• Asian-Australasian Journal of Animal Sciences
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• v.12 no.1
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• pp.129-138
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• 1999

If rumen bacteria can be manipulated to utilize nutrients (i.e., ammonia and plant cell wall carbohydrates) more completely and efficiently, the need for protein supplementation can be reduced or eliminated and the digestion of fiber in forage or agricultural residue-based diets could be enhanced. However, these approaches require a complete and accurate description of the rumen community, as well as methods for the rapid and accurate detection of microbial density, diversity, phylogeny, and gene expression. Molecular ecology techniques based on small subunit (SSU) rRNA sequences, nucleic acid probes and the polymerase chain reaction (PCR) can potentially provide a complete description of the microbial ecology of the rumen of ruminant animals. The development of these molecular tools will result in greater insights into community structure and activity of gut microbial ecosystems in relation to functional interactions between different bacteria, spatial and temporal relationships between different microorganisms and between microorganisms and reed panicles. Molecular approaches based on SSU rRNA serve to evaluate the presence of specific sequences in the community and provide a link between knowledge obtained from pure cultures and the microbial populations they represent in the rumen. The successful development and application of these methods promises to provide opportunities to link distribution and identity of gastrointestinal microbes in their natural environment with their genetic potential and in situ activities. The use of approaches for assessing pupulation dynamics as well as for assessing community functionality will result in an increased understanding and a complete description of the gastrointestinal communities of production animals fed under different dietary regimes, and lead to new strategies for improving animal growth.

• Animal Systematics, Evolution and Diversity
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• v.27 no.3
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• pp.220-227
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• 2011

The morphology of the two marine urostyloid ciliates, Pseudokeronopsis carnea (Cohn, 1866) and Uroleptopsis citrina Kahl, 1932, in the family Pseudokeronopsidae, collected from the Yellow Sea, and the East Sea, Korea, respectively, were studied using live observation and protargol impregnation. Additionally, the small subunit ribosomal RNA (SSU rRNA) gene was sequenced. These two species are firstly recorded in Korea. The main diagnostic key is as follows. Pseudokeronopsis carnea: body outline elongate-elliptical, brown-reddish or orange-red in colour in vivo; bicorona of 16-24 frontal cirri; one buccal and two frontoterminal cirri; 7-10 transverse cirri; 5-7 dorsal kineties; two types of cortical granules (one orange-red pigment, mainly grouped around cirri and dorsal bristles, arranged in typical rubra-pattern; the other, colourless and blood-cell-shaped, and densely distributed); contractile vacuole in the posterior half of the cell on the left side, usually in posterior 1/3-2/5. Uroleptopsis citrina: body outline elongate-elliptical, lemon-yellow in colour in vivo; two types of cortical granules (one yellow pigment; the other, blood-cell-shaped, densely distributed); bicorona of 12-18 frontal cirri; 2-3 frontoterminal cirri; two midventral rows comprising 26-35 cirri (consisting of anterior paired cirri, non-paired single cirri, and posterior paired cirri); three dorsal kineties. In addition, the SSU rRNA sequences of the two species were compared with public database of these species and consequently, showed high similarity.

• Animal Systematics, Evolution and Diversity
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• v.36 no.2
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• pp.113-122
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• 2020

From a moss sample, we isolated and identified Notohymena gangwonensis Kim et al., 2019 based on morphological and molecular data. The moss and type population has completely identical 18S rRNA (nuclear small subunit ribosomal RNA) gene sequences and both are highly similar in morphological and morphometric attributes, except for the diameter and arrangement of the cortical granules. Thus, we reexamined the type materials(i.e., micrographs and gDNA) and resulted in finding mistakes made by the authors of the species. Based on these data and supporting materials newly obtained (i.e., internal transcribed spacer [ITS] 1, ITS2, 5.8S, and partial 28S rDNA sequences, and scanning electron micrographs), we provide improved diagnosis of the species to clarify its identity. In addition, a key for Notohymena species is provided.

• The Plant Pathology Journal
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• v.22 no.1
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• pp.36-45
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• 2006

Twenty isolates of Didymella bryoniae were isolated from infected cucurbit plants in various growing areas of southern Korea in 2001 and 2002. Random Amplified Polymorphic DNA (RAPD) group [RG] I of D. bryoniae was more virulent than RG IV to watermelon. Virulence of the RG I isolate was strong to moderate to cucumber, whereas that of the RG IV varied from strong, moderate to weak. Two hundred seventy-three amplified fragments were produced with 40 primers, and were analyzed by a cluster analysis using UPGMA method with an arithmetic average program of NTSYSPC. At the distance level of 0.7, two major genomic DNA RAPD groups were differentiated among 20 isolates. The RG I included 7 isolates from watermelon and one isolate from melon, whereas the RG IV included 12 isolates from squash, cucumber, watermelon and melon. Amplification of internal transcribed spacer (ITS) region and small subunit rRNA region from the 20 isolates yielded respectively a single fragment. Restriction pattern with 12 restriction enzymes was identical for all isolates tested, suggesting that variation in the ITS and small subunit within the D. bryoniae were low. Amplification of the genomic DNAs of the tested isolates with the sequence characterized amplified regions (SCAR) primer RG IF-RG IR specific for RG I group resulted in a single band of 650bp fragment for 8 isolates out of the 20 isolates. Therefore, these 8 isolates could be assigned into RG I. The same experiments done with RG IIF-RG IIR resulted in no amplified PCR product for the 20 isolates tested. An about 1.4 kb-fragment amplified from the RG IV isolates was specifically hybridized with PCR fragments amplified from genomic DNAs of the RG IV isolates only, suggesting that this PCR product could be used for discriminating the RG IV isolates from the RG I isolates as well other fungal species.

• Parasites, Hosts and Diseases
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• v.58 no.1
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• pp.73-79
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• 2020

Echinostoma revolutum is a zoonotic food-borne intestinal trematode that can cause intestinal bleeding, enteritis, and diarrhea in human and birds. To identify a suspected E. revolutum trematode from a red-crowned crane (Grus japonensis) and to reveal the genetic characteristics of its mitochondrial (mt) genome, the internal transcribed spacer (ITS) and complete mt genome sequence of this trematode were amplified. The results identified the trematode as E. revolutum. Its entire mt genome sequence was 15,714 bp in length, including 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one non-coding region (NCR), with 61.73% A+T base content and a significant AT preference. The length of the 22 tRNA genes ranged from 59 bp to 70 bp, and their secondary structure showed the typical cloverleaf and D-loop structure. The length of the large subunit of rRNA (rrnL) and the small subunit of rRNA (rrnS) gene was 1,011 bp and 742 bp, respectively. Phylogenetic trees showed that E. revolutum and E. miyagawai clustered together, belonging to Echinostomatidae with Hypoderaeum conoideum. This study may enrich the mitochondrial gene database of Echinostoma trematodes and provide valuable data for studying the molecular identification and phylogeny of some digenean trematodes.

• Journal of Microbiology and Biotechnology
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• v.14 no.5
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• pp.959-966
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• 2004

Twenty-three cultures of harmful algal bloom (HAB)-(causing dinoflagellates were isolated from the coastal waters of Korea. For each of the 14 morphospecies, the nuclearencoded small subunit (SSU) rDNA was analyzed to determine the phylogenetic relatedness of the species. Despite temporal and spatial isolation, 3-4 clonal cultures of Alexandrium catenella, Cochlodinium polykrikoides, and Gymnodinium catenatum had 100% identical SSU rDNA sequences. In contrast, heterogeneities in the SSU rDNA sequences were observed in Akashiwo sanguinea and Lingulodinium polyedrum strains. Extreme sequence polymorphism was shown within the SSU rRNA genes of an Al. tamarense clonal culture. A homology search in GenBank revealed that 11 dinoflagellate species were located in clusters corresponding to their morphological classification. The SSU rDNA sequences of C. polykrikoides, Gyrodinium instriatum, and Pheopolykrikos hartmannii, which were determined for the first time in this study, showed the following phylogenetic relationships: C. polykrikoides formed an independent branch separated from other dinoflagellates; Gyr. instriatum was placed in a monophyletic group with Gyr. dorsum and Gyr. uncatenum; and Ph. hartmanii, which forms a distinct two-celled pseudocolony, belonged to Gymnodinium sensu Hansen and Moestrup.

• Research in Plant Disease
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• v.21 no.4
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• pp.330-333
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• 2015

In June 2013, we collected leaf spot disease samples of Datura metel from Gangneung, Gangwon Province, Korea. The symptoms observed were small circular to oval dark brown spots with irregular in shape or remained circular with concentric rings. We isolated the pathogen from infected leaves and cultured the fungus on potato dextrose agar. We examined the fungus morphologically and confirmed its pathogenicity according to Koch's postulates. The results of morphological examinations, pathogenicity tests, and the rDNA sequences of the internal transcribed spacer regions (ITS1 and ITS4), glycerol-3-phosphate dehydrogenase (G3PDH) and the RNA polymerase II second largest subunit (RPB2) gene sequence revealed that the causal agent was Alternaria tenuissima. To the best of our knowledge, this is the first report of leaf spot of D. metel caused by A. tenuissima in Korea as well as worldwide.

• Mycobiology
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• v.30 no.1
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• pp.13-17
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• 2002

The genomic DNAs were extracted from roots of Glycine max and Sorghum bicolor, and compared with those from spores of two arbuscular mycorrhizal(AM) fungi, Glomus mosseae and Scutellospora heterogama. The partial small subunit(SSU) of ribosomal RNA genes were synthesized and amplified by polymerase chain reaction with the fungal specific primers, AM1 and NS31. By the recent molecular techniques, the presence of another AM fungal DNA were confirmed in the roots of two plants, and three sequences of rDNA fragments amplified were identified to be close to those of G. caledonium, G. fasiculatum and G. proliferum. The two AM fungi, both, were found to colonize at the cortical layers of plant roots collected in the fields, together.

• Journal of Environmental Health Sciences
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• v.35 no.3
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• pp.187-190
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• 2009

Cryptosporidium spp. were detected in 17 of 135 swine lagoon samples from five farms by 18S ribosomal DNA locus and PCR. Seventeen positive samples identified were included two distinctive genotypes C. suis and Cryptosporidium sp. based on a small-subunit rRNA gene-based PCR-restriction fragment length polymorphism analysis. Cryptosporidium spp. were detected out of farrowing, farrowing and nursery (mix), and finishing. Prevalence rate was 12.6% with infection rates between 3.7 and 18.5%. We concluded that Cryptosporidium oocysts can persist in treated lagoon and potentially contaminate surface water through improper discharge. This study was undertaken for the evaluation of the infection status of the genotypes of Cryptosporidium spp. in swine lagoon.

• Animal Systematics, Evolution and Diversity
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• v.27 no.2
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• pp.115-122
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• 2011

The morphology of the two marine hypotrichous ciliates Apokeronopsis bergeri and A. ovalis, isolated from the Yellow Sea, Korea, are described based on live and protargol-impregnated specimens. It is the first time that these species have been recorded in Korea. In addition, the small subunit ribosomal RNA gene was sequenced for comparison with the public database. The genus Apokeronopsis has recently been established in the family Pseudokeronopsidae, and the two congeners of the Korean population share the following characteristics: one row of one or more buccal cirri; usually two frontoterminal cirri; midventral complex composed of two distinctly separated rows; one left and one right marginal row; number of transverse cirri, more than eight; absence of caudal cirri; two types of cortical granules. Apokeronopsis bergeri differs from A. ovalis primarily in body shape (fusiform vs. oval form), size (usually $260{\times}80{\mu}m$ vs. $160{\times}55{\mu}m$), type II cortical granules (oval vs. round shape; yellow-green vs. mostly colourless and only a few yellow-green in colour), and morphometric data (75-106 vs. 53-70 in adoral membranelles; 37-47 vs. 24-36 in frontal cirri; 9-15 vs. 1-2 in buccal cirri), as well as molecular data (2.87% of pairwise distance).