• Journal of Life Science
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• v.17 no.12
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• pp.1610-1615
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• 2007

Genus Sorbus is a long lived woody species that is primarily distributed throughout Asia and Europe. This species is regarded as very important herbal medicines in Korea and China. Sorbus commixta is primarily distributed throughout Europe. We evaluated a representative sample of the four taxa with nuclear ribosomal DNA internal transcribed spacer sequences (ITS) to estimate genetic relationships within genus. Aligned nucleotide sequences of the length of ITS1 were nearly constant within genus Sorbus varying from 219 in S. aucuparia to 218 in the rest species. Especially, the 5.8S subunit of all taxa of Sorbus was found to constant of 165 bp nucleotides. However, aligned nucleotide sequences of the length of ITS2 vary from 240 in S. sambucifolia var. pseudogrcilisto 245 in S. aucuparia. Total alignment length is 629 positions, of which 35 are parsimony-informative, 32 variable but parsimony-uninformative, and 552 constant characters. The base furtherance showed the difference to the by a total taxon: an average A and T are 17.7% and G and C are 30.4%, 34.2%, respectively. All the four taxa beginning with conserved base paired triplets emerging from single strand regions (domain I). Noteworthy, in the RNA secondary structure proposed for the three Korean Sorbus taxa RNA transcript ITS2, which shows a remarkedly well-conserved folding (domain II). When compared to the European Sorbus (S. aucuparia) of ITS2. ITS analysis may be useful in germ-plasm classification several taxa of genus Sorbus.

• Journal of Life Science
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• v.23 no.2
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• pp.190-196
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• 2013

The sea squirt, Halocynthia roretzi, has experienced mass mortality due to softness syndrome. The identification of disease-induced genes can provide insights into the development of this syndrome. To identify the genes, we performed differentially expressed gene (DEG) analysis. The expression of the phosphoglycerate kinase (HrPGK) gene was significantly decreased in diseased sea squirts compared to normal ones. We confirmed the result of the DEG analysis through RT-PCR and real-time PCR. In addition, we detected single nucleotide polymorphisms at position -106 (A/T) and -254 (G/T) in the HrPGK gene promoter by genotyping analysis. At the -106 site of the HrPGK gene, the frequency of the AA allele in disease-resistant sea squirts was about two-fold higher than that of sensitive ones, and the frequency of the TT allele in the disease-resistant sea squirts was about six-fold lower. At the -254 site of the HrPGK gene, the frequency of the GT and the GG allele was approximately two-fold higher and two-fold lower, respectively, in the disease-resistant sea squirts compared to the disease-sensitive ones. Analysis of the relationship between the genotypic variation at the -106/-254 promoter and the expression of HrPGK mRNA showed that HrPGK mRNA expression was higher in the -106/-254 AA/GT genotype samples than in the -106/254 TT/GG genotype ones. These results show that sea squirts harboring the AA/GT genotype may have more resistance to mortality than the sea squirts with other genotypes.

• Korean Journal of Clinical Laboratory Science
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• v.51 no.4
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• pp.406-413
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• 2019

This study was undertaken to investigate the distribution of human papillomavirus (HPV) subtypes and cervical lesions in Busan. Furthermore, the cytological and histological findings of cervical lesions were compared to determine the usefulness of the currently released vaccines. HPV subtypes of 2,130 patients who visited Haeundae Paik Hospital between January 2013 and March 2016 were analyzed by the HPV 9G DNA chip. Liquid-based cytological examination was performed, and subtypes were classified according to the 2001 guidelines of The Bethesda System. Biopsy or hysterectomy specimens were subjected to hematoxylin and eosin staining for histological examinations. Of the total 2,130 cases, 1,254 (58.9%) were positive for HPV, and 876 (41.1%) were negative. Of these, 152 (7.1%), 97 (4.6%) and 80 (3.8%) were identified as HPV 16, 68 and 56, respectively. Of the 329 cases encompassing the above three HPV subtypes, histopathological analysis diagnosed 155 (47.1%) cases with CIN2 or higher grade. Notably, the occurrences of HPV subtypes 16, 68, 56, 58 and 51 were most frequently diagnosed in Busan. Further analysis revealed that administration of Gardasil^Ⓡ 9, the currently available vaccine in the market, exerts no protection against subtypes 68, 59 and 51. This study aims to provide an important reference for future HPV vaccination programs in Busan.

• Journal of Life Science
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• v.12 no.1
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• pp.96-105
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• 2002

To investigate expression of the artificial gene encoding a repeated tripeptide lysyl-glutamyl-tryptophan in tobacco plant, the plant binary vector, pART404 has been constructed, which contains the duplicated CaMV 35S promoter, an artificial gene coding for repetitive polymer (Lys-Glu-Trp)$_{64}$, and nopaline synthase (nos) terminator. The recombinant expression vector was introduced in Nicotiana tabacum (var. Xanthi) via Agrobacterium tumefaciens-mediated trans-formation. The transgenic calli selected by kanamycin containing medium were then regenerated to whole plants. Southern blot analysis indicated that five transgenic plants (No. 1, 7, 9, 43, 45) showed the hybridizing signals at 1.1 kb of the expected size on EcoRI digestion and each of the transgenic plants contained 1 or 3 copies of the artificial gene inserted into its genome. By northern blot analysis, the size of the hybridized total RNA was estimated to be approximately 1.2 kb and the RNA appeared generally to have the integrity. Western blot indicated that the protein was detected at the position of 33 kDa and the expression level of the polypeptide in the transgenic plant (No. 45) was measured to approximately 0.1% of the total protein.

• Genes and Genomics
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• v.40 no.11
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• pp.1181-1197
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• 2018

Tropical plant rubber tree (Hevea brasiliensis) is the sole source of commercial natural rubber and low-temperature stress is the most important limiting factor for its cultivation. To characterize the gene expression profiles of H. brasiliensis under the cold stress and discover the key cold stress-induced genes. Three cDNA libraries, CT (control), LT2 (cold treatment at $4^{\circ}C$ for 2 h) and LT24 (cold treatment at $4^{\circ}C$ for 24 h) were constructed for RNA sequencing (RNA-Seq) and gene expression profiling. Quantitative real time PCR (qRT-PCR) was conducted to validate the RNA-Seq and gene differentially expression results. A total of 1457 and 2328 differentially expressed genes (DEGs) in LT2 and LT24 compared with CT were respectively detected. Most significantly enriched KEGG pathways included flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, cutin, suberine and wax biosynthesis, Pentose and glucuronate interconversions, phenylalanine metabolism and starch and sucrose metabolism. A total of 239 transcription factors (TFs) were differentially expressed following 2 h or/and 24 h of cold treatment. Cold-response transcription factor families included ARR-B, B3, BES1, bHLH, C2H, CO-like, Dof, ERF, FAR1, G2-like, GRAS, GRF, HD-ZIP, HSF, LBD, MIKC-MADS, M-type MADS, MYB, MYB-related, NAC, RAV, SRS, TALE, TCP, Trihelix, WOX, WRKY, YABBY and ZF-HD. The genome-wide transcriptional response of rubber tree to the cold treatments were determined and a large number of DEGs were characterized including 239 transcription factors, providing important clues for further elucidation of the mechanisms of cold stress responses in rubber tree.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2019.05a
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• pp.533-536
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• 2019

Recombinant baculoviruses are widely used to express heterologous genes in cultured insect cells. Recombinant baculoviruses can serve as gene-transfer vectors for expression of recombinant proteins in a wide range of mammalian cell types. Baculovirus system has significant benefits in view of safety, large-scale, and high level of gene expression. In this study, baculoviral vectors which were reconstructed from pOPINEneo-3C-GFP vector, were recombined with cytomegalovirus (CMV) promoter, green fluorescent protein (GFP), and p53 with NcoI and XhoI. These recombinant vectors were infected with various cells and cell lines. The baculovirus vector thus developed was analyzed by comparing the metastasis and expression of the recombinant genes with conventional vectors. These results suggest that the baculovirus vector has higher efficiency in metastasis and expression than the control vector. This work was supported by a grant from Mid-Career Researcher Program(NRF-2016R1A2B4016552) through the National Research Foundation of Korea(NRF) funded by the Ministry of Science, ICT & Future Planning(MSIP).

• Journal of Plant Biotechnology
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• v.48 no.1
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• pp.34-43
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• 2021

Targeted genome editing using the CRISPR/Cas9 system is a ground-breaking technology that is being widely used to produce plants with useful traits. However, for woody plants, only a few successful attempts have been reported. These successes have used Agrobacterium-mediated transformation, which has been reported to be very efficient at producing genetically modified trees. Nonetheless, there are unresolved problems with plasmid sequences that remain in the plant genome. In this study, we demonstrated a DNA-free genome editing technique in which purified CRISPR/Cas9 ribonucleoproteins (RNPs) are delivered directly to the protoplasts of a hybrid poplar (Populus alba × Populus glandulosa). We designed three single-guide RNAs (sgRNAs) to target the stress-associated protein 1 gene (PagSAP1) in the hybrid poplar. Deep sequencing results showed that pre-assembled RNPs had a more efficient target mutagenesis insertion and deletion (indel) frequency than did non-assembled RNPs. Moreover, the RNP of sgRNA3 had a significantly higher editing efficacy than those of sgRNA1 and sgRNA2. Our results suggest that the CRISPR/Cas9 ribonucleoprotein-mediated transfection approach is useful for the production of transgene-free genome-edited tree plants.

• Parasites, Hosts and Diseases
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• v.61 no.3
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• pp.317-324
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• 2023

Standard- and large-sized eggs of Trichuris trichiura were found in the feces of schoolchildren in Yangon, Myanmar during epidemiological surveys and mass deworming with albendazole in 2017-2019. The standard-sized eggs were identified as those of T. trichiura, but it was necessary to exclude the possibility of the large-sized eggs belonging to Trichuris vulpis, a dog whipworm. We conducted morphological and molecular studies to determine the species of the 2 types of Trichuris eggs. Individual eggs of both sizes were isolated from Kato-Katz fecal smears (n=20) and mechanically destroyed using a 23G injection needle. Nuclear DNA was extracted, and the 18S rRNA region was sequenced in 15 standard-sized eggs and 15 large-sized eggs. The average size of standard-sized eggs (T. trichiura) was 55.2×26.1 ㎛ (range: 51.7-57.6×21.3-28.0 ㎛; n=97), whereas the size of large-sized eggs was 69.3×32.0 ㎛ (range: 65.1-76.4×30.1-34.5 ㎛; n=20), slightly smaller than the known size of T. vulpis. Regarding standard-sized eggs, the 18S rRNA nucleotide sequences exhibited 100% homology with T. trichiura deposited in GenBank and 88.6-90.5% homology with T. vulpis. Regarding large-sized eggs, the nucleotide sequences showed 99.8-100% homology with T. trichiura in GenBank and 89.6-90.7% homology with T. vulpis. Both standard- and large-sized eggs of Trichuris spp. found in Myanmar schoolchildren during 2017-2019 were morphologically and molecularly confirmed to belong to T. trichiura. The conversion of eggs from smaller to large sizes might be due to anthelmintic treatments with albendazole.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.30-30
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• 2022

Philippines is the second world supplier of coconut by-products. As its first major genomics project, the Philippine Genome Center program for Agriculture (PGC-Agriculture) took the challenge to sequence and assemble the whole coconut genome. The project aims to provide advance genetics tools for our collaborating coconut researchers while taking the opportunity to initiate local capacity. Combination of different NGS platforms was explored and the Philippine 'Catigan Green Dwarf' (CATD) variety was selected with the breeders to be the crop's reference genome. A high quality genome assembly of CATD was generated and used to characterize important genes of coconut towards the development of resilient and outstanding varieties especially for added high-value traits. The talk will present the significant results of the project as published in various papers including the first report of whole genome sequence of a dwarf coconut variety. Updates will include the challenges hurdled and specific applications such as gene mining for host insect resistance and screening for least damaged coconuts (thus potentially insect resistant varieties). Genome-wide DNA markers as published and genes related to coconut oil qualitative/quantitative traits will also be presented, including initial molecular/biochemical studies that support nutritional and medicinal claims. A web-based genome database is currently built for ease access and wider utility of these genomics tools. Indeed, a major milestone accomplished by the coconut genomics research team, which was facilitated with the all-out government support and strong collaboration among multidisciplinary experts and partnership with advance research institutes.

• The korean journal of orthodontics
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• v.27 no.2
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• pp.335-347
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• 1997

Vitamin D is known to exert its action by activating DNA and RBA within target cells to produce proteins and enzymes that can be used in bone resorption process. Particularly, the active form of vitmain D, 1,25-dihydroxycholecalciferol $[1,25-(OH)_2D_3]$, is considered to be one of the most potent stimulators of osteoclatic acitivity in vitro. The purpose of this study was to evaluate the effect of 1,25-Dihydroxyvitamin $D_3$ on the avtivity of periodotal ligament cells and, the experimental tooth movement. Human periodontal ligament cells were collected from the first premolar tooth extracted for the orthodontic treatment, and were incubated in the environment of $37^{\circ}C$, 5% $CO_2$ and 95% humidity. Microtitration(MIT) assay was done at 10, 25, 50 and 100ng/ml of 1,25-Dihydroxyvitamin $D_3$. 21 Sprague-Daft rats were divided into a control gmup(3), and experimental groups(18) where 100g of force from helical spring was applied across the maxillary incisors 1,25-Dihydroxyvitamin $D_3$ was injected into periodontal ligament at the mesial or distal surface of maxillary incisors so that we can compare the control side and the experimental side. Expreimental groups were sac rifled at 12, 24, 36, 48, 72hours and 7 days after force application, respectively. And the obtained tissues were evaluated histologically. The observed results were as follows. 1. The activity of periodontal ligament cells in l0ng/ml or 25ng/ml of 1,25-Dihydroxyvitamin $D_3$ 1,25-Dihydroxyvitamin $D_3$ was not significantly different to the control at the cultivation of 1, 2 and 3 days. 2. The activity of periodontal ligament cells was significantly increased at 3 days in 50 ng/ml of 1,25-Dihydroxyvitamin $D_3$ and 2, 3 days in 100g/ml of 1,25-Dihydroxyvitamin $D_3$. 3. Up to 7 days after force application, there was no difference in osteoblastic activity, tearing of periodontal ligament and proliferation of capillary at tension side between 1,25-Dihydroxyvitamin $D_3$ injection side and the control side. 4. The osteoclastic activity and the resorption of alveolar bone was greater in 1,25-Dihydroxyvitamin $D_3$ injection side than the control side at 36 hours after force application.