• The Korean Journal of Mycology
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• v.39 no.3
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• pp.217-222
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• 2011

Job's tears (Coix lacryma-jobi) is native to East Asia, and grains of the plant are used as health food and medicinal material. Head blight symptoms of the plant were frequently observed during disease surveys in Korea from 2006 to 2008. The symptoms were characterized as discoloration of husks, and subsequently inside of mature grains were shriveled or emptied. One hundred fifty nine isolates of Fusarium species were obtained from the disease symptoms of the plant collected from several locations in the country. Out of the isolates, the most frequently isolated Fusarium species were F. graminearum (34%), F. proliferatum (14.5%), F. verticillioides (10.1%), F. equiseti (6.9%), and F. fujikuroi (6.3%). Other Fusarium species isolated were F. subglutinans, F. semitectum, F. poae, and F. sporodochioides. Elongation factor 1 alpha gene sequences of the isolates were used for phylogenetic analysis. Analyses of the sequences revealed that the isolates were confirmed to be identical with each reference species of NCBI GenBank. Pathogenicity tests showed that F. graminearum, F. proliferatum and F. verticillioides were strongly virulent to grains of Job's tears. The present study is the first report of head blight of Job's tears caused by Fusarium species in Korea.

• 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.

• The Journal of Advanced Prosthodontics
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• v.7 no.6
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• pp.468-474
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• 2015

PURPOSE. The aim of this study was to characterize and compare bacterial diversity on the removable partial denture (RPD) framework over time. MATERIALS AND METHODS. This descriptive pilot study included five women who were rehabilitated with free-end mandibular RPD. The biofilm on T-bar clasps were collected 1 week ($t_1$) and 4 months ($t_2$) after the RPD was inserted ($t_0$). Bacterial 16S rDNA was extracted and PCR amplified. Amplicons were cloned; clones were submitted to cycle sequencing, and sequences were compared with GenBank (98% similarity). RESULTS. A total of 180 sequences with more than 499 bp were obtained. Two phylogenetic trees with 84 ($t_1$) and 96 ($t_2$) clones represented the bacteria biofilm at the RPD. About 93% of the obtained phylotypes fell into 25 known species for $t_1$ and 17 for $t_2$, which were grouped in 5 phyla: Firmicutes ($t_1=82%$; $t_2=60%$), Actinobacteria ($t_1=5%$; $t_2=10%$), Bacteroidetes ($t_1=2%$; $t_2=6%$), Proteobacteria ($t_1=10%$; $t_2=15%$) and Fusobacteria ($t_1=1%$; $t_2=8%$). The libraries also include 3 novel phylotypes for $t_1$ and 11 for $t_2$. Library $t_2$ differs from $t_1$ (P=.004); $t_1$ is a subset of the $t_2$ (P=.052). Periodontal pathogens, such as F. nucleatum, were more prevalent in $t_2$. CONCLUSION. The biofilm composition of the RPD metal clasps changed along time after RPD wearing. The RPD framework may act as a reservoir for potentially pathogenic bacteria and the RPD wearers may benefit from regular follow-up visits and strategies on prosthesis-related oral health instructions.

• The Korean Journal of Mycology
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• v.41 no.3
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• pp.142-148
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• 2013

Sorghum (Sorghum bicolor Moench) was traditionally grown on a small scale, however, at present its cultivation is getting momentum in terms of food and animal feed crop throughtout the Korea. Grain mold symptoms of the plant were frequently observed during disease surveys in Korea from 2007 to 2009. The symptoms were highly variable. Severely infected grain was fully covered with mold and partially infected grain may look normal or discolored. Ninety isolates of Fusarium species were obtained from the diseased plants collected from several locations in the country. Among the collected Fusarium isolates, 41 were identified as Fusarium thapsinum, 23 as F. proliferatum, 12 as F. graminearum, 5 as F. incarnatum, and 3 as F. equiseti based on their morphological and cultural characteristics. Elongation factor 1 alpha gene sequences of the isolates were used for phylogenetic analysis. Analyses of the sequences revealed that the isolates were confirmed to be identical with related species of NCBI GenBank. Pathogenicity tests showed that three dominant species, F. thapsinum, F. proliferatum and F. graminearum were strongly virulent to grains of sorghum. This study is the first report of sorghum grain mold caused by Fusarium species in Korea.

• The Korean Journal of Mycology
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• v.48 no.3
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• pp.297-312
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• 2020

Wilted soybean plants were collected from soybeans cultivation fields in Korea from 2014 to 2016. Fusarium spp., Colletotrichum spp., Rhizoctonia spp., Macrophomina sp., Phytophthora spp., and Calonectria ilicicola were obtained from the infected samples. Out of these, Fusarium spp. were the dominant species (79.1%). In total, 53 isolates were identified as F. solani species complex, F. oxysporum species complex, F. graminearum species complex, and F. fujikuroi species complex based on mycological characteristics. Sequence typing analysis was conducted using translation elongation factor 1 alpha (TEF) to confirm the identification of isolates. All isolates were identified as F. solani, F. oxysporum, F. commune, F. asiaticum, and F. fujikuroi based on phylogenetic analysis of TEF sequences. Pathogenicity of 44 isolates was tested on three cultivars of soybean using the root dip inoculation method. Out of 5 Fusarium species, only F. asiaticum could not cause the symptoms or be weak. Ten isolates were selected based on pathogenic characters and species identification to investigate the host range and screen soybean cultivars for resistance. Fusarium solani, F. oxysporum, and F. commune were aggressive only to soybean, and F. fujikuroi was aggressive to kidney bean, yellow cowpea, black cowpea, adzuki bean as well as soybean. All 13 Korean soybean cultivars were susceptible to F. commune and F. fujikuroi. Out of 13 cultivars, cv. Janggi, cv. Poongsannamul, and cv. Socheongja were resistant to Fusarium wilt, while cv. Hwanggeumol and Chamol were susceptible to Fusarium wilt.

• Journal of Ginseng Research
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• v.44 no.1
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• pp.135-144
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• 2020

Background: Panax species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven Panax species, two (P. quinquefolius and P. trifolius) from North America and five (P. ginseng, P. notoginseng, P. japonicus, P. vietnamensis, and P. stipuleanatus) from Asia. Methods: We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven Panax whole chloroplast genomes. Results: We identified 1,128 single nucleotide polymorphisms (SNP) in coding gene sequences, distributed among 72 of the 79 protein-coding genes in the chloroplast genomes of the seven Panax species. The other seven genes (including psaJ, psbN, rpl23, psbF, psbL, rps18, and rps7) were identical among the Panax species. We also discovered that 12 large chloroplast genome fragments were transferred into the mitochondrial genome based on sharing of more than 90% sequence similarity. The total size of transferred fragments was 60,331 bp, corresponding to approximately 38.6% of chloroplast genome. We developed 18 SNP markers from the chloroplast genic coding sequence regions that were not similar to regions in the mitochondrial genome. These markers included two or three species-specific markers for each species and can be used to authenticate all the seven Panax species from the others. Conclusion: The comparative analysis of chloroplast genomes from seven Panax species elucidated their genetic diversity and evolutionary relationships, and 18 species-specific markers were able to discriminate among these species, thereby furthering efforts to protect the ginseng industry from economically motivated adulteration.

• Horticultural Science & Technology
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• v.34 no.1
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• pp.142-153
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• 2016

The present study investigated identification of cultivars through phylogenetic analysis of 108 Citrus varieties and related cultivars using simple sequence repeat (SSR) markers. Two hundred three SSR primer pairs were used to detect polymorphic markers among 8 Citrus cultivars consisting of 4 mandarins, 1 orange, 1 tangor, 1 tangelo, and 1 pumelo. Eighteen SSR primer pairs were reproducible and showed highly polymorphic alleles. These markers were applied to assess genetic variations of the 108 varieties. Each marker detected 5-14 alleles, with an average of 9.28. The polymorphism information content varied from 0.417 to 0.791 with an average of 0.706. Cluster analysis with SSR markers resulted in 13 major groups reflecting cultivar types and pedigree information. Twelve orange cultivars in the $I-1^{st}$ sub-cluster and 23 mandarin cultivars in the $II-1^{st}$ sub-cluster, respectively, were not discriminated using the SSR markers. This could be due to narrow genetic backgrounds originated through bud mutation or nucellars seedlings. The SSR profile database of Citrus cultivars will be useful as a tool for protection of plant breeders' intellectual property rights in addition to assessing genetic diversity in Citrus cultivars and germplasms.

• Journal of Life Science
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• v.29 no.5
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• pp.524-529
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• 2019

Medicinal plants resources are becoming important assets since their usages have been expanded to the development of functional foods for human health, cosmetics and pharmaceutical industries. However, their phylogenetic origins and names are different from each country and quite often they are mixed each other resulting in the confusion for consumers. Particularly when they are very similar based on their morphological characteristics and distributed, it is extremely difficult to differentiate their origins even by specialists. Therefore, identification of each plant species is important for standardizing herbal medicine. Thistle is a medicinal and perennial plant. Obtaining information about the genetic diversity of plant populations is highly important for conservation and germplasm utilization. Although thistle is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish from other similar species from different countries. In this study, we developed single nucleotide polymorphism (SNP) markers derived from chloroplast genomic sequences to identify distinct Korean-specific thistle species via high resolution melting (HRM) curve analyses. We performed molecular authentication of four different kinds of thistle species from different regions using DNA sequences in the trnL-F and matK chloroplast intergenic region. The SNP markers developed in this study are useful for rapidly identifying specific thistle species from different country.

• Korean Journal of Environmental Biology
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• v.39 no.2
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• pp.147-155
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• 2021

To investigate the incidence of plant-parasitic nematodes (PPNs) in perilla fields in Korea, 55 soil samples were collected from open fields and plastic-film house fields and were analyzed during January 2020 to October 2020. Root-lesion nematodes (RLNs), spiral nematodes, root-knot nematodes, and stunt nematodes were detected in perilla fields, and the incidences of RLNs (39%) and spiral nematodes (55%) were higher than those of other nematodes. Among PPNs, RLNs are very important species found on economic crops. The detection frequency of RLNs was increased due to continuous crop cultivation, and the frequency of fields that cultivated only one crop continuously for over 11 years was twice higher than the frequency of fields that cultivated only one crop for less than 5 years. The PPN species diversity and density were different between leaf-perilla cultivation fields and seed-perilla cultivation fields. In phylogenetic analysis of RLNs, Pratylenchus penetrans, P. vulnus, and Pratylenchoides leiocauda were identified in perilla fields. These results suggest the RLNs should be considered for establishing nematode management strategies in perilla fields in Korea.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.26 no.3
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• pp.248-262
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• 2021

Marine planktonic ciliates include two major groups, loricated tintinnids and naked oligotrichs. The study of marine ciliate plankton in Korea began with taxonomic efforts on tintinnids based on the morphology of lorica, a vase-shaped shell. Despite polymorphism in the lorica, it is utilized as a key characteristic in identification of tintinnid species. However, oligotrichs have been studied only recently in Korea due to challenges associated with the observation of ciliary arrangements and the technical development for cell staining. Species diversity and phylogenetic classification of the ciliates have been informed by recent advances in morphological and molecular analyses. Illustrations of the planktonic ciliate in Korea have been published on the basis of taxonomic data of tintinnids and oligotrichs. Planktonic ciliates acting as the major consumers of pico- and nanoplankton as well as the prey of mesozooplankton, has been monitored by spatial and temporal investigations in Korean coastal waters. A practical approach addressing the limitations and potential of marine ciliate studies in Korea is proposed here to improve the data quality of planktonic ciliates, providing an enhanced basis for quality control of ciliate monitoring.