• 한국수산과학회지
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• 제50권5호
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• pp.624-629
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• 2017

A rainbow trout Onchorhynchus mykiss farm located in Gangwon province, South Korea, experienced approximately 10% mortality in June 2017. Most diseased fish had a markedly distended, gas-filled stomach, and exhibited abnormal behavior at the water surface. In this study, we attempted to identify the cause of stomach distension syndrome in those rainbow trout. The stomach of most of the affected fish were full of unidentified gases and some exudate, and yeast was isolated from the stomach mucosa. Pure cultures of yeast were identified using a multilocus sequence typing scheme based on 18S rRNA, internal transcribed spacers, large subunit rRNA, and the gene encoding the largest subunit of RNA polymerase II (RPB1). The RPB1 gene sequences were compared with those of related species available in a database. The yeast was identified as Scheffersomyces coipomoensis (Candida coipomoensis) based on sequence analyses. This is the first study to reveal that Sch. coipomoensis is a potential causative agent of stomach distension syndrome in farmed rainbow trout. Our results will be helpful for future related studies, and indicate that farmers and stakeholders should observe this emerging disease closely.

• Journal of Computing Science and Engineering
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• 제11권4호
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• pp.111-120
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• 2017

Post-translational modifications (PTMs) of proteins play substantial roles in the gene regulation of cell physiological functions and in the generation of major diseases. However, the majority of existing studies only explored a certain PTM of proteins, while very few have investigated the PTMs of two or more domains and the effects of their interactions. In this study, after collecting data regarding a large number of breast cancer-related and validated PTMs, a sequence and domain analysis of breast cancer proteins was carried out using bioinformatics methods. Then, protein-protein interaction network-related tools were applied in order to determine the crosstalks between the PTMs of the proteins. Finally, statistical and functional analyses were conducted to identify more modification sites of domains and proteins that may interact with at least two or more PTMs. In addition to exploring the associations between the interactive effects of PTMs, the present study also provides important information that would allow biologists to further explore the regulatory pathways of biological functions and related diseases.

• Fisheries and Aquatic Sciences
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• 제7권3호
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• pp.122-129
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• 2004

Harmful Cochlodinium polykrikoides is a notorious harmful algal bloom (HAB) species that is causing mass mortality of farmed fish along the Korean coast with increasing frequency. We analyzed the sequence of the large subunit (LSD) rDNA D1-D3 region of C. polykrikoides and conducted phylogenetic analyses using Bayesian inference of phylogeny and the maximum likelihood method. The molecular phylogeny showed that C. polykrikoides had the genetic relationship to Amphidinium and Gymnodinium species supported only by the relatively high posterior probabilities of Bayesian inference. Based on the LSU rDNA sequence data of diverse dinoflagellate taxa, we designed the C. polykrikoides-specific PCR primer set, CPOLY01 and CPOLY02 and developed PCR detection assays for its sensitive, accurate HAB monitoring. CPOLY01 and CPOLY02 specifically amplified C. polykrikoides and did not cross-react with any dinoflagellates tested in this study or environmental water samples. The effective annealing temperature $(T_{p})$ of CPOLY01 and CPOLY02 was $67^{\circ}C$. At this temperature, the conventional and nested PCR assays were sensitive over a wide range of C. polykrikoides cell numbers with detection limits of 0.05 and 0.0001 cells/reaction, respectively.

• Fisheries and Aquatic Sciences
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• 제11권1호
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• pp.36-40
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• 2008

We analyzed the nucleotide sequences of about 500 bp of the mitochondrial NADH dehydrogenase subunit 3 (ND3) gene to estimate the genetic variation of Korean masu salmon (Oncorhynchus masou) populations. DNA samples were collected from 104 river-only specimens and 52 anadromous specimens from three hatcheries and one river. There are no records of artificial release into the river. We amplified the ND3 gene by polymerase chain reaction, targeting areas that included parts of the cytochrome oxidase III gene and the NADH dehydrogenase subunit 4L gene, and defined 14 haplotypes based on 12 variable nucleotide sites in the examined region. Among the haplotypes, ten were specific to river-only specimens within hatchery populations. Haplotype diversity of river-only populations in hatcheries was higher than that of anadromous and wild populations. Pairwise population $F_{ST}$ estimates and neighbor-joining tree analyses inferred that anadromous and river-only populations were distinct. These results suggest that sequence polymorphism in the ND3 region may be a useful marker for analyzing the genetic variation and population structure of masu salmon.

• BMB Reports
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• 제29권1호
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• pp.52-57
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• 1996

A specific DNA fragment from Korean radish (Raphanus sativus L.) was amplified by performing PCR with oligonucleotide primers which correspond to the highly conserved regions of plant peroxidases. The size of the PCR product was ca. 400 bp, as expected from the known plant peroxidase genes. Comparison of the nucleotide and deduced amino acid sequences of the PCR product to those of other plant peroxidase-encoding genes revealed that the amplified fragment corresponded to the highly conserved region I and III of plant peroxidases. By screening a genomic library of Korean radish using the amplified fragment as a probe, two positive clones, named prxK1 and prxK2, were isolated. Restriction mapping studies indicated that the 5.2 kb Sail fragment of the prxK1 clone and the 4.0 kb EcoRI fragment of the prxK2 clone encode separate isoperoxidase genes. Analyses of the promoter region of the prxK1 clone shows that putative CAAT box, CMT box, and TGA1b binding sequence (5' TGACGT) are present 718 bp upstream from the start codon.

• Parasites, Hosts and Diseases
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• 제43권3호
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• pp.101-110
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• 2005

In this study, the trypsin gene (bgtryp-1) from the German cockroach, Blattella germanica, was cloned via the immunoscreening of patients with allergies to cockroaches. Nucleotide sequence analysis predicted an 863 bp open reading frame which encodes for 257 amino acids. The deduced amino acid sequence exhibited $42-57\%$ homology with the serine protease from dust mites, and consisted of a conserved catalytic domain (GOSGGPLV). bgtryp-1 was determined by both Northern and Southern analysis to be a 0.9 kb, single-copy gene. SDS-PAGE and Western blotting analyses of the recombinant protein (Bgtryp-1) over-expressed in Escherichia coli revealed that the molecular mass of the expressed protein was 35 kDa, and the expressed protein was capable of reacting with the sera of cock-roach allergy patients. We also discussed the possibility that trypsin excreted by the digestive system of the German cockroach not only functions as an allergen, but also may perform a vital role in the activation of PAR-2.

• ALGAE
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• 제31권4호
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• pp.303-315
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• 2016

Compsopogon specimens collected in China were examined based on morphology and DNA sequences. Five molecular markers from different genome compartments including rbcL, COI, 18S rDNA, psbA, and UPA were identified and used to construct a phylogenetic relationship. Phylogenetic analyses indicated that two different morphological types from China clustered into an independent clade with Compsopogon specimens when compared to other global samples. The Compsopogon clade exhibited robust support values, revealing the affiliation of the samples to Compsopogon caeruleus. Although the samples were distributed in a close geographical area, unexpected sequence divergences between the Chinese samples implied that they were introduced by different dispersal events and from varied origins. It was speculated that Compsopogon originated in North America, a portion of the Laurentia landmass situated in the Rodinia supercontinent at approximately 573.89-1,701.50 million years ago during the Proterozoic era.Although Compsopogonhad evolved for a rather long time, genetic conservation had limited its variability and rate of evolution, resulting in the current monospecific global distribution. Additional global specimens and sequence information were required to increase our understanding of the evolutionary history of this ancient red algal lineage.

• The Plant Pathology Journal
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• 제23권3호
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• pp.187-192
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• 2007

The anthracnose disease on pepper fruits in Korea was caused by Colletotrichum acutatum as well as C. gloeosporioides. Since C. acutatum showed less sensitivity to benomyl, it was analyzed whether the less sensitivity was given by the same mechanism for the fungicide resistance of C. gloeosporioides. The isolates of C. acutatum were less sensitive to the three benzimidazole fungicides tested, benomyl, carbendazim, and thiophanate-methyl. However, the of C. acutatum isolates were different from the resistant isolates of C. gloeosporioides in their response to diethofencarb, one of N-phenyl-carbamates; the former was still less sensitive to diethofencarb than the latter. The differences in the resistance mechanisms in two species were conspicuous in sequence analysis of the tub2 genes. The genes from C. acutatum did not show any non-synonymous base substitutions at the regions known to be correlated with the benzimidazole-resistance. All of these data may indicate that the less sensitivity of C. acutatum to benomyl is based on different mechanism(s) from that of C. gloeosporioides.

• 식물병연구
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• 제19권1호
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• pp.49-54
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• 2013

Sclerotinia white rot disease was observed on 5 and 6-year-old ginseng (Panax ginseng) roots in Hongchun, Cheorwon, and Yanggu, Gangwon Province, Korea from 2006 to 2010. Symptoms included a brownish watery soft rot of the roots, and black sclerotia were often found on the rotten roots. The causal agent of the disease was identified as Sclerotinia nivalis based on cultural characteristics and sequence analyses of the internal transcribed spacer region of rDNA and ${\beta}$-tubulin gene with 100% sequence similarity. Pathogenicity tests were performed on 2-year-old ginseng roots with mycelium plugs without wounds. A watery soft rot of the roots and black sclerotia were observed 10 days after inoculation. These symptoms were identical to those observed on naturally infected roots. The same fungus was re-isolated from the lesions induced by artificial inoculation. This is the first report of sclerotinia white rot caused by S. nivalis on P. ginseng in Korea.

• Parasites, Hosts and Diseases
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• 제43권1호
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• pp.7-13
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• 2005

The taxonomy of Acanthamoeba spp., an amphizoic amoeba which causes granulomatous amoebic encephalitis and chronic amoebic keratitis, has been revised many times. The taxonomic validity of some species has yet to be assessed. In this paper, we analyzed the morphological characteristics, nuclear 18s rDNA and mitochondrial 16s rDNA sequences and the Mt DNA RFLP of the type strains of four Acanthamoeba species, which had been previously designated as A. divionensis, A. parasidionensis, A. mauritaniensis, and A. rhysodes. The four isolates revealed characteristic group II morphology. They exhibited 18S rDNA sequence differences of $0.2-1.1\%$ with each other, but more than $2\%$ difference from the other compared reference strains. Four isolates formed a different clade from that of A. castellanii Castellani and the other strains in morphological group lion the phylogenetic tree. In light of these results, A. paradivionensis, A. divionensis, and A. mauritaniensis should be regarded as synonyms for A. rhysodes.