• Journal of Microbiology and Biotechnology
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• v.20 no.12
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• pp.1637-1646
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• 2010

The bacterium Deinococcus radiodurans is one of the most resistant organisms to ionizing radiation and other DNA-damaging agents. Although, at present, 30 Deinococcus species have been identified, the whole-genome sequences of most species remain unknown, with the exception of D. radiodurans (DRD), D. geothermalis, and D. deserti. In this study, comparative genomic hybridization (CGH) microarray analysis of three Deinococcus species, D. radiopugnans (DRP), D. proteolyticus (DPL), and D. radiophilus (DRPH), was performed using oligonucleotide arrays based on DRD. Approximately 28%, 14%, and 15% of 3,128 open reading frames (ORFs) of DRD were absent in the genomes of DRP, DPL, and DRPH, respectively. In addition, 162 DRD ORFs were absent in all three species. The absence of 17 randomly selected ORFs was confirmed by a Southern blot. Functional classification showed that the absent genes spanned a variety of functional categories: some genes involved in amino acid biosynthesis, cell envelope, cellular processes, central intermediary metabolism, and DNA metabolism were not present in any of the three deinococcal species tested. Finally, comparative genomic data showed that 120 genes were Deinococcus-specific, not the 230 reported previously. Specifically, ddrD, ddrO, and ddrH genes, previously identified as Deinococcus-specific, were not present in DRP, DPL, or DRPH, suggesting that only a portion of ddr genes are shared by all members of the genus Deinococcus.

• Journal of Microbiology and Biotechnology
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• v.26 no.11
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• pp.1924-1932
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• 2016

Mycophenolic acid (MPA) is an antibiotic produced by Penicillium brevicompactum. MPA has antifungal, antineoplastic, and immunosuppressive functions, among others. ${\beta}-Hydroxy-{\beta}-methylglutaryl-CoA$ (HMG-CoA) lyase is a key enzyme in the bypass metabolic pathway. The inhibitory activity of HMG-CoA lyase increases the MPA biosynthetic flux by reducing the generation of by-products. In this study, we cloned the P. brevicompactum HMG-CoA lyase gene using the thermal asymmetric interlaced polymerase chain reaction and gene walking technology. Agrobacterium tumefaciens-mediated transformation (ATMT) was used to insert a mutated HMG-CoA lyase gene into P. brevicompactum. Successful insertion of the HMG-CoA lyase gene was confirmed by hygromycin screening, PCR, Southern blot analysis, and enzyme content assay. The maximum MPA production by transformants was 2.94 g/l. This was 71% higher than wild-type ATCC 16024. Our results demonstrate that ATMT may be an alternative practical genetic tool for directional transformation of P. brevicompactum.

• KSBB Journal
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• v.13 no.2
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• pp.214-219
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• 1998

Polymerase chain reaction(PCR) was conducted to obtain the gene encoding glucose oxidase(GOD) from Aspergillus niger(ATCC 2110) and the DNA sequence determined was coincided with published GOD sequence from A. niger. Recombinant transforming vector containing GOD and hygromycin B(hyg.B) resistant gene(hph) was constructed and used for further transformation of A. niger ATCC 2110. Selectivity of hyg.B against A. niger differed depending on which media were used i.e., nutrient-rich media such as potato dextrose agar(PDA) and complete medium(CM) showed only 50% growth inhibition at 400 $\mu$m ml$^-1$ of hyg.B while the minimal media inhibited mycelial growth completely at 200 $\mu$m ml$^-1$ of hyg.B. Twenty to sixty putative transformants were isolated from the hyg.B-containing minimal top agar, transferred successively onto alternating selective and nonselective media for a mitotic stability of hyg.B resistance and, then, single-spored. Among the stable transformants, the transformant(GOD1-6) grown by flask culture showed the considerable increase of extracellular GOD activity, which was estimated to the degree of 50% - 100% comparing to that of wild type. Transformation of tGOD1-6 was resulted from integration of the vectors into heterologous as well as homologous regions of the A. niger genome. Southern blot analysis revealed that there were two independent integrations of vector into fungal genome and one into the GOD gene due to homologous recombination. In addition, GOD activity and sodium gluconate production when tGOD1-6 was fed-batch fermented were enhanced 11 fold and 2.25 fold, respectively, compared to that of the wild type.

• BMB Reports
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• v.38 no.3
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• pp.320-327
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• 2005

Five ripening-related ACC synthase cDNA isoforms were cloned from 80% ripe papaya cv. 'Sinta' by reverse transcription-PCR using gene-specific primers. Clone 2 had the longest transcript and contained all common exons and three alternative exons. Clones 3 and 4 contained common exons and one alternative exon each, while clone 1, the most common transcript, contained only the common exons. Clone 5 could be due to cloning artifacts and might not be a unique cDNA fragment. Thus, there are only four isoforms of ACC synthase mRNA. Southern blot analysis indicates that all five clones came from only one gene existing as a single copy in the 'Sinta' papaya genome. Multiple sequence alignment indicates that the four isoforms arise from a single gene, possibly through alternative splicing mechanisms. All the putative alternative exons were present at the 5'-end of the gene comprising the N-terminal region of the protein. 'Sinta' ACC synthase cDNAs were of the capacs 1 type and are most closely related to a 1.4 kb capacs 1-type DNA(AJ277160) from Eksotika papaya. No capacs 2-type cDNAs were cloned from 'Sinta' by RT-PCR. This is the first report of possible alternative splicing mechanism in ripening-related ACC synthase genes in hybrid papaya, possibly to modulate or fine-tune gene expression relevant to fruit ripening.

• Proceedings of the Botanical Society of Korea Conference
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• 1987.07a
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• pp.261-282
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• 1987

Plants store a significant amount of their nitrogen, sulfur and carbon reserves as storage proteins in seed tissues. The major proteins present in rice seeds are the glutelins. Glutelins are initially synthesized at 4-6 days postanthesis and deposited into protein bodies via Golgi apparatus. Based on nucleic acid sequences and Southern blot analysis, the three isolated glutelin genomic clones were representative members of three gene subfamilies each containing 5 to 8 copies. A comparison of DNA sequences displayed by relevant regions of these genomic clones showed that two subfamilies, represented by clones, Gt1 and Gt2, were closely, related and probably evolved by more recent gene duplication events. The 5' flanking and coding sequences of Gt1 and Gt2 displayed at least 87% homolgy. In contrast, Gt3 showed little or no homolgy in the 5' flanking sequences upstream of the putative CAAT boxes and exhibited significant divergence in all other portions of the gene. Conserved sequences in the 5' flanking regions of these genes were identified and discussed in light of their potential regulatory role. The derived primary sequences of all three glutelin genomic clones showed significant homology to the legume 11S storage proteins indicating a common gene origin. A comparison of the derived glutelin primary sequences showed that mutations were clustered in three peptide regions. One peptide region corresponded to the highly rautable hypervariable region of legume peptide region of legume 11S storage proteins, a potential target area for protein modification. Expression studies indicated that glutelin mRNA transcripts are differentially accumulated during endosperm development. Promoterss of Gt2 and Gt3 were functional as they direct transient expression of chloramphenicol acetyltransferase in cultured plant cell.

• Journal of Physiology & Pathology in Korean Medicine
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• v.21 no.4
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• pp.998-1003
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• 2007

The green marine algae, Capsosiphon fulvescens (CF) is a food supplement cultivated in south coast of Southern Korea. The purpose of this study was to investigate the mechanism of CF-induced hypopigmentation. The present study was designed to determine the effect of CF extracton melanogenesis in B16 cells, particularly its specific effects on tyrosinase and tyrosinase-related protein 2 (TRP-2). We measured melanin contents and analyzed melanosome associated protein levels using Western blot and Reverse transcription-polymerase chian reaction (RT-PCR) analysis. CF extract markedly inhibited melanin synthesis and tyrosinase activity. In addition, cellular dendricity was slightly decreased by CF extract. In further experiments, CF extract significantly reduced the protein levels of tyrosinase and TRP-2 in B16 cells. RT-PCR analysis revealed that tyrosinase and TRP-2 mRNA levels were unaffected by CF treatment. Therefore, these results suggest that hypopigmentary effect of CF was due to post-translational degradationof tyrosinase and TRP-2.

• Journal of Applied Biological Chemistry
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• v.43 no.1
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• pp.5-11
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• 2000

Three cDNA clones encoding rice calmodulin (CaM) isoforms (OsCaM-1, OsCaM-2, and OsCaM-3) were isolated from a rice cDNA library constructed from suspension-cultured rice cells treated with fungal elicitor. The coding regions of OsCaM-1 and O.sCaM-2 were 89% homologous at DNA Ievel, whereas the 5' and 3' untranslated regions were highly divergent. The polypeptides encoded by OsCaM-1 and OsCaM-2 was identical except two conservative substitution at position 8 and 75. The coding region of OsCaM-3 was consist of a typical conserved CaM domain and an additional C-terminal extension. The amino acid sequence of conserved CaM domain of OsCaM-3 shared only 86% identity with that OsCaM-1. The OsCaM-3 cDNA is belongs to a novel group of calmodulin gene due to its C-terminal extension of 38 amino acids, a large number of which are positively charged. The extension also contains a C-terminal CaaX-box prenylation site (CVlL). Genomic Southern analysis revealed at least six copies of CaM or CaM-related genes, suggesting that calmodulin may be represented by a small multigene family in the rice geneme. Expression of OsCaM gene was examined through Northern blot analysis. Transcript level of OsCaM-3 was increased by treatment with a fungal elicitor, whereas the OsCaM-1 and OsCaM-2 genes did not respond to the fungal elicitor. The expression of OsCaM-3 gene was remarkable inhibited in the rice cells treated with cyclosporine A, calcinurin inhibitor.

• The Korean Journal of Mycology
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• v.38 no.1
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• pp.48-53
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• 2010

Agrobacterium-mediated transformation was conducted in order to generate DNA insertional mutants of Flammulina velutipes. Agrobacterium tumefaciens AGL-1 harboring pBGgHg was transformed into gill tissues of Flammulina velutipes strain KACC42777. The transformants resistant on hygromycine ($30\;{\mu}g/ml$) were confirmed by PCR. The targeted insertional sites were amplified by inverse PCR and sequenced. To find the phenotype variation of all generated transformants, bottle cultivation which followed by the standard cultivation protocol were conducted. Color variation was observed on the cultivated fruiting bodies. Furthermore, the transformant pool will be used as a good genetic resources for studying gene function.

• Journal of Microbiology
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• v.43 no.4
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• pp.331-336
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• 2005

The objective of this study was to assess the strain-specificity of a DNA probe, Fu12, for Fusobacterium nucleatum subsp. nucleatum ATCC $25586^T$ (F. nucleatum ATCC $25586^T$), and to develop sets of strain-specific polymerase chain reaction (PCR) primers. Strain-specificity was tested against 16 strains of F. nucleatum and 3 strains of distinct Fusobacterium species. Southern blot hybridization revealed that the Fu12 reacted exclusively with the HindIII-digested genomic DNA of F. nucleatum ATCC $25586^T$. The results of PCR revealed that three pairs of PCR primers, based on the nucleotide sequence of Fu12, generated the strain-specific amplicons from F. nucleatum ATCC $25586^T$. These results suggest that the DNA probe Fu12 and the three pairs of PCR primers could be useful in the identification of F. nucleatum ATCC $25586^T$, especially with regard to the determination of the authenticity of the strain.

• Korean Journal of Plant Tissue Culture
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• v.21 no.5
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• pp.315-318
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• 1994

To obtain transformed plants, we cocultured cotyledonary explants of Codonopsis lanceolata with Agrobacterium tumefaciens LBA4404, a disamed strain harboring a binary vector pBI121 carrying the CaMV35S promoter-$\beta$-glucuronidase (GUS) gene fusion used as a reporter gene and NOS promoter-neomycin phosphotransferase gene as a positive selection marker in MS liquid medium with 1mg/L BA. After 48 h of culture, explants were transferred onto MS solid medium with Img/L BA, 250mg/L carbenicillin, and 100mg/L kanamycin sulfate and cultured in the dark. Numerous adventitious buds formed on the cut edges of the explants after 2 weeks of culture. When subjected to GUS histochemical assay buds showed a positive response at a frequency of 15%. Explants formed adventitious shoot at a frequency of 56.7%, after 6 weeks of culture. Upon transfer onto the basal medium, most of the shoots were rooted and subsequently the regenerants were transplanted to potting soil. Southern blot analysis confirmed that the GUS gene was incorporated into the genomic DNA of the GUS-positive regenerants.