• Journal of Microbiology and Biotechnology
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• v.23 no.8
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• pp.1154-1158
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• 2013

Ganciclovir resistance of human cytomegalovirus is associated with mutations in the viral UL97 gene and poses severe problems for immunocompromised patients. In this study, PCR-based restriction fragment length polymorphism and sequencing analyses detected the UL97 D605E mutation in all five clinical isolates from patients with ganciclovir-resistant human cytomegalovirus infection during prolonged ganciclovir therapy, whereas the M460V mutation was only present in 1 of 5 isolates. On the other hand, the detection rates of the D605E mutation in the stored available DNA samples from the donor and allogeneic stem cell transplantation recipients were 66.7% and 93.7%, respectively, suggesting that the presence of D605E mutation was not associated with the ganciclovir exposure. Although the D605E mutation may not be related to ganciclovir resistance, we suggest that this mutation could be an important molecular marker of human cytomegalovirus evolution in East Asian countries. Moreover, the restriction fragment length polymorphism method using the restriction enzyme HaeIII, which is generally used to detect the UL97 A591V mutation, could also detect the D605E mutation and may therefore be a useful tool for future research on the investigation of UL97 gene mutations.

• The KIPS Transactions:PartA
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• v.16A no.3
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• pp.143-152
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• 2009

One of the main issues in comparative genomics is to study chromosomal gene order in one or more related species. For this purpose, the whole genome alignment is usually applied to find the horizontal gene transfer, gene duplication, and gene loss between two related genomes. Also it is well known that the novel visualization tool with whole genome alignment is greatly useful for us to understand genome organization and evolution process. There are a lot of algorithms and visualization tools already proposed to find the "gene clusters" on genome alignments. But due to the huge size of whole genome, the previous visualization tools are not convenient to discover the relationship between two genomes. In this paper, we propose AlignScope, a novel visualization system for whole genome alignment, especially useful to find gene clusters between two aligned genomes. This AlignScope not only provides the simplified structure of genome alignment at any simplified level, but also helps us to find gene clusters. In experiment, we show the performance of AlignScope with several microbial genomes such as B. subtilis, B.halodurans, E. coli K12, and M. tuberculosis H37Rv, which have more than 5000 alignment pairs (matched DNA subsequence).

• Animal Systematics, Evolution and Diversity
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• v.28 no.3
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• pp.215-219
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• 2012

To examine genetic divergences of two endemic Sorex caecutiens subspecies from Korea (S. c. hallamontanus in Korean Jeju Island and S. c. annexus in the mainland Korean Peninsula), we obtained partial cytochrome oxidase I (COI) sequences (429 bp) and complete cytochrome b sequences (1,140 bp) from the two Korean subspecies, and we compared these sequences to the corresponding sequences of S. caecutiens, obtained from GenBank. We found that Jeju S. c. hallamontanus is one of three clades within S. caecutiens, with an average Jukes-Cantor distance of 1.57% in the COI sequences and the distance of 2.07% and 11 fixed site differences in the cytochrome b sequences, indicating that Jeju S. c. hallamontanus is one endemic subspecies with concordant genetic distinctness, although further analyses with nuclear DNA sequences are necessary to confirm these findings. However, S. c. annexus from the mainland Korean Peninsula was not divergent from S. c. macropygmaeus from northeastern China and adjacent Russia, indicating that S. c. annexus from the mainland Korean Peninsula is another endemic subspecies with only morphological differences, although it is necessary to reexamine the subspecies status of S. c. annexus.

• Animal Systematics, Evolution and Diversity
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• v.26 no.1
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• pp.15-19
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• 2010

The Russian ratsnake, Elaphe schrenckii, is found in Russia, China, and Korea, and is considered to be an endangered species by the Ministry of Environment in South Korea. Due to habitat loss and use in oriental medicine, their population has been severely decimated. In South Korea, two subspecies of E. schrenckii has been defined according to body color: E. s. schrenckii (blackish) and E. s. anomala (yellow-brownish). Molecular genetic studies on Elaphe schrenckii are very scarce and the taxonomy of Elaphe schrenckii subspecies is uncertain. From the present study, we attempted to identify the genetic differences of these two subspecies using species-specific microsatellites developed from the genomic library of E. schrenckii. Nine polymorphic loci were tested on 19 individuals from E. s. schrenckii (n=10) and E. s. anomala (n=9) in South Korea. The mean number of alleles was 3.78 in E. s. schrenckii and 4.11 in E. s. anomala. The average expected heterozygosity was 0.542 and 0.511 in E. s. schrenckii and E. s. anomala, respectively. We found a lack of genetic structure between two subspecies ($F_{ST}=0.016$) and no genetic discrimination between two subspecies was found. Based on the present findings by microsatellites, two subspecies can be considered as one species, E. schrenckii. However, further investigations on taxonomical status using mitochondrial and nuclear DNA sequences need to be performed and morphological & ecological data should be revised. The genetic markers should benefit future studies of the endangered species of other Elaphe species for the study of genetic diversity and potential conservation management.

• Animal Systematics, Evolution and Diversity
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• v.32 no.4
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• pp.272-280
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• 2016

Most scyphomedusae jellyfishes recorded in Korean waters are temperate and subtropical species. In the present study, two cold-water jellyfishes from Korean waters are first described. Scyphomedusae were collected from the coasts of Gangneung and Ulsan of the East Sea, and Boryeong, and the eastern area of the Yellow Sea from June 2006 to May 2015. Scyphomedusae collected in Ulsan and Gangneung were identified morphologically as Aurelia limbata Brandt, 1835. Their umbrella was 250-500 mm in width and 30-50 mm in height; the exumbrella was white and the subumbrella was dark brown in color. The vascular system was complex with anastomosed branches. Individuals of this species lived at about 6.6-9.9℃ and 30-50 m depth in Korean waters. Scyphomedusae collected from the center of the Yellow Sea and from Boryeong were identified as Parumbrosa polylobata Kishinouye, 1910. Their umbrella was disc-shaped, 80-200 mm in width and 20-40 mm in height. Its milky white gonads could be seen through the transparent exumbrella. The stomach cavity was round and flat with four interradial cavities connected by subgenital cavities, and the four oral arms were bifurcated and spear-head shaped. Individuals were found at about 6.4-10.0℃ and 40-90 m depth in Korean waters. The identities of both species were confirmed by molecular analysis using nuclear ribosomal DNA sequences.

• Korean Journal of Ichthyology
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• v.23 no.3
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• pp.217-224
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• 2011

The seven leptocephali (14.6~68.0 mm in total length) of the family Ophichthidae, from the East Sea of Korea, were identified using 12S rRNA 861-bp sequences and their morphological development were described. Our seven leptocephali were identified to Echelus uropterus based on genetic distance (d=0.000) being well consistent with that of adult E. uropterus. Our seven leptocephali of E. uropterus are characterized by morphological combinations: caudal fin present; the melanophores present in series of nine gut swellings; total myomeres 154~158; body depth in total length less than 10%; eight black horizontal bands present from anus to caudal fin base. Our morphological and molecular results suggest that E. uropterus may be an intermediate group between subfamily Ophichthinae and Myrophinae.

• Animal Systematics, Evolution and Diversity
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• v.27 no.1
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• pp.1-17
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• 2011

Thais Roding, 1798, commonly known as rock-shell, is among the most frequently found gastropod genera worldwide on intertidal rocky shores including those of Japan, China, Taiwan and Korea. This group contains important species in many marine environmental studies but species-level taxonomy of the group is quite complicated due to the morphological variations in shell characters. This study examined the genetic variations and relationships among three Korean Thais species based on the partial nucleotide sequences of mitochondrial cox1 gene fragments. Phylogenetic trees from different analytic methods (maximum parsimony, neighbor-joining, and maximum likelihood) showed that T. bronni and T. luteostoma are closely related, indicating the most recent common ancestry. The low sequence divergence found between T. luteostoma and T. bronni, ranging from 1.53% to 3.19%, also corroborates this idea. Further molecular survey using different molecular marker is required to fully understand a detailed picture of the origin for their low level of interspecific sequence divergence. Sequence comparisons among conspecific individuals revealed extensive sequence variations within the three species with maximum values of 2.43% in T. clavigera and 1.37% in both T. bronni and T. luteostoma. In addition, there is an unexpectedly high level of mitochondrial genotypic diversity within each of the three Korean Thais species. The high genetic diversity revealed in Korean Thais species is likely to reflect genetic diversity introduced from potential source populations with diverse geographic origins, such as Taiwan, Hong Kong, and a variety of different coastal regions in South China and Japan. Additional sequence analysis with comprehensive taxon sampling from unstudied potential source populations will be also needed to address the origin and key factors for the high level of genetic diversity discovered within the three Korean Thais species studied.

• Genomics & Informatics
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• v.4 no.4
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• pp.147-160
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• 2006

GATA transcription factors are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif in the form $CX_{2}CX_{17-20}CX_{2}C$followed by a basic region. In fungi, they act as transcriptional activators or repressors in several different processes, ranging from nitrogen source utilization to mating-type switching. Using an in-house bioinformatics portal system, we surveyed 50 fungal and 9 out-group genomes and identified 396 putative fungal GATA transcription factors. The proportion of GATA transcription factors within a genome varied among taxonomic lineages. Subsequent analyses of phylogenetic relationships among the fungal GATA transcription factors, as well as a study of their domain architecture and gene structure, demonstrated high degrees of conservation in type IVa and type IVb zinc finger motifs and the existence of distinctive clusters at least at the level of subphylum. The SFH1 subgroup with a 20-residue loop was newly identified, in addition to six well-defined subgroups in the subphylum Pezizomycotina. Furthermore, a novel GATA motif with a 2f-residue loop ($CX_{2}CX_{21}CX_{2}C$, designated 'zinc finger type IVc') was discovered within the phylum Basidiomycota. Our results suggest that fungal GATA factors might have undergone multiple distinct modes of evolution resulting in diversified cellular modulation in fungi.

• Development and Reproduction
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• v.23 no.4
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• pp.333-344
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• 2019

In vertebrate reproductive system, estrogen receptor (ER) plays a pivotal role in mediation of estrogenic signaling pathways. In the present study, we report the cDNA cloning, expression analysis, and transcriptional activity of ERβ1 subtype from medaka Oryzias dancena. The deduced O. dancena ERβ1 (odERβ1; 519 amino acids) contained six characteristic A/B to E/F domains with very short activation function 2 region (called AF2). A phylogenetic analysis indicated that odERβ1 was highly conserved among teleost ERβ1 subgroup. A conventional RT-PCR revealed that the odERβ1 transcripts were widely distributed in the multiple tissues, the ovary, brain, gill, intestine, kidney, and muscle. Further, the relatively higher odERβ1 expressions in the ovary and brain were clearly reproduced in RT-qPCR assay. When HA-fused odERβ1 expression vector was transfected into HEK293 cells, an immunoreactivity for odERβ1 was mainly detected in the nucleus part. Finally, an estrogen responsive element driven luciferase reporter assays demonstrated that the transcriptional activity of odERβ1 significantly increased by estradiol-17β (E2) in a dose dependent manner (p<0.05). However, fold-activation of odERβ1 in the presence of E2 was markedly weak, when it compared with those of O. latipes ERβ1. Taken together, these data suggest that odERβ1 represents a functional variant of teleost ERβ subtype and provides a basic tool allowing future studies examining the function of F domain of ERβ1 subtype and expanding our knowledge of ERβ evolution.

• The Plant Pathology Journal
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• v.28 no.2
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• pp.123-136
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• 2012

Diseases caused by begomoviruses (family Geminiviridae, genus Begomovirus) constitute a serious constraint to tropical and sub-tropical agro-ecosystems worldwide. In recent years, they have also introduced in temperate regions of the world where they have great impact and are posing a serious threat to a variety of greenhouse crops. Begomoviral diseases can in extreme cases reduce yields to zero leading to catastrophic losses in agriculture. They are still evolving and pose a serious threat to sustainable agriculture across the world, particularly in tropics and sub-tropics. Till recently, there have been no records on the occurrence of begomoviral disease in South Korea, however, the etiology of other plant viral diseases are known since last century. The first begomovirus infected sample was collected from sweet potato plant in 2003 and since then there has been gradual increase in the begomoviral epidemics specially in tomato and sweet potato crops. So far, 48 begomovirus sequences originating from various plant species have been submitted in public sequence data base from different parts of the country. The rapid emergence of begomoviral epidemics might be with some of the factors like evolution of new variants of the viruses, appearance of efficient vectors, changing cropping systems, introduction of susceptible plant varieties, increase in global trade in agricultural products, intercontinental transportation networks, and changes in global climatic conditions. Another concern might be the emergence of a begomovirus complex and satellite DNA molecules. Thorough understanding of the pathosystems is needed for the designing of effective managements. Efforts should also be made towards the integration of the resistant genes for the development of transgenic plants specially tomato and sweet potato as they have been found to be widely infected in South Korea. There should be efficient surveillance for emergence or incursions of other begomoviruses and biotypes of whitefly. This review discusses the general characteristics of begomoviruses, transmission by their vector B. tabaci with an especial emphasis on the occurrence and distribution of begomoviruses in South Korea, and control measures that must be addressed in order to develop more sustainable management strategies.