantitative results in ratios of relative light units and positive cutoff values (RLU/PC). Twenty-five thousand and five patients were included in this study to analyze the correlation between the ratio of RLU/PC and stage of cervical dysplasia. The results show that the RLU/PC ratios ranged from 0-3500 while almost normal cases, ASC-US and ASC-H, had values below 200. Of those samples negative for cytology markers, 94.6% were normal and their RLU/PC ratios were less than 4. With an RLU/PC ratio greater than 4 and less than or equal to 300, the percentages in all age groups were normal 53.6%, LSIL 20.2%, ASC-US 17.2%, HSIL 6.13%, ASC-H 2.72%, and AGC 0.11%, respectively. In contrast, 64.0% of samples with a RLU/PC ratio greater than 300 and less than or equal to 3500 were LSIL. These results should contribute to cost effective cervical cancer management strategies. Further studies of associations with particular HPV genotypes would be useful to predict the risk of progression to cancer.

• Journal of Genetic Medicine
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• v.12 no.2
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• pp.85-91
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• 2015

Purpose: Noninvasive prenatal test (NIPT) by massively parallel sequencing (MPS) of cell-free fetal DNA in maternal plasma marks a significant advancement in prenatal screening, minimizing the need for invasive testing of fetal chromosomal aneuploidies. Here, we report the initial clinical performance of NIPT in Korean pregnant women. Materials and Methods: MPS-based NIPT was performed on 910 cases; 5 mL blood samples were collected and sequenced in the Shenzhen BGI Genomic Laboratory to identify aneuploidies. The risk of fetal aneuploidy was determined by L-score and t-score, and classified as high or low. The NIPT results were validated by karyotyping for the high-risk cases and neonatal follow-up for low-risk cases. Results: NIPT was mainly requested for two clinical indications: abnormal biochemical serum-screening result (54.3%) and advanced maternal age (31.4%). Among 494 cases with abnormal biochemical serum-screening results, NIPT detected only 9 (1.8%) high-risk cases. Sixteen cases (1.8%) of 910 had a high risk for aneuploidy: 8 for trisomy 21, 2 for trisomy 18, 1 for trisomy 13, and 5 for sex chromosome abnormalities. Amniocentesis was performed for 7 of these cases (43.8%). In the karyotyping and neonatal data, no false positive or negative results were observed in our study. Conclusion: MPS-based NIPT detects fetal chromosomal aneuploidies with high accuracy. Introduction of NIPT as into clinical settings could prevent about 98% of unnecessary invasive diagnostic procedures.

• Interdisciplinary Bio Central
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• v.3 no.3
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• pp.10.1-10.8
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• 2011

Introduction: Hash functions are computer algorithms that protect information and secure transactions. In response to the NIST's "International Call for Hash Function", we developed a biological hash function using the computing capabilities of bacteria. We designed a DNA-based XOR logic gate that allows bacterial colonies arranged in a series on an agar plate to perform hash function calculations. Results and Discussion: In order to provide each colony with adequate time to process inputs and perform XOR logic, we designed and successfully demonstrated a system for time-delayed bacterial growth. Our system is based on the diffusion of ${\ss}$-lactamase, resulting in destruction of ampicillin. Our DNA-based XOR logic gate design is based on the op-position of two promoters. Our results showed that $P_{lux}$ and $P_{OmpC}$ functioned as expected individually, but $P_{lux}$ did not behave as expected in the XOR construct. Our data showed that, contrary to literature reports, the $P_{lux}$ promoter is bidirectional. In the absence of the 3OC6 inducer, the LuxR activator can bind to the $P_{lux}$ promoter and induce backwards transcription. Conclusion and Prospects: Our system of time delayed bacterial growth allows for the successive processing of a bacterial hash function, and is expected to have utility in other synthetic biology applications. While testing our DNA-based XOR logic gate, we uncovered a novel function of $P_{lux}$. In the absence of autoinducer 3OC6, LuxR binds to $P_{lux}$ and activates backwards transcription. This result advances basic research and has important implications for the widespread use of the $P_{lux}$ promoter.