• Asian Pacific Journal of Cancer Prevention
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• v.15 no.2
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• pp.651-656
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• 2014

Background: Cervical cancer is the third commonest type of cancer among women in Malaysia. Our aim was to determine the distribution of human papilloma virus (HPV) genotypes in cervical cancer in our multi-ethnic population. Materials and Methods: This was a multicentre study with a total of 280 cases of cervical cancer from 4 referral centres in Malaysia, studied using real-time polymerase chain reaction (qPCR) detection of 12 high risk-HPV genotypes. Results: Overall HPV was detected in 92.5% of cases, in 95.9% of squamous cell carcinomas and 84.3%of adenocarcinomas. The five most prevalent high-risk HPV genotypes were HPV 16 (68.2%), 18 (40%), 58 (10.7%), 33 (10.4%) and 52 (10.4%). Multiple HPV infections were more prevalent (55.7%) than single HPV infections (36.8%). The percentage of HPV positive cases in Chinese, Malays and Indians were 95.5%, 91.9% and 80.0%, respectively. HPV 16 and 18 genotypes were the commonest in all ethnic groups. We found that the percentage of HPV 16 infection was significantly higher in Chinese (75.9%) compared to Malays (63.7%) and Indians (52.0%) (p<0.05), while HPV 18 was significantly higher in Malays (52.6%) compared to Chinese (25.0%) and Indians (28%) (p<0.05). Meanwhile, HPV 33 (17.9%) and 52 (15.2%) were also more commonly detected in the Chinese (p<0.05). Conclusions: This study showed that the distribution of HPV genotype in Malaysia is similar to other Asian countries. Importantly, we found that different ethnic groups in Malaysia have different HPV genotype infection rates, which is a point to consider during the implementation of HPV vaccination.

• KSBB Journal
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• v.24 no.5
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• pp.432-438
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• 2009

Here, we demonstrated simple nucleic acid, RNA, concentration method using polymer micro chip containing glass bead ($100\;{\mu}m$). Polymer micro chip was fabricated by PDMS ($1.5\;cm\;{\times}\;1.5\;cm$, $100\;{\mu}m$ in the height) including pillar structure ($160\;{\mu}m\;(I)\;{\times}\;80\;{\mu}m\;(w)\;{\times}\;100\;{\mu}m\;(h)$, gap size $50\;{\mu}m$) for blocking micro bead. RNA could be adsorbed on micro glass bead at low pH by hydrogen bonding whereas RNA was released at high pH by electrostatic force between silica surface and RNA. Amount of glass beads and flow rate were optimized in aspects of adsorption and desorption of RNA. Adsorption and desorption rate was measured with real time PCR. This concentrated RNA was applied to amplification micro chip in which NASBA (Nucleic Acid Sequence Based Amplification) was performed. As a result, E.coli O157 : H7 in the concentration of 10 c.f.u./10 mL was successfully detected by these serial processes (concentration and amplification) with polymer micro chips. It implies this simple concentration method using polymer micro chip can be directly applied to ultra sensitive method to measure viable bacteria and virus in clinical samples as well as environmental samples.

• The Korean Journal of Food And Nutrition
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• v.33 no.2
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• pp.142-148
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• 2020

The purpose of this study was to investigate the prevalence, toxin gene profiles, and enterotoxin producing ability of Bacillus cereus isolated from environment-friendly vegetables and good agricultural practices (GAP) vegetables. A total of 49 vegetables including 40 environment-friendly vegetables and 9 GAP vegetables were tested. The Vitek 2 system was used to identify B. cereus and the PCR was used to detect 6 toxin genes, respectively. B. cereus was detected in 34 (69.3%) of 49 vegetables and the prevalence of B. cereus in GAP vegetables (44.4%) was lower than in the environment-friendly vegetables (75.0%). The detection rates of entFM, nheA, hblC, and cytK enterotoxin genes, respectively, among all isolates were 100%, 97.0%, 88.2%, and 73.5%, respectively. All of the isolates had at least one or more enterotoxin gene and 20 isolates (58.8%) had hemolysin BL enterotoxin producing ability. The risk of food poisoning from the environment-friendly vegetables and the GAP vegetables has been shown as constant. Thus, it is necessary to expand the supply of GAP vegetables showing lower B. cereus contamination than the environment-friendly vegetables. The characteristics of the environment-friendly vegetables and the GAP vegetables that must be consumed after cleaning should be disseminated to consumers regarding food poisoning prevention.

• Journal of Plant Biotechnology
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• v.39 no.3
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• pp.196-204
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• 2012

This study was carried out to develop reliable systems for somatic embryogenesis in oil palm tree (Elaeis guineensis Jacq.), and to verify the somaclonal variants by RAPD analysis. Embryogenic callus was induced successfully on modified half-strength MS medium containing $NaH_2PO_4{\cdot}2H_2O$ and casein. Embryogenic callus was further developed to somatic embryo mass (SEM), which is very hard and bonded tightly each other. Plantlets were proliferated when SEM was cultured on modified MS medium containing half strength $NH_4NO_3$, casein and L-ascorbic acid. Plantlets were transplanted into pots containing artificial soils. When RAPD analysis was conducted using randomly selected 95 in vitro plantlets and 19 random primers, somaclonal variation was detected using BNR35 primer. There was missing band around 1 kb in #22, #28, #35, and #77 plantlets. In addition, bands obtained from #28, #35, and #77 was much stronger than other normal bands. The blast results at NCBI revealed that somaclonal variation observed in this study was related to chloroplast genome of oil palm. The results also revealed that oil palm reproduction system through somatic embryogenesis is quite reliable and early detection of somaclonal variants seem to be possible at in vitro stage by RAPD analysis.

• Korean Journal of Medicinal Crop Science
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• v.11 no.2
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• pp.102-108
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• 2003

This experiment was conducted to evaluate the diversity and purity of the Korean ginseng (Panax gjnseng) lines developed by the pure line selection using RAPD markers. Four primer (OPA 19, OPM 11, URP 3 and UBC 98) out of the 48 primer tested produced band which showed within-line polymorphisms at least in one line. Within-line polymorphisms were detected in six lines by OPA 19, in four lines by URP 03, in five lines by OPM 11, and in one line by UBC 98 respectively. Five plants obtained from the commercial cultivar 'Cheonpung' were differentiated using the primers OPA 19 and OPM 11. Five plants obtained from the 'Yeonpung were differentiated using the primer OPM 11. Detection of within-line RAPD polymorphisms might be attributed to the fact that cross pollination appear in P. gjnseng and a long period of three to four years required to reach the reproductive stage thereby delay the process to homozygosity.

• Korean Journal of Microbiology
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• v.37 no.4
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• pp.265-272
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• 2001

The diversity of acid-tolerant epiphytic bacterial communities on deciduous oak tree (Quercus dentate Thunb.) leaves was examined both in the natural forest area with a clean air and in the industrial estate to assess effects of acidic depositions to the phyllosphere using 16S rDNA sequence data. A total of 444 acid-tolerant epiphytic bacterial clones were obtained, resulting in 17 phylotypes by performing a analysis of restriction fragment length polymorphism (RFLP) for PCR-amplified 16S rDNA products. A very low diversity of dominating acid tolerant bacterial communities in both areas was found, just 2 subphyla groups, $\gamma$-Proteobacteria and low-G+C gram-positive bacteria. As tree leaves grow older, diversities of acid-tolerant bacteria on them significantly increased. The community structure of acid-tolerant epiphytic bacteria consisted of Pseudomonas and Enterobacteriaceae groups in the $\gamma$-Proteobacteria subphylum, and Streptococcaceae and Staphylococcus groups in the low-G+C gram-positive bacteria subphylum. The direct influence of acidic depositions on bacterial phylogenetic composition could not be detected especially when higher taxonomic levels such as subphylum, but at narrower or finer levels it could be observed by a detection of Xanthomonadales group belonged to the $\gamma$-Proteobacteria only in the industrial area and of Acetobacteraceae group belonged to the $\alpha$-Proteobacteria. There remains that these specific acid-tolerant epiphytic bacterial groups could be used as indicators for assessing effects of acidic depositions on the phyllosphere.

• Korean Journal of Poultry Science
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• v.40 no.3
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• pp.223-234
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• 2013

Poultry industry is abounding day by day as it engrosses less cost of investment per bird as compared to large animals. Poultry have the most copious genomic tool box amongst domestic animals for the detection of quantitative trait loci (QTL) and marker assisted selection (MAS). Use of multiple markers and least square techniques for mapping of QTL affecting quality and production traits in poultry is in vogue. Examples of genetic tests that are available to or used in industry programs are documented and classified into causative mutations (direct markers), linked markers in population-wide linkage disequilibrium (LD) with the QTL (LD markers), and linked markers in population wide equilibrium with the QTL (LE markers). Development of genome-wide SNP assays, role of 42 K, 60 K (Illumina) and 600 K (Affymetrix$^{(R)}$ Axim$^{(R)}$) SNP chip with next generation sequencing for identification of single nucleotide polymorphism (SNP) has been documented. Hybridization based, PCR based, DNA chip and sequencing based are the major segments of DNA markers which help in conducting of MAS in poultry. Economic index-marker assisted selection (EI-MAS) provides platform for simultaneous selection for production traits while giving due weightage to their marginal economic values by calculating predicted breeding value, using information on DNA markers which are normally associated with relevant QTL. Understanding of linkage equilibrium, linkage dis-equilibrium, relation between the markers and gene of interest are quite important for success of MAS. This kind of selection is the most useful tool in enhancing disease resistance by identifying candidate genes to improve the immune response. The application of marker assisted selection in selection procedures would help in improvement of economic traits in poultry.

• Korean Journal of Veterinary Research
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• v.41 no.2
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• pp.157-165
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• 2001

Amplified fragment length polymorphism(AFLP) technique is based on the polymorphism detection through selective PCR amplification of restriction fragments from digested genomic DNA and thus includes the procedures of the total DNA digestion by endonucleases, ligation of adapters to the ends of the fragments, and following the selective amplification of the restricted DNA fragments. This study were aimed to : (1) determine the genetic variability of S aureus strains, (2) estimate genetic diversity within and among these strains, (3) compare phylogenetic relationships among these strains as genetic markers using AFLP techniques. Genomic DNA was digested with a particular combination of three restriction enzymes with specific recognition sites and the DNA fragments were ligated to restriction specific adapters and amplified using the selective primer combinations. In the S aureus strain, the number of scorable AFLP bands detected per each primer combination varied from 29 to 102, with an average of 61.59 using 27 primer combinations. A total of 1,663 markers were generated, 904 bands of which were polymorphic, showing a 33.48% level of polymorphism with these primer combinations. Among the primer combinations, E02/T02, E02/T03, E04/H02, E02/T01 and E04/H03 primer combinations showed a high level of polymorphism with 0.78, 0.76, 0.74, 0.71 and 0.70, respectively. But T03/H01, E01/T02 and E01/T03 primer combinations showed a low level of polymorphism with 0.38, 0.37 and 0.15, respectively, Therefore, the former primer combinations will be the most effective for AFLP analysis of S aureus. In SA1 sub-types the level of polymorphism of S aureus KCTC 1927 was similar to that of S aureus CU 01(0.825) and higher than those of other strains such as S aureus CU 02 (0.715), S aureus KCTC 2199(0.625), S aureus KCTC 1916(0.607) and S aureus KCTC 1621 (0.553). In SA2 sub-types the level of polymorphism of S aureus CU 07 was similar to that of S aureus CU 08(0.935) and higher than those of both S aureus CU 04(0.883) and S aureus CU 05(0.883) and lower than those of S aureus CU 03(0.583). In SA3 subtypes the level of polymorphism of S aureus CU 11 was similar to that of S aureus CU 12(0.913) and lower than that of S aureus CU 15(0.623). The results proved that AFLP marker analysis of S aureus strain could be used to study the epidemiology of mastitis and in addition, common genotype in geographic region could be useful for the development of an effective vaccine or DNA marker for easy diagnosis of mastitis caused by S aureus infection.

• Food Science of Animal Resources
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• v.34 no.6
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• pp.799-807
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• 2014

Meat source fraud and adulteration scandals have led to consumer demands for accurate meat identification methods. Nucleotide amplification assays have been proposed as an alternative method to protein-based assays for meat identification. In this study, we designed Loop-mediated isothermal amplification (LAMP) assays targeting species-specific mitochondrial DNA to identify and discriminate eight meat species; cattle, pig, horse, goat, sheep, chicken, duck, and turkey. The LAMP primer sets were designed and the target genes were discriminated according to their unique annealing temperature generated by annealing curve analysis. Their unique annealing temperatures were found to be $85.56{\pm}0.07^{\circ}C$ for cattle, $84.96{\pm}0.08^{\circ}C$ for pig, and $85.99{\pm}0.05^{\circ}C$ for horse in the BSE-LAMP set (Bos taurus, Sus scrofa domesticus and Equus caballus); $84.91{\pm}0.11^{\circ}C$ for goat and $83.90{\pm}0.11^{\circ}C$ for sheep in the CO-LAMP set (Capra hircus and Ovis aries); and $86.31{\pm}0.23^{\circ}C$ for chicken, $88.66{\pm}0.12^{\circ}C$ for duck, and $84.49{\pm}0.08^{\circ}C$ for turkey in the GAM-LAMP set (Gallus gallus, Anas platyrhynchos and Meleagris gallopavo). No cross-reactivity was observed in each set. The limits of detection (LODs) of the LAMP assays in raw and cooked meat were determined from $10pg/{\mu}L$ to $100fg/{\mu}L$ levels, and LODs in raw and cooked meat admixtures were determined from 0.01% to 0.0001% levels. The assays were performed within 30 min and showed greater sensitivity than that of the PCR assays. These novel LAMP assays provide a simple, rapid, accurate, and sensitive technology for discrimination of eight meat species.

• Journal of Periodontal and Implant Science
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• v.38 no.2
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• pp.143-152
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• 2008

Purpose: Specific bacteria are believed to play an important role in chronic periodontitis. Although extensive microbial analyses have been performed from subgingival plaque samples of periodontitis patients, systemic analysis of subingival microbiota has not been carried out in a Korean population so far. The purpose of this study was to investigate the prevalence of 29 putative periodontal pathogens in Korean chronic periodontitis patients and evaluate which pathogens are more associated with Korean chronic periodontitis. Material and Methods: A total of 86 subgingival plaque samples were taken from 15 chronic periodontits(CP) patients and 13 periodontally healthy subjects in Korea. CP samples were obtained from the deepest periodontal pocket (>3 mm probing depth[PD]) and the most shallow periodontal probing site ($\leq$3 mm PD) in anterior tooth and posterior tooth, respectively, of each patient. Samples in healthy subjects were obtained from 1 anterior tooth and 1 posterior tooth. Polymerase chain reaction (PCR) of 16S ribosomal DNA (rDNA) of subgingival plaque bacteria was performed. Detection frequencies(% prevalence) of 29 putative periodontal pathogens were investigated as bacterium-positive sites/total sites. Results: With the exception of Olsenella profuse and Prevotella nigrescens, the sites of diseased patients generally showed higher prevalence than the healthy sites of healthy subjects for all bacteria analyzed. Tanerella forsythensis (B.forsythus), Campylobacter rectus, Filifactor alocis, Fusobacterium nucleatum, Porphyromonas endodontalis and Porphyromonas gingivalis were detected in more than 80% of sites with deep probing depths in CP patients. In comparison between the sites (deep or shallow PD) of CP patients and the healthy sites of healthy subjects, there was statistically significant difference(P<0.05) of prevalence in T.forsythensis (B.forsythus), C.rectus, Dialister invisus, F.alocis, P.gingivalis and Treponema denticola. Conclusion: Our results demonstrate that the four putative periodontal pathogens, T.forsythensis (B.forsythus), C.rectus, P.gingivalis and F.alocis are closely related with CP patients in the Korean population.