• Journal of Marine Life Science
• /
• v.6 no.2
• /
• pp.47-57
• /
• 2021

In the fishery industry, global aquaculture production has stagnated due to overfishing of aquatic products, restrictions between countries, and climate change. The aquaculture suggests the possibility of a blue revolution that can be expanded in a new way. The aquaculture industry now accounts for more than half of the fishery products from the sea as a raw material for seafood for human consumption. Various latest biological research methods are being applied for the development of a sustainable aquaculture industry. Genomics has made significant progress in recent years. Since the genome sequence of Atlantic cod was sequenced in 2011, the genomes of more species have been sequenced. The genome information is providing a more robust and productive knowledge base for the aquaculture industry, including breeding and breeding of superior traits, improving disease resistance quality, and optimizing aquaculture feed and feed methods. This review looked at the status of genome analysis technology and the current status of genome research of aquaculture species. The development of genome research technology and massive genomic information is important in solving the challenges of the aquaculture industry and will help sustainable fisheries and aquaculture.

• Journal of Life Science
• /
• v.32 no.2
• /
• pp.94-100
• /
• 2022

Chronic infection by hepatitis B virus (HBV) greatly increases the risk for liver cirrhosis and hepatocellular carcinoma (HCC). The outcome of HBV infection is shaped by the complex interplay of the mode of transmission, host genetic factors, viral genotype, adaptive mutations, and environmental factors. The pregenomic RNA transcription of HBV for their replication is regulated by the core promoter activation. Core promoter mutations have been the reason for acute liver failure and are associated with HCC development. We obtained HBV genes from a patient in Myanmar who was infected with HBV and identified gene variations in the core promoter region. For measuring the relative transactivation activity of the core promoter, we prepared the core-promoter reporter construct. Among the gene variations of the core promoter, the mutations of C1731T and G1806A were associated with increase in the transactivation of the HBV core promoter. Through computer analysis for searching for a tentative transcription factor binding site, we showed that the mutations of C1713T and G1806A newly created C/EBPβ and XBP1-responsive elements of the core promoter, respectively. The ectopic expression of C/EBPβ largely increased the HBV core promoter containing the C1713T mutation and that of XBP1 activated the M95 promoter containing the G1806A mutation. Our efforts to treat and prevent HBV infections are hampered by the emergence of drug-resistant mutations and vaccine-escape mutations. Our results provide the biological properties and clinical significance of specific HBV core promoter mutations.

• Journal of Microbiology and Biotechnology
• /
• v.33 no.7
• /
• pp.909-914
• /
• 2023

While searching for the bacteria which are responsible for degradation of pesticide in soybean field soil, a novel bacterial strain, designated 5-5^T, was isolated. The cells of the strain were Gram-staining-positive, aerobic and non-motile rods. Growth occurred at 10-42℃ (optimum, 30℃), pH 5.5-9.0 (optimum, pH 7.0-7.5), and 0-2% (w/v) NaCl (optimum, 1%). The predominant fatty acids were C_15:0 anteiso, C_17:0 anteiso, and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). The predominant menaquinone was MK-9 (H₂). Diphosphatidylglycerol, glycolipids, phosphatidylinositol, and phosphatidylglycerol were the major polar lipids. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain 5-5^T is a member of the genus Sinomonas and its closest relative is Sinomonas humi MUSC 117^T, sharing a genetic similarity of 98.4%. The draft genome of strain 5-5^T was 4,727,205 bp long with an N50 contig of 4,464,284 bp. Genomic DNA G+C content of strain 5-5^T was68.0 mol%. The average nucleotide identity (ANI) values between strain 5-5^T and its closest strains S. humi MUSC 117^T and S. susongensis A31^T were 87.0, and 84.3 % respectively. In silico DNA-DNA hybridization values between strain 5-5^T and its closest strains S. humi MUSC 117^T and S. susongensis A31^T were 32.5% and 27.9% respectively. Based on the ANI and in silico DNA-DNA hybridization analyses, the 5-5^T strain was considered as novel species belonging to the genus Sinomonas. On the basis of the results from phenotypic, genotypic and chemotaxonomic analyses, strain 5-5^T represents a novel speciesof the genus Sinomonas, for which the name Sinomonas terrae sp. nov. is proposed. The type strain is 5-5^T (=KCTC 49650^T =NBRC 115790^T).

• Research in Plant Disease
• /
• v.28 no.4
• /
• pp.231-236
• /
• 2022

Oxypetalum coeruleum, commonly known as Tweedia, is a perennial herbaceous plant of the Apocynaceae family native to southern Brazil and Uruguay. Tweedia plants are grown as one of the most popular ornamental flowers for floral arrangement in Korea. In May 2021, several tweedia plants in a single greenhouse in Gimje, Jeollabuk-do were found to show virus-like symptoms including necrotic rings, vein-clearing, chlorotic mottle, and mosaic on the leaves, and necrosis on the stems. Here, we have identified tomato spotted wilt virus (TSWV) in symptomatic tweedia leaves by applying high-throughput RNA sequencing. In the result, a single infection by TSWV was verified without mixed infections of different virus species. To confirm the presence of TSWV, a reverse transcription polymerase chain reaction was performed with a specific primer set to the N gene of TSWV. The complete genomic sequence of L, M, and S segments of TSWV 'Oxy' isolate were determined and deposited in GenBank under accession numbers LC671525, LC671638, and LC671639, respectively. In the phylogenetic tree analysis by maximum likelihood method, 'Oxy' isolate showed a high relationship with TSWV 'Gumi' isolate from Gerbera jamesonii in Gyeongsangbuk-do, Korea; for all three RNA segments. To our knowledge, this is the first report of TSWV infection of O. coeruleum in Korea.

• The Korea Journal of Herbology
• /
• v.24 no.4
• /
• pp.115-120
• /
• 2009

Objectives : Due to the morphological similarity and frequent occurrence of intermediate forms as well as morphological variations of aerial part, the correct identification between Rhei Radix et Rhizoma and Rhei Undulatai Rhizoma is very difficult. To develop a reliable method for correct identification and improving the quality standards of Rhei Radix et Rhizoma and Rhei Undulatai Rhizoma, we analyzed RAPD and developed SCAR marker. Methods : To amplify target DNA at the genomic level, 32 Operon 10-mer random primers were applied with four Rheum species, R. officinale, R. palmatum, R. tanguticum and R. undulatum. The nucleotide sequences were determined and species-specific primers were prepared depending on the species-specific RAPD amplicons after subcloned into the pGEM-Teasy vector. To develop the SCAR markers, species-specific PCR amplification and multiplex-PCR were carried out using the single species-specific primer pairs and combinations of them, respectively. Results : We used RAPD analysis of four Rheum plant species to obtain several species-specific RAPD amplicons. From nucleotide sequences of these RAPD amplicons, we developed two SCAR markers that amplified 314 bp and 390 bp DNA fragments in only R. undulatum but not in R. officinale, R. palmatum, R. tanguticum and R. undulatum, for distinguishing Rhei Undulatai Rhizoma and Rhei Radix et Rhizoma. Furthermore, we established SCAR markers for the simultaneous discrimination of the three species within a single reaction by using multiplex-PCR. Conclusions : These genetic markers can be used for the efficient discrimination of plants species and commercial herbal medicines between Rhei Undulatai Rhizoma and Rhei Radix et Rhizoma, to ultimately prevent indiscriminate distribution and prescription of these herbal medicines.

• Korean Journal of Environmental Biology
• /
• v.41 no.1
• /
• pp.1-13
• /
• 2023

Broad bean wilt virus 2 (BBWV2) is a species in the genus Fabavirus and family Secoviridae, which is transmitted by aphids and has a wide host range. The BBWV2 genome is composed of two single-stranded, positive-sense RNAs, RNA-1 and RNA-2. The representative symptoms of BBWV2 are mosaic, mottle, vein clearing, wilt, and stunting on leaves, and these symptoms cause economic damage to various crops. In 2019, Perilla fructescens leaves with mosaic and yellowing symptoms were found in Geumsan, South Korea. Reverse-transcription polymerase chain reaction (RT-PCR) was performed with specific primers for 10 reported viruses, including BBWV2, to identify the causal virus, and the results were positive for BBWV2. To characterize a BBWV2 isolate (BBWV2-GS-PF) from symptomatic P. fructescens, genetic analysis and pathogenicity tests were performed. The complete genomic sequences of RNA-1 and RNA-2 of BBWV2-GS-PF were phylogenetically distant to the previously reported BBWV2 isolates, with relatively low nucleotide sequence similarities of 76-80%. In the pathogenicity test, unlike most BBWV2 isolates with mild mosaic or mosaic symptoms in peppers, the BBWV2-GS-PF isolate showed typical ring spot symptoms. Considering these results, the BBWV2-GS-PF isolate from P. fructescens could be classified as a new strain of BBWV2.

• Korean Journal of Animal Reproduction
• /
• v.25 no.3
• /
• pp.237-242
• /
• 2001

We recently demonstrated that both linear- and supercoil-form B1/B2 SINE (short interspersed elements) sequences could increase an integration frequency of a reporter gene in preimplatation mouse embryos. In those reports, when either a control or SINE-flanked DNA was separately applied to microinjection, the proportions of $\beta$-gal positives were 16% and 63%, respectively, in linear-form DNA, and 6% and 25%, respectively, in circular-form DNA. Here, we examined the contribution of a circular-form DNA moiety to integration frequency by using a mixed-farm (linear and circular-form) DNA in microinjection. When examined in the blastocyst stage, the proportion of $\beta$-gal-positive embryos was 17.3% and 46.6% in control and SINE-flanked DNA, respectively. These results suggest that there is little contribution of circular-form DNA moiety to the resultant integration frequency, and that the majority of the integration events are mediated through a linear conformation of vector DNA. In addition, some clues on integration process could be obtained from the analysis of microinjection results.

• Korean Journal of Ichthyology
• /
• v.34 no.3
• /
• pp.208-217
• /
• 2022

We wanted to develop a real-time PCR assay capable of detecting Liobagrus obesus in environmental DNA (eDNA) extracted from freshwater samples using a pair of species-specific primers and probe for the endangered fish, L. obesus. The species-specific primers and probe were designed in consideration of single nucleotide polymorphisms between 65 species of freshwater fish living in the Republic of Korea within the cytochrome b (cytb) gene of mitochondrial DNA. The species-specific primers and probe, in the real-time PCR assay, showed high specificity as only the L. obesus genomic DNA (gDNA) was found to be positive in the specificity verification using 65 species gDNA of freshwater fish in the Republic of Korea. In addition, in the detection limit analysis using the serial dilution concentrations of L. obesus gDNA, it was found that it was possible to detect up to 0.2 pg, showing high sensitivity. Afterwards, using the species-specific primers and probe, real-time PCR assay was performed on freshwater samples obtained from 8 stations in the mid-upper basin of Geum River. As a result, the cytb gene of L. obesus was detected in total 5 stations including all 3 stations where this species was collected at the time of field survey. Therefore, the species-specific primers and probe developed in present study, and the real-time PCR assay using them, can accurately detect the cytb gene of L. obesus from eDNA samples, which can be utilized to monitor the existing habitats of this species and to discover potential new habitats.

• Journal of the Korean Society of Radiology
• /
• v.81 no.3
• /
• pp.632-643
• /
• 2020

Purpose To investigate the correlation between magnetic resonance (MR) image-based radiomics features and the genomic features of breast cancer by focusing on biomolecular intrinsic subtypes and gene expression profiles based on risk scores. Materials and Methods We used the publicly available datasets from the Cancer Genome Atlas and the Cancer Imaging Archive to extract the radiomics features of 122 breast cancers on MR images. Furthermore, PAM50 intrinsic subtypes were classified and their risk scores were determined from gene expression profiles. The relationship between radiomics features and biomolecular characteristics was analyzed. A penalized generalized regression analysis was performed to build prediction models. Results The PAM50 subtype demonstrated a statistically significant association with the maximum 2D diameter (p = 0.0189), degree of correlation (p = 0.0386), and inverse difference moment normalized (p = 0.0337). Among risk score systems, GGI and GENE70 shared 8 correlated radiomic features (p = 0.0008-0.0492) that were statistically significant. Although the maximum 2D diameter was most significantly correlated to both score systems (p = 0.0139, and p = 0.0008), the overall degree of correlation of the prediction models was weak with the highest correlation coefficient of GENE70 being 0.2171. Conclusion Maximum 2D diameter, degree of correlation, and inverse difference moment normalized demonstrated significant relationships with the PAM50 intrinsic subtypes along with gene expression profile-based risk scores such as GENE70, despite weak correlations.

• Journal of Korean Society of Forest Science
• /
• v.90 no.2
• /
• pp.169-175
• /
• 2001

Genomic DNAs were extracted from the leaves of 182 ginkgo trees (Ginkgo biloba L.) planted in 6 regions and subjected to the analysis of both I-SSR and RAPD markers. A total of 227 amplicon variants were generated by PCR using 15 I-SSR primers and 67 amplicons by PCR with 5 RAPD primers. Levels of genetic diversity within 6 populations were turned out to be similar (Shannon's Index, I-SSR : 0.35~0.40; mean of 0.38, RAPD : 0.31~0.38; mean of 0.35, combined : 0.35~0.40; mean of 0.37). Ranks of the level of genetic diversity estimated from I-SSR, RAPD, and combined data were not coincided each other. Majority of genetic diversity was allocated among individuals within populations (I-SSR : 94.31%, RAPD : 93.62%, combined : 93.57%), which resulted in pretty low level of population differentiation. Genetic differentiation between male and female groups was turned out to be quite low (I-SSR : 0.03, RAPD : 0.091, combined : 0.043), which slightly fluctuated when analysis was restricted to the data obtained from 3 regions where both male and female trees were sampled (I-SSR : 0.038, RAPD : 0.084, combined : 0.047). Genetic relationships among the populations, reconstructed by UPGMA, were not coincided with geographic affinity, which might be resulted from sharing of seed sources in some regions. Whereas independent cluster analyses with I-SSR data and RAPD data, respectively, reclassified by sexes revealed two sexual groups in which all the male and the female populations were clustered together, cluster analysis with combined data did not show clear sexual grouping.