• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.04a
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• pp.32-32
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• 2019

Mutation breeding is the useful tool to improve agronomic traits in various crop species. Soybean is most important crop and is rich in protein and oil contents. Despite of the importance as economic value and various genetic resource of soybean, there have been limited studies of genetic relationship among mutant resources through radiation breeding. In this study, the agronomical phenotype for selecting various genetic resources was evaluated in 528 soybean mutant lines. As a result, 210 soybean mutants with their original cultivars were selected with various traits. We named 210 selected lines as Mutant Diversity Pool (MDP). The genetic diversity and the relationship of the MDP were investigated using TRAP and TE-TRAP markers. In TRAP analysis, sixteen primer combination (PC)s were used and a total of 551 fragments were amplified. The highest (84.00%) and the lowest (32.35%) polymorphism levels were showed in PC MIR157B+Ga5 and B14G14B+Ga3, respectively. The mean of PIC values was 0.15 ranging from 0.07 in B14G14B+Sa12 to 0.23 in MIR157B+Sa4. Phylogenetic and population structure analysis indicated that the 210 MDP lines dispersed to four groups among the wild types and their mutants. The highest genetic diversity among populations was observed between lines Paldal and 523-7 (Fst=0.409), whereas the lowest genetic diversity was between population KAS360-22 and 94seori (Fst=0.065). AMOVA showed 11.583 (21.0%) and 43.532 (79.0%) variations in inter and intra mutant population, respectively. Overall, the genetic similarity of each intra mutant populations was closer than that of inter mutant population. A total of 408 fragments were amplified in the 210 MDP using twelve PCs of TE-TRAP markers that were obtained from a combination of three TIR sequence of transposable elements (MITE-stowaway; M-s, MITE-tourist; M-t, PONG). The highest (77.42%) and the lowest (56.00%) polymorphism levels were showed in PONG+Sa4 and PONG+Sa12, respectively. The mean of PIC values was 0.15 ranging from 0.09 in M-s+Sa4 and M-s+Ga5 to 0.21 in M-t+Ga5. AMOVA of M-s showed 2.209 (20%) and 8.957 (80%) variations in inter and intra mutant population, respectively. AMOVA of M-t showed 2.766 (18%) and 12.385 (82%) variations in inter and intra mutant population, respectively. AMOVA of PONG showed 3.151 (29%) and 7.646 (71%) variations in inter and intra mutant population, respectively. According to our study, the PONG had higher inter mutant population and lower intra mutant population. This mean was that for aspect of radiation sensitivity, M-s and M-t showed higher mobility than that of PONG. Our results suggest that the TRAP and the TE-TRAP markers may be useful for assessing the genetic diversity and relationship among soybean MDP and help to improve our knowledge of soybean mutation/radiation breeding.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.5
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• pp.614-628
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• 2019

Objective: The inhibitory leukocyte immunoglobulin-like receptors (LILRBs) play an important role in innate immunity. The present study represents the first description of the cloning and structural and functional analysis of LILRB1 and LILRB3 isolated from two genetically disparate chicken lines. Methods: Chicken LILRB1-3 genes were identified by bioinformatics approach. Expression studies were performed by transfection, quantitative polymerase chain reaction. Signal transduction was analyzed by western blots, immunoprecipitation and flow cytometric. Cytokine levels were determined by enzyme-linked immunosorbent assay. Results: Amino acid homology and phylogenetic analyses showed that the homologies of LILRB1 and LILRB3 in the chicken line 6.3 to those proteins in the chicken line 7.2 ranged between 97%-99%, while homologies between chicken and mammal proteins ranged between 13%-19%, and 13%-69%, respectively. Our findings indicate that LILRB1 and LILRB3 subdivided into two groups based on the immunoreceptor tyrosine-based inhibitory motifs (ITIM) present in the transmembrane domain. Chicken line 6.3 has two ITIM motifs of the sequence LxYxxL and SxYxxV while line 7.2 has two ITIM motifs of the sequences LxYxxL and LxYxxV. These motifs bind to SHP-2 (protein tyrosine phosphatase, non-receptor type 11) that plays a regulatory role in immune functions. Moreover, our data indicate that LILRB1 and LILRB3 associated with and activated major histocompatibility complex (MHC) class I and ${\beta}2-microglobulin$ and induced the expression of transporters associated with antigen processing, which are essential for MHC class I antigen presentation. This suggests that LILRB1 and LILRB3 are transcriptional regulators, modulating the expression of components in the MHC class I pathway and thereby regulating immune responses. Furthermore, LILRB1 and LILRB3 activated Janus kinase2/tyrosine kinase 2 (JAK2/TYK2); signal transducer and activator of transcription1/3 (STAT1/3), and suppressor of cytokine signaling 1 genes expressed in Macrophage (HD11) cells, which induced Th1, Th2, and Th17 cytokines. Conclusion: These data indicate that LILRB1 and LILRB3 are innate immune receptors associated with SHP-2, MHC class I, ${\beta}2-microglobulin$, and they activate the Janus kinase/signal transducer and activator of transcription signaling pathway. Thus, our study provides novel insights into the regulation of immunity and immunopathology.

• Journal of fish pathology
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• v.33 no.2
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• pp.127-138
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• 2020

We attempted to isolate and identify potentially pathogenic bacteria from geoduck clam (Panopea japonica) larvae, juvenile and adult, focusing on Vibrios. The isolates were identified by molecular approach and biochemical characterization. In particular, we applied MLSA (multilocus sequence analysis) to the isolated Vibrios for clear identification and phylogenetic relationships, by combining 16s rDNA and several houskeeping genes (pyrH, recA, rpoA). We obtained 141 isolates; 10 from healthy adults, 52 from moribund adults with blisters and 79 from larvae. 46 from the moribund adults and 39 from the larvae were identified as Vibrio species, while the rest of these samples and all the isolates from healthy adult were identified as marine general bacteria. Among Vibrio species, Vibrio splendidus was the most frequently identified from the moribund adults and clustered with the known V. splendidus in GenBank by MLSA. However, it was still unclear that V. splendidus was the cause of blisters because the artificial infection experiment was not conducted and V. splendidus was isolated also from the larvae. Further studies are necessary to clarify the etiological agent of the blisters found in geoduck clam in this study.

• 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.

• Journal of Life Science
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• v.33 no.7
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• pp.593-604
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• 2023

The ocean accounts for over 70% of the Earth's surface and is a space of largely unexplored unknowns and opportunities. Korea is a peninsula surrounded by the sea on three sides, emphasizing the importance of marine research. The ocean has an extremely complex environment with immense biological diversity. In terms of microbiology, the marine environment has varying factors like extreme temperature, pressure, solar radiation, salt concentration, and pH, providing ecologically unique habitats. Due to this variety, marine organisms have very different phylogenetic classifications compared with terrestrial organisms. Although various microorganisms inhabit the ocean, studies on the diversity, isolation, and cultivation of marine microorganisms and the secondary metabolites they produce are still insufficient. Research on bioactive substances from marine microorganisms, which were rarely studied until the 1990s, has accelerated in terms of natural products from marine Actinomycetes since the 2000s. Since then, industries for bioplastic and biofuel production, carbon dioxide capture, probiotics, and pharmaceutical discovery and development of antibacterial, anticancer, antioxidant, and anti-inflammatory drugs using bacteria, archaea, and algae have significantly grown. In this review, we introduce current research findings and the latest trends in life science and biotechnology using marine microorganisms. Through this article, we hope to create consumer awareness of the importance of basic and applied research in various natural product-related discovery fields other than conventional pharmaceutical drug discovery. The article aims to suggest pathways that may boost research on the optimization and application of future marine-derived materials.

• Horticultural Science & Technology
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• v.34 no.2
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• pp.305-313
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• 2016

Brassica juncea (2n = 4x = 36, AABB genome, 1,068 Mb) is a U's triangle species and an amphidiploid derivative of B. rapa and B. nigra. Fifteen varieties were used to study the ITS (internal transcribed spacer) regions of ribosomal DNA and MITEs (miniature inverted-repeat transposable elements) with a view of developing specific molecular markers. ITSs and MITEs are an excellent resource for developing DNA markers for genomics and evolutionary studies because most of them are stably inherited and present in high copy numbers. The ITS (ITS1 and ITS2) sequence was compared with the consensus sequence of B. rapa and B. nigra. Variation in ITS1 created two separate groups among 15 varieties, with 10 varieties in one group and 5 in the other. Phylogenetic analysis revealed two major clusters for those 10 and 5 varieties. Among the 160 different MITE primers used to evaluate the selected 15 varieties of B. juncea, 70 were related to the Stowaway, 79 to the Tourist, 6 to the hAT, and 5 to the Mutator super-families of MITEs. Of 160 markers examined, 32 were found to be polymorphic when fifteen different varieties of B. juncea were evaluated. The variety 'Blackgat' was different from the other mustard varieties with respect to both phenotype and genotype. The diversity of 47 additional accessions could be verified using eight selected molecular markers derived from MITE family sequences. The polymorphic markers identified in this study can be used for varietal classification, variety protection, and other breeding purposes.

• Journal of Applied Biological Chemistry
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• v.62 no.3
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• pp.287-292
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• 2019

Pseudomonas tolaasii causes brown blotch disease on the oyster mushroom (Pleurotus ostreatus). Various pathogenic strains of P. tolaasii were isolated and divided into three subtypes, $P1{\alpha}$, $P1{\beta}$, and $P1{\gamma}$. For phage therapy, bacteriophages against to these subtype strains were applied to mushroom cultivation and very successful to prevent from the disease. In this study, bacteriophages were isolated against the representative strains of subtype pathogens and their polyclonal antibodies were synthesized to investigate structural relationship among capsid proteins of phages. Phage preparations over $10^{10}pfu/mL$ were injected to rabbit thigh muscle and polyclonal antibodies were obtained after three times of boost injection. Titers of the antibodies obtained were over $2{\times}10^7Ab/mL$ for the phage ${\phi}6264$, $1{\times}10^6Ab/mL$ for the phage ${\phi}HK2$, and $1{\times}10^7Ab/mL$ for the phage ${\phi}HK19$ and phage ${\phi}HK23$. High specific activities were observed between antibodies and the corresponding bacteriophages. Some cross-reactivities between the antibodies and non-corresponding bacteriophages were also measured. Antibody $Ab{\phi}6264$ inactivated all phages of $P1{\alpha}$ subtype and only phage ${\phi}HK16$ among $P1{\beta}$ subtype phages. Antibody $Ab{\phi}HK23$ of $P1{\gamma}$ subtype neutralized all phages of $P1{\beta}$ subtype as well as the phage ${\phi}HK23$, showing the widest phage-inactivation range. When the structural-similarity studies of phages were investigated by using phage antibodies, closeness obtained by phylogenetic analysis of 16S rRNA genes of pathogenic strains were quite different from that of polyclonal antibody-specific structural similarity of phage capsid proteins. In conclusion, there is weak correlation between the host strain specificity of bacteriophage and its capsid structural similarity measured by phage antibodies.

• Journal of Life Science
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• v.32 no.3
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• pp.202-209
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• 2022

The green alga Chlamydomonas reinhardtii, a unicellular haploid eukaryote, has long been used by researchers and industries as a cell factory to produce high value-added microalgae substances using genetic modification. Microalga K01, presumed to be Chlamydomonas, was isolated from 12 freshwater samples from the Chungcheong and Jeolla regions to replace C. reinhardtii, an introduced species currently used in most basic and industrial research. The isolated K01 strain was identified as C. reinhardtii through morphological and phylogenetic studies of the 18S rDNA gene sequence (NCBI accession number KC166137). The growth and lipid content of the isolated C. reinhardtii K01 were compared with three wild and four mutant strains in TAP medium, and it was found that the K01 strain could produce 1.74×10⁷ cells/ml by the third day of culture. The growth rate of C. reinhardtii K01 was 1.5 times faster than UTEX2244, which showed the highest number of cells (1.20×10⁷ cells/ml) among the compared strains. The lipid content of the isolated C. reinhardtii K01 (20.67%) was similar to those of the wild strains, although the fatty acid oleate C18:1 was not detected in the isolated strain but was identified in the seven others. The cell density of the isolated strain increased to 0.87 g/l during a six-day culture in BG11 medium, where nitrate (NaNO₃) was introduced as a nitrogen source, while the seven acquired strains showed almost no cell proliferation.

• Korean Journal of Plant Resources
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• v.36 no.4
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• pp.369-380
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• 2023

Developing and breeding improved legume-based food resources require collecting useful genetic traits with heritability even though requiring some time-consuming, costly, and labor intensive. We attempted to infer heritability of nine genetic traits-days to flowering, days to maturity, period from flowering to maturity, the number of seeds per pod, 100-seeds weight, and four contents such as crude protein, crude oil, crude fiber, and dietary fiber-using 455 homologous chloroplast gene sets of six species of legumes. Correlation analysis between genetic trait differences and phylogenetic distance of homologous gene sets revealed that days to flowering, the number of seeds per pod, and crude oil content were influenced by genetic factors rather than environmental factors by 62.86%, 69.45%, 57.14% of correlated genes (P-value ≤ 0.05) and days to maturity showed intermediate genetic effects by 62.42% (P-value ≤ 0.1). The period from flowering to maturity and 100-seeds weight showed different results compared to those of some previous studies, which may be attributed to highly complicated internal (epistatic or additive gene effects) and external effects (cultural environment and human behaviors). Despite being slightly unexpected, our results and method can widely contribute to analyze heritability by including genetic information on mitochondria, nuclear genome, and single nucleotide polymorphisms.