• Horticultural Science & Technology
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• v.35 no.3
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• pp.333-343
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• 2017

Bloomless cucumber fruits are commercially produced by grafting onto the pumpkin stocks (Cucurbita moschata) to restricted silicon ($SiO_2$) absorption. Inhibition of silicon absorption in bloomless stocks is conferred by a mutant allele of the CmLsi1 homologous to Lsi1 in rice. In this study, we characterized the Lsi1 homologs in pumpkin (C. moschata) and its cold-tolerant wild relative C. ficifolia ('Heukjong') in order to develop a DNA marker for selecting a bloomless trait and to establish the molecular basis for breeding bloomless stock cultivars of C. ficifolia. A Cleaved amplified polymorphic sequence (CAPS) marker (CM1-CAPS) was designed based on a non-sysnonymous single nucleotide polymorphism (SNP, C>T) of the CmLsi1 mutant-type allele, and its applicability for Marker-assisted selection (MAS) was confirmed by evaluating three bloom and five bloomless pumpkin stock cultivars. Quantitative RT-PCR of the CmLsi1 for these stock cultivers implied that expression level of the CmLsi1 gene does not appear to be associated with the bloom/bloomless trait and may differ depending on plant species and tissues. A full length cDNA of the Lsi1 homolog [named CfLsi1($B^+$)] of 'Heukjong' (C. ficifolia), was cloned and sequence comparison between CmLsi1($B^+$) and CfLsi1($B^+$) revealed that there exists total 24 SNPs, of which three were non-synonymous. Phylogenetic analysis of CfLsi1($B^+$) and Lsi1 homologs further revealed that CfLsi1($B^+$) is closesly related to Nodulin 26-like intrinsic proteins (NIPs) and most similar to CpNIP1 of C. pepo than C. moschata.

• Journal of Life Science
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• v.21 no.6
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• pp.819-828
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• 2011

To inspect norovirus contamination of groundwater in south eastern areas of Korea, a systematic survey of groundwater in Busan, Ulsan, and Gyeongsangnam-do was performed for two years from 2009 to 2010. For this purpose, we first optimized the nested reverse transcription-PCR condition by designing two sets of primers for the detection of norovirus genogroups, GI and GII. Of 145 samples, 21 (25.9%) and 15 (23.4%) were norovirus positive in the dry season (April to June) and wet season (July to August), respectively. The detection frequencies of norovirus in Busan, Ulsan, and Gyeongsangnam-do were 15%, 7%, and 32%, respectively, reflecting a geographical difference in their distribution. The GI and GII isolates were 5 and 31, respectively, indicating the prevalence of GII in the tested areas. According to phylogenetic analysis of their nucleotide sequences, all of the GI isolates were identified to genotype GI.5 whilst the GII isolates were divided into two genotypes, GII.3 and GII.4. Neither physical-chemical parameters such as pH, temperature, oxidation-reduction potential, and dissolved oxygen, nor microbial indicators of water quality such as total bacteria, total coliforms, and Escherichia coli were statistically correlated with contamination of norovirus in the groundwater. Interestingly, however, the presence of norovirus was closely correlated with low turbidity (<0.50 NTU). The present study suggests that periodical monitoring of norovirus in groundwater is necessary to prevent epidemic waterborne diseases and to secure better sanitary conditions for public health.

• Journal of Life Science
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• v.19 no.6
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• pp.711-719
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• 2009

We determined a portion of mitochondrial 16S rRNA gene sequences (416 bp) to investigate the genetic structure of the octopus (Octopus minor Ssaki) population in Korea and China. Samples were obtained from Korea (Yeosu, Namhae, Jindo, Muan, Geomundo and Seosan) and China (Sandong) during the period of August 2006 to September 2007. Sequence analyses of 28 individual specimens collected from 7 localities revealed 11 haplotypes, ranging in a sequence divergence of 0.2% - 1.2%. Phylogenetic analyses using PHYLIP and networks subdivided the octopus into two clades (termed clade A and B) and the nucleotide divergence between them was 0.4%. This haplotype subdivision was in accordance with geographic separation: one at Yeosu, Namhae, Muan and Jindo, and the other at Seosan, Geomundo and Sandong. On the basis of hierarchial genetic analysis, genetic distance between localities in Korea and China were also found, but a significant population differentiation was not shown in this study (p>0.05). Consequently, most of the octopus populations in Korea had considerable distribution due to the mitochondrial gene flow that resulted in a formation of a genetically homogenous structure, whereas some of the Korean and Chinese populations had different genetic structures. Gene flow among populations may be restricted due to impassable geographic barriers that promote genetic differentiation.

• Journal of Life Science
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• v.16 no.5
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• pp.812-827
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• 2006

To investigate the population structure and geographic distance among anchovies (Engraulis japonicus) in Korea, we compared and analyzed the mitochondrial DNA control region sequences (227 bp) of anchovies from 12 localities in inshore and offshore waters. The sequence analysis of 84 individuals showed 29 haplotypes, ranging in sequence divergence by pairwise comparisons from 0.3% to 3.5% (1 bp-12 bp). E9 haplotype of anchovies were found largely in inshore waters and also in offshore waters, which was regarded as the major source in Korean waters (58.3%). However, E26, E27, E28, and E29 haplotypes were found in westsouthern (locality 10, four among 7). Phylogenetic analysis using PHYLIP was divided into two clades (clade A and B). Most of the haplotypes, excluding E26, E27, E28, and E29, were strongly supported by bootstrap analysis (>75%), whereas the relationship between clade A and B was weakly supported by bootstrap analysis (51%). High levels of genetic diversity were found; haplotype diversity (H)=0.75-1.00, and nucleotide diversity $({\pi})=0.015-0.0244$. Analysis of $F_{ST}$ between populations in inshore waters ranged in 0.01-0.05, whereas those of offshore waters ranged in 0.01-0.58. A high gene flow occurred in inshore (Nm=22.61-34.22) and offshore (Nm=11.57-45.67) populations. The distribution of mitochondrial DNA haplotypes between westsouthern and other populations was suggestive of significantly different differentiation ($F_{ST}$=0.20-0.59, p<0.05; d=0.52, p=0.00; ${\phi}=0.02-0.41$, p＜0.05). These results suggested that the overall anchovy population in the Korean peninsula caused considerable migration due to the mitochondrial gene flow between inshore and offshore populations to form a genetically homogenous and panmictic structure, although a heterogeneous population was found in this study.

• Research in Plant Disease
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• v.21 no.3
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• pp.235-242
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• 2015

A 2014 nationwide survey in radish fields investigated the distribution of common viruses and possible emerging viruses. Radish leaves with virus-like symptoms were collected and 108 samples assayed by RT-PCR using specific primers for Radish mosaic virus (RaMV), Cucumber mosaic virus (CMV), and Turnip mosaic virus (TuMV); 47 samples were TuMV positive, and RaMV and CMV were detected in 3 and 2 samples, respectively. No samples showed double infection of TuMV/RaMV, or RaMV/CMV, but two double infections of TuMV/CMV were detected. TuMV isolates were sorted by symptom severity, and three isolates (R007-mild; R041 and R065-severe) selected for BLAST and phylogenetic analysis, which indicated that the coat protein (CP) of these isolates (R007, R041, and R065) have approx. 98-99% homology to a previously reported TuMV isolate. RaMV CP showed approx. 99% homology to a previously reported isolate, and the CMV CP is identical to a previously reported Korean isolate (GenBank : GU327368). Three isolates of TuMV showing different pathogenicity (degree of symptom severity) will be valuable to study determinants of pathogenicity.

• Parasites, Hosts and Diseases
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• v.56 no.3
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• pp.275-280
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• 2018

In the present study, we identified a Spirometra species of Myanmar origin (plerocercoid) by molecular analysis using mitochondrial cox1 and nad1 genes, as well as by morphological observations of an adult tapeworm. Spargana specimens were collected from a paddy-field in Taik Kyi Township Tarkwa Village, Yangon, Myanmar in December 2017. A total of 5 spargana were obtained from 20 frogs Hoplobatrachus rugulosus; syn: Rana rugulosa (Wiegmann, 1834) or R. tigrina (Steindachner, 1867). The plerocercoids were used for experimental infection of a dog. After 4 weeks of infection, an adult tapeworm was recovered from the intestine of the dog. Morphologically, the distinct features of Spirometra sp. (Myanmar origin) relative to S. erinaceieuropaei and S. decipiens include a uterine morphology comprising posterior uterine coils that larger than the terminal uterine ball and coiling of the uteri diagonally (swirling) rather than spirally. The cox1 sequences (1,566 bp) of the Myanmar-origin Spirometra species showed 97.9% similarity to a reference sequence of S. decipiens (GenBank no. KJ599679) and 90.5% similarity to a reference sequence of S. erinaceieuropaei (GenBank no. KJ599680). Phylogenetic tree topologies were identical and presented high confidence level of values for the 3 major branches of the 3 Spirometra species in cox1 and nad1 genes. These results indicated that Myanmar-origin Spirometra species coincided with those of S. ranarum and may be considered as a valid species.

• Journal of Life Science
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• v.20 no.11
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• pp.1697-1703
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• 2010

Asarum consists of low-growing herbs and is a genus in the Aristolochiaceae family with species found in the north temperate zones with most species in Asia. We evaluated the nine taxa with the trnL - trnT region of the chloroplast genome to estimate phenotypic relationships within genus Asarum in Korea. Alignment of the DNA sequences required the addition of numerous gaps. Sequence variation within the Asarum was mostly due to nucleotide inserts/deletions, although several indels and inserts were found. Another source of sequence divergence was length variation due to stretches of short repeats that occur at the trnL - trnT region in all the Asarum. A + T content for nine Korean species of genus Asarum ranged between 74.7% and 78.3%. These values were higher than those for the angiosperm alignments of the total trnL and trnT region (64.5~67.1%). Within genus Asarum, A. patens was strikingly different from the others in the three phylogenetic analyses (MP, ML, and NJ). However, some internal nodes were poorly supported. Within Korean Asarum, four species were unsolved portions. Possible reasons for the striking non-congruence between the previous morphological traits and the trnL - trnT based on phylogeny were discussed.

• Journal of Life Science
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• v.24 no.7
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• pp.757-761
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• 2014

Olive flounder (Paralichthys olivaceus) is an important aquaculture fish species in Jeju Island, South Korea. Due to the intensification of flounder fish farming, huge amounts of chemical antibiotics are used against several fish diseases. This has many harmful side effects on fish, as well as human consumers. Hence, an alternative to chemical antibiotic agents is needed for disease control. In this study, three strains of rhizobacteria (BRH433-2, TRH415-2, and THJ609-3) were isolated from the rhizosphere of plants. Assays of their antibacterial activity against fish pathogens, such as S. iniae, S. parauberis, V. anguillarum, and E. tarda, were performed with untreated broth culture (without cell separation), supernatant, and precipitated pellets separated by centrifugation. Among these, the cell suspension prepared from the precipitated pellet showed significant antimicrobial activity when compared with that of the untreated broth culture and centrifugal supernatant. These results indicate that the three isolated rhizobacterial strains exhibit antibacterial activity. Analysis of the 16S rDNA sequences of the BRH-433-2, THJ609-3, and TRH415-2 strains showed the highest similarity to Burkholderia gladioli (99.5%), Pseudomonas baetica (97.7%), and P. koreensis and P. baetica (98.4%), respectively. We suggest that the strains hold promise in disease management of fish.

• Journal of Life Science
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• v.23 no.1
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• pp.110-115
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• 2013

A microorganism (strain AR1) producing an extracellular lipolytic enzyme was isolated from hot springs located in Beppu, Japan. Phylogenetic analysis based on the 16S rDNA sequence and biochemical studies indicated that AR1 belongs to the genus Geobacillus. This study focused on novel strategies to increase extracellular lipolytic enzyme production by this novel Geobacillus sp. AR1. Cultures of the AR1 strain grew within a wide temperature range (from 35 to $75^{\circ}C$); the optimum temperature was $65^{\circ}C$. The pH for optimal growth was 6.5, whereas the optimum pH for lipolytic enzyme production was 8.5. The presence of oils in the culture medium led to improvements in lipolytic enzyme activity. Soybean oil was the most efficient inducer, and it yielded better results when added in the exponential phase. On the other hand, the addition of chemical surfactants led to lipolytic enzyme production. Their addition to the culture could affect the location of the enzyme activity. The addition of Tween 20 in the stationary phase significantly increased the proportion of the extracellular enzyme activity. According to the results, following the addition of soybean oil and Tween 20 in the exponential and stationary phases, the extracellular lipolytic activity was increased 2.4-fold compared with that of a control.

• Journal of Life Science
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• v.23 no.1
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• pp.95-101
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• 2013

In this study, plant samples of five species were collected from the Dokdo islands in South Korea. Plant samples such as Asparagus schoberioides, Corydalis platycarpa, Festuca rubra, Sedum oryzifolium, and Setaria viridis were collected from the Dongdo and Seodo. Endophytic fungal strains were isolated from the roots of five plants from the Dokdo islands. Thirty-three fungal strains were isolated from these native plants. All the endophytic fungi were analyzed by internal transcribed spacer (ITS) sequencing (ITS containing ITS1, 5.8s, and the ITS2 region). Waito-c rice seedlings were treated with fungal culture filtrates to test their plant growth-promoting activity. A bioassay of the D-So-1-1 fungal strain isolated from S. oryzifolium confirmed that it has the highest plant growth-promoting activity. All the endophytic fungi belong to four orders: Eurotiales (86%), Capnodiales (3%), Hypocreales (4%), and Incertae sedis (7%). The endophytic fungi were classified as Ascomycota, which contained Aspergillus (12%), Cladosporium (3%), Eurotium (3%), Fusarium (18%), Microsphaeropsis (6%), and Penicillium (58%) at the genus level.