• Korean Journal of Microbiology
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• v.49 no.2
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• pp.156-164
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• 2013

Actinomycetes produce diverse secondary metabolites which have the primary importance in medicine, agriculture and food production, and key to this is their ability to interact with other organisms in natural habitats. In this study, we have investigated the taxonomical and functional diversity of actinomycetes in fecal sample of rhinoceros beetle larvae (Allomyrina dichotoma L.) by using culture-dependent and -independent approaches. For the culture-independent approach, the community DNA was extracted from the sample and 16S rRNA genes of actinomycetes were amplified using actinomycetes-specific PCR primers. Thirty-seven clones were classified into 15 genera and 24 species of actinomycetes. For the culture-dependent approach, 53 strains were isolated from larval feces, of which 27 isolates were selected based on morphological characteristics. The isolates were classified into 4 genera and 14 species, and 24 isolates (89%) were identified as the genus Streptomyces. Many of the representative isolates had antimicrobial activities against plant pathogenic fungi and Gram-positive bacteria. In addition, most of the isolates (78%) showed biochemical properties to hydrolyze cellulose and casein. The results demonstrated that diverse and valuable actinomycetes could be isolated from insect fecal samples, indicating that insect guts can be rich sources for novel bioactive compounds.

• Research in Plant Disease
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• v.16 no.3
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• pp.306-311
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• 2010

To detect Fusarium mycotoxins, grain samples were collected from 32 rice fields all over the country and from 19 maize fields in eastern and midland provinces in Korea in 2009. Maize contamination with Fusarium species (54.9%) was higher than in rice (8.2%). Using Fusarium species specific PCR primer sets (Fg16 and VERT), 58 and 354 of total 506 isolates from maize samples were putatively identified as F. graminearum (11.5%) and F. verticillioides (70.0%), respectively. From rice samples, 276 of 315 isolates (87.8%) were putatively identified as F. graminearum but F. verticillioides was not identified. LC or LC-MS analysis of the samples revealed that fumonisin was the most commonly detected mycotoxin in maize samples but its level was below the regulation limit. Only two maize samples were contaminated with deoxynivalenol and zearalenone at the levels above the regulation limit. In rice samples, contamination with zearalenone was common but the levels were below the regulation limit. This study showed that most of the Korean maize and rice samples collected in 2009 were contaminated with Fusarium mycotoxins but the levels were below the Korean regulations for deoxynivalenol, fumonisin and zearalenone.

• Journal of the korean academy of Pediatric Dentistry
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• v.34 no.2
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• pp.247-254
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• 2007

Mutans streptococci have been reported to be implicated in dental caries. Of these streptococcal species, Streptcoccus mutans and Streptococcus sobrinus are most commonly found in human dental caries. Prevalence of these bacterial species in dental caries is found to be varied in different races and countries. Therefore, importance of these bacteria in dental caries remains to be determined The present study was performed to find out correlation S. mutans and S. sobrinus with dental caries in 125 Korean children with mixed dentition between 6 to 11 years of age. They were classified as group A(6-8 years) and group B(9-11 years) by age. For the study, stimulated saliva samples were collected from each subject. The vials containing saliva specimens were serially diluted (1:10) in saline and plated in duplicate on tryptone-yeast extract-cysteine with sucrose and bacitracin (TYCSB) for S. mutans and S. sobrinus. After genomic DNA was extracted from the samples, polymerase chain reaction (PCR) amplification was performed for identification using universal primers and specific primers to S. mutans and S. sobrinus. Data of microbial variables were compared to caries status of the subjects. According to this study, the result were as follows : 1. S. mutans versus S. sobrinus were moderate positive linear correlated in both group A(r=0.70) and group B(r=0.50). 2. Between S. mutans and dental caries there were weak positive linear correlation in both group A(r= 0.25) and group B(r=0.34). 3. S. sobrinus versus dental caries were not correlated in group A but slightly correlated in group B(r=0.21). 4. Between S. mutans and age, there were not correlation in both group. 5. S. sobrinus versus age were weak correlated in group A(r=0.32) but not correlated in group B.

• Korean Journal of Plant Taxonomy
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• v.41 no.4
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• pp.299-314
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• 2011

The choice of molecular markers is the first step when selecting experimental plans in the field of population genetics. The popular molecular markers in population genetic studies are mainly allozyme, RAPD, RFLP, AFLP, microsatellite, SNP and ISSR. Among these, microsatellites are frequently found in nuclear, chloroplast and mitochondrial genome, showing a high level of polymorphism and nuclear microsatellites are codominant. Thus, it is a favorable molecular marker for population structure analyses and genetic diversity studies. Microsatellites are composed of tandem repeated 1~6 base pair nucleotide motifs and can be easily amplified by PCR reactions using locus specific primers. Because microsatellites have low cross-species transferability, however, they are only applicable between phylogenetically close species. In wild plants, the lack of genomic information and the high development cost of the microsatellite obstruct the wider use of microsatellites in plant population genetics research. In this review, we introduce the basis for microsatellite markers, the development process, and analytical methods as well as evolutionary models and their applications. In addition, possible genotyping errors which lead to erroneous conclusions are discussed.

• Journal of Animal Science and Technology
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• v.45 no.6
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• pp.911-916
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• 2003

The mitochondrial DNA(mtDNA) D-loop region was amplified from Duroc(Sus scrofa) by polymerase chain reaction(PCR). The oligonucleotide primer used to amplify the Sus scrofa mtDNA D-loop region was designed using tRNA-Pro and tRNA-Phe sequence in mtDNA regions highly conserved in many other animal species. There were 1,145 base pairs(bp) in the D-loop region. The middle of the region contained 10 tandem repeat of an 10-bp Sus scrofa-specific sequence, TACACGTGCG. We designed primers for PCR-mediated single stranded conformation polymorphism(SSCP) analysis that amplified a 345 bp fragment, which contained the most variable region according to our sequencing data. SSCP analysis of denatured amplification products was carried out by polyacrylamide(8%) gel electrophoresis followed by ethidium bromide staining. The SSCP analysis identified two band patterns(A and B) and comparision of these two nucleotide sequences identified 21 base substitutions. These results show that SSCP analysis of the D-loop region is useful for detecting the genetic polymorphism.

• Environmental Mutagens and Carcinogens
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• v.22 no.3
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• pp.142-148
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• 2002

Although ionizing radiation (IR) has been used to treat the various human cancers, IR is cytotoxic not only to cancer cells but to the adjacent normal tissue. Since normal tissue complications are the limiting factor of cancer radiotherapy, one of the major concerns of IR therapy is to maximize the cancer cell killing and to minimize the toxic side effects on the adjacent normal tissue. As an attempt to develop a method to monitor the degree of radiation exposure to normal tissues during radiotherapy, we investigated the transcriptional responses of human peripheral blood lymphocytes (PBL) following IR using cDNA microarray chip containing 1,221 (1.2 K) known genes. Since conventional radiotherapy is delivered at about 24 h intervals at 180 to 300 cGy/day, we analyzed the transcriptional responses ex-vivo irradiated human PBL at 200 cGy for 24 h-period. We observed and report on 1) a group of genes transiently induced early after IR at 2 h, 2) of genes induced after IR at 6 h, 3) of genes induced after IR at 24 h and on 4) a group of genes whose expression patters were not changed after IR. Since Biological consequences of IR involve generation of various reactive oxygen species (ROS) and thus oxidative stress induced by the ROS is known to damage normal tissues during radiotherapy, we further tested the temporal expression profiles of genes involved in ROS modulation by RT-PCR. Specific changes of 6 antioxidant genes were identified in irradiated PBL among 9 genes tested. Our results suggest the potential of monitoring post-radiotherapy changes in temporal expression profiles of a specific set of genes as a measure of radiation effects on normal tissues. This type of approach should yield more useful information when validated in in vivo irradiated PBL from the cancer patients.

• Reproductive and Developmental Biology
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• v.29 no.4
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• pp.213-221
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• 2005

We used nine decamer primers to generate DNA fragment sizes ranging from 100 bp to 1,600 bp from two bullhead (Pseudobagrus fulvidraco) populations of Dangjin in Korea. 376 fragments were identified in the cultured bullhead population, and 454 in the population of wild bullhead from Dangjin: 287 specific fragments $(76.3\%)$ in the cultured bullhead population and 207 $(45.6\%)$ in the wild bullhead population. On average, a decamer primer was used to generate 34.2 amplified products in a cultured bullhead. A RAPD primer was used to generate an average of 3.1 amplified bands per sample, ranging between 2.5 and 6.0 fragments in this population. Nine primers also generated 24 polymorphic fragments (24/376 fragment, $6.4\%$) in the cultured bullhead population, and 24 (24/454 fragments, $5.2\%$) in the wild bullhead population. The OPA-16 primer, notably, produced which 11 out of 11 bands $(100\%)$ were monomorphic in the wild bullhead population. 110 intra-population-specific fragments, with an average of 12.2 per primer, were observed in the cultured bullhead population. 99 fragments, with an average of 11.0 per primer, were identified in the wild bullhead. Especially, 55 inter-population-common fragments, with an average of 6.1 per primer, were observed in the two bullhead populations. The bandsharing value (BS value) of individuals within the wild bullhead population was substantially higher than was determined in the cultured bullhead population. The average bandsharing value was $0.596\pm0.010$ within the cultured bullhead population,. and $0.657\pm0.010$ within the wild bullhead population. The dendrogram obtained with the nine primers indicates two genetic clusters, designated cluster $1\;(CULTURED\;01\~CULTURED\;11)$, and cluster $2\;(WILD\;12\~WILD\;22)$. Ultimately, the longest genetic distance displaying significant molecular differences was determined to exist between individuals in the two bullhead populations, namely between individuals WILD no. 19 of the wild bullhead population and CULTURED no. 03 of the cultured bullhead population (genetic distance = 0.714). RAPD-PCR allowed us to detect the existence of population discrimination and genetic variation in Korean population of bullhead. This finding indicates that this method constitutes a suitable tool for DNA comparison, both within and between individuals, populations, species, and genera.

• International Journal of Oral Biology
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• v.48 no.2
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• pp.9-18
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• 2023

The rapid detection of bacteria in the oral cavity, its species identification, and bacterial count determination are important to diagnose oral diseases caused by pathogenic bacteria. The existing clinical microbial diagnosis methods are time-consuming as they involve observing patients' samples under a microscope or culturing and confirming bacteria using polymerase chain reaction (PCR) kits, making the process complex. Therefore, it is required to analyze the development status of substances and systems that can rapidly detect and analyze pathogenic microorganisms in the oral cavity. With research advancements, a close relationship between oral and systemic diseases has been identified, making it crucial to identify the changes in the oral cavity bacterial composition. Additionally, an early and accurate diagnosis is essential for better prognosis in periodontal disease. However, most periodontal disease-causing pathogens are anaerobic bacteria, which are difficult to identify using conventional bacterial culture methods. Further, the existing PCR method takes a long time to detect and involves complicated stages. Therefore, to address these challenges, the concept of point-of-care (PoC) has emerged, leading to the study and implementation of various chair-side test methods. This study aims to investigate the different PoC diagnostic methods introduced thus far for identifying pathogenic microorganisms in the oral cavity. These are classified into three categories: 1) microbiological tests, 2) microchemical tests, and 3) genetic tests. The microbiological tests are used to determine the presence or absence of representative causative bacteria of periodontal diseases, such as A. actinomycetemcomitans, P. gingivalis, P. intermedia, and T. denticola. However, the quantitative analysis remains impossible, and detecting pathogens other than the specific ones is challenging. The microchemical tests determine the activity of inflammation or disease by measuring the levels of biomarkers present in the oral cavity. Although this diagnostic method is based on increase in the specific biomarkers proportional to inflammation or disease progression in the oral cavity, its commercialization is limited due to low sensitivity and specificity. The genetic tests are based on the concept that differences in disease vulnerability and treatment response are caused by the patient's DNA predisposition. Specifically, the IL-1 gene is used in such tests. PoC diagnostic methods developed to date serve as supplementary diagnostic methods and tools for patient education, in addition to existing diagnostic methods, although they have limitations in diagnosing oral diseases alone. Research on various PoC test methods that can analyze and manage the oral cavity bacterial composition is expected to become more active, aligning with the shift from treatment-oriented to prevention-oriented approaches in healthcare.

• Asian Journal of Turfgrass Science
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• v.23 no.2
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• pp.307-316
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• 2009

Creeping bentgrass (Agrostis palustrics Huds.) is cool season turfgrasse that is used for putting green in golf course. Creeping bentgrass cultivars are difficult to distinguish with the same species because of similar morphological characters and low level of genetic diversity. The SCAR markers using the specific DNA can be useful for differentiating between creeping bentgrass cultivars. Five RAPD primers were used for specific band detection among creeping bentgrass cultivars, penncross, penn A-4, crenshaw, L-93, CY-2, T-1. The pairs of SCAR primers for six cultivers were designed by the specific sequences of the bands that amplified by RAPD. Three of the six SCAR primers could not make the use as SCAR primers because the specific false bands were detected in all cultivars. The remaining pairs of SCAR primer, CY850F/R, T700F/R, L2900F/R, amplified the specific band at expected size for three cultivars, CY-2, T-1, L-93, respectively. The CY850F/R primer amplified a band of 850bp in CY-2 cultivar, the T700F/R primer amplified a band of 700bp in T-1 cultivar, and the L2900F/R primer amplified a band of 2.9kb in L-93 cultivar. In this study we developed the SCAR markers to identify and distinguish the inerseeded creeping bentgrass cultivars in a golf course green.

• Korean Journal of Veterinary Service
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• v.41 no.3
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• pp.157-163
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• 2018

In order for monitoring of pathogenic bacterial contamination in the freshly slaughtered poultry meats produced in Gyeong-Nam province, we first isolated 4 strains of Salmonella spp. and 32 strains of Enterococcus faecalis from the total 164 samples, then we analyzed potential virulence gene profiles of the bacterial isolates by PCR using species-specific primer. The potential virulence genes we selected in this study were stn, invA, fimA, spvR, and spvC for the isolates of Salmonella spp. and those of esp, cylM, cylA, cylB, gelE, fsrA, fsrB, and fsrC were for the isolates of E. faecalis. The PCR results showed that all 5 virulence genes were detected simultaneously in the all isolates of Salmonella spp. However, there was a diverse occurrence pattern of the virulence genes in the case of E. faecalis. The gene for enterococcal surface protein (esp) was not detected among the isolates (0/32), and the haemolysin gene prevalence rate of cylA, cylB, and cylM were 3.1% (1/32), 9.3% (3/32), and 9.3% (3/32), respectively. Moreover, the genes of gelE, fsrA, fsrB, and fsrC that associated with gelatinase activity were detected in the rate of 53.1% (17/32), 53.1% (17/32), 53.1% (17/32), and 53.1% (17/32), respectively. In conclusion, in the isolates of Salmonella spp., all possessed 5 virulence genes tested, suggesting that they are all related with each other clonally. However, in the case of E. faecalis isolates, the occurrence of the haemolysin genes (cylM, cylA, cylB) and the gelatinase genes (gelE, fsrABC) was highly variable among the isolates.