• Journal of Microbiology and Biotechnology
• /
• v.31 no.6
• /
• pp.882-889
• /
• 2021

In order to use an enzyme industrially, it is necessary to increase the activity of the enzyme and optimize the reaction characteristics through molecular evolution techniques. We used the error-prone PCR method to improve the reaction characteristics of LipCA lipase discovered in Antarctic Croceibacter atlanticus. Recombinant Escherichia coli colonies showing large halo zones were selected in tributyrin-containing medium. The lipase activity of one mutant strain (M3-1) was significantly increased, compared to the wild-type (WT) strain. M3-1 strain produced about three times more lipase enzyme than did WT strain. After confirming the nucleotide sequence of the M3-1 gene to be different from that of the WT gene by four bases (73, 381, 756, and 822), the secondary structures of WT and M3-1 mRNA were predicted and compared by RNAfold web program. Compared to the mean free energy (MFE) of WT mRNA, that of M3-1 mRNA was lowered by 4.4 kcal/mol, and the MFE value was significantly lowered by mutations of bases 73 and 756. Site-directed mutagenesis was performed to find out which of the four base mutations actually affected the enzyme expression level. Among them, one mutant enzyme production decreased as WT enzyme production when the base 73 was changed (T→ C). These results show that one base change at position 73 can significantly affect protein expression level, and demonstrate that changing the mRNA sequence can increase the stability of mRNA, and can increase the production of foreign protein in E. coli.

• The Korea Journal of Herbology
• /
• v.28 no.5
• /
• pp.1-6
• /
• 2013

Objectives : This study was conducted to identify the original Sinomini Caulis et Rhizoma plant among Stephania tetrandra, Cocculus trilobus, and Aristolochiae fangchi to develop the genetic marker for Sinomini Caulis et Rhizoma. Methods : Sinomenium acutum was identified by the classification and identification committee of the National Center for Standardization of Herbal Medicines. The chloroplast ndhF gene was amplified. We performed sequences alignment analysis of Sinomenium acutum, Stephania tetrandra, C. trilobus, and A. fangchi using BioEdit program. The SFR markers designed were consisted of SF01, SR04, and SR05 primers. Results : Many variations of Sinomeni Caulis et Rhizoma are currently commercialized as herbal medicine. We compared the base sequences of the ndhF intergenic space of chloroplast DNA with Sinomenium acutum, Stephania tetrandra, C. trilobus, and A. fangchi. According to the results, it showed that the nucleotide variations were seen in 30 genes of four species. Phylogenetic analysis revealed that 4 species were classified into five groups based on an inter-group divergence in nucleotide sequence of 9%. We developed SFR marker nucleotides enough to authenticate respective species and confirmed its application on the band size at 419 base pair. These sequence differences at corresponding positions were available genetic markers to identity the Sinomeni Caulis et Rhizoma. Conclusions : Base on these results, the ndhF region was effective in distinguishing Sinomini Caulis et Rhizoma The SFR genetic marker was useful for identifying Sinomini Caulis et Rhizoma with other species.

• Journal of the Korean Magnetic Resonance Society
• /
• v.18 no.2
• /
• pp.52-57
• /
• 2014

The TCP domain is a DNA-binding domain present in plant transcription factors and plays important roles in various biological functions. The hydrogen exchange rate constants of the imino protons were determined for the three DNA duplexes containing the DNA-binding sites for the TCP11, TCP15, and TCP20 transcription factors using NMR spectroscopy. The M11 duplex displays unique hydrogen exchange property of the five base pairs in the first binding site (5'-GTGGG-3'). However, the M15 and M20 duplexes lead to clear changes in thermal stabilities of these five base pairs. The unique dynamic features of the five base pairs in the first binding site might play crucial roles in the sequence-specific DNA binding of the class I TCP transcription factors.

• Asian Pacific Journal of Cancer Prevention
• /
• v.14 no.2
• /
• pp.1155-1157
• /
• 2013

Cancer is a highly complex medical problem with ramifications for public health throughout the world. Most studies have mainly focused on change in the nuclei as being aetiologically responsible. Few have examined the relationship between the cytoplasm and cancer, despite the fact that research has indicated that the cytoplasmic environment is an important factor for cellular differentiation and that the genetic information provided by the nucleus is entirely dependent on this environment for its expression. Gene mutations may be the result, rather than the cause of carcinogenesis. We submit a new concept - "short base sequences" (50-500 bps, including DNA or RNA sequences) in the cytoplasm which could play an important role in carcinogenesis. This is a new theory to explain the origin of the cancer.

• Proceedings of the Korean Society of Plant Pathology Conference
• /
• 1995.06b
• /
• pp.1-19
• /
• 1995

The plasmid pJEL 101 contains a highly repetitive element from the genome of Xanthomonas oryae pv. oryzae that has properties of an insertional element. The insertional nature of the element, hereto referred to as IS203, was confirmed by molecular analyses of the element and three related elements that were isolated from X. oryzae. The related sequences were isolated on the basis of transposition to the transposon-trapping vector pL3SAC and hybridization with pJEL101. The trapped elements (IS203a, IS203b, and IS203c) were each composed of 1,055 base pairs with 25 base terminal inverted repeats. The elements caused a three base pair target site duplication at the site of insertion in the sacRB gene. The sequence of pJEL 101 has 96% base pair identity with IS203a and 99% identity with IS203a and IS203c but lacks three nucleotides of the consensus left terminal repeat. IS203b has the same DNA sequences as IS203c but is inserted ito the sacRB gene in the opposite orientation. The longest open reading frame of IS203a could code for a protein of 318 amino acids and molecular weight of 37, 151. A search of the Genbank database revealed that IS203 has 51% identity with 909 nucleotides of IS4551 from Escherichia coli. The predicted protein of ORF1 has 40% and 30% amino acid identity to the ORF1 of Tn4551 and the transposase of IS30, respectively.

• Animal cells and systems
• /
• v.3 no.3
• /
• pp.303-309
• /
• 1999

Inter- and intraspecific genetic relationships between Rana amurensis from Korea and Russia and other brown frogs were investigated by nucleotide sequence of a 504 base pair (bp) fragment of the mitochondrial cytochrome b gene. Nucleotide sequence similarities among Korean populations of R. amurensis ranged from 99.6% to 97.6% and 98.8% within Russian populations. The nucleotide sequence similarity between Korean and Russian R. amurensis ranged from 86.9% to 85.5%. Based on Kimura-2-parameter distance, the sequence divergence between R. amurensis from Korea and Russia was 16.18% and 18.04% among other related brown frogs. interspecific sequence divergences among R. amurensis and other related brown frogs diverged by 20.3%. Using an estimate of 2-4% mitochondrial DNA sequence divergence per million years, Korean and Russian R. amurensis diverged about 8 to 4 million years ago (Mya) and other brown frogs diverged about 9 to 5 Mya from ancestral frogs and distributed from North Asia to Sakhalin in a short time. In the neighbor-joining and UPGMA tree R. amurensis was clustered into two groups with Korean and Russian populations and the other brown frogs were grouped separately with diverged trichotomous clusters (R. dybowskii and R. pirica, R. okinavana and R. tsushimensis, and R. japonica and R. longicrus).

• The Korean Journal of Quaternary Research
• /
• v.18 no.2 s.23
• /
• pp.33-42
• /
• 2004

In South Korea a Pedo-sedimentary Sequence(PS) indicating the Last Glacial Maximun(LGM) is typified y a brown to dark brown, relatively stiff paleosol layers formed by repetitive freezing and thawing processes which in turn left characteristi glossic textures in soil-solum, polygolnal structures with a flagipans, vertical soil wedges or freezing cracks, and horizontal foliations, As a pre-LGM sedimentary sequences (older than 25Ka), the Old Fluvial Sequence(OFS) overlain by the Slope Sedimentary Sequence(SS) are distributed commonly at the base level higher than 14-15m above present river-bed along the major river basin. After the LGM (ca. 18Ka), the Young Fluvial Sequence(YFS) appears at an altitude ascending order of sedimentary profiles. In this fluvial organic muds of Jangheungri site(Jinju), Sorori site(Cheonwon), and Youngsan estruarine rivermouth(Mokpo) were exemplified in order to interpret their formation ages and environments. As result of $^{14}C$ datings, the formation ages of te organic muds are Boelling to Alleroed (MIS-1). These organic muds were fomed in fluvial backswamp or local pond/bog in response to shifting fluvial system. On the basis of palynological production dominant with Abies/Picea-Betula and Ranunculaceae, Compositae, Cyperaceae, and Graminae, it was interpreted that more boreal to subboreal condition was prevailed rather than temperate like today during the formation of organic muds and soil moisture condition was a repetition of wet and dry condition.

• Journal of Microbiology and Biotechnology
• /
• v.8 no.6
• /
• pp.650-655
• /
• 1998

The chromosomal DNA fragment from Phaffia rhodozyma CBS 6938 which is able to autonomously replicate in the yeast Saccharomyces cerevisiae was cloned on an integrative URA3 plasmid. Its minimal fragment exhibiting autonomously replicating activiy in the S. cerevisiae gave a higher frequency transformation efficiency than that found for centromere-based plasmid, and enabled extrachromosoma1ly stable transmission of the plasmids in one copy per yeast cell under non-selective culture condition. The 836-bp DNA element lacked an ORF and did not contain any acceptable match to an ARS core consensus. Sequence analysis, however, displayed a cluster of three hairpin-Ioop-sequences with individual $\triangle {G_{25}}^{\circ}C$ free energy value of -10.0, -17.5, and -17.0 kcal. $mor^{-l}$as well as a 9-bp sequence with two base pair mismatches to the S. cerevisiae/E. coli gyrase-binding site. This 836-bp sequence also included one 7-bp sequence analogous to the core consensus of centromeric DNA element III (CDEIII) of S. cerevisiae, but CDEIII-like 7 bp sequence alone did not give a replicative function in this yeast.

• The KIPS Transactions:PartD
• /
• v.12D no.1 s.97
• /
• pp.111-120
• /
• 2005

Software development creates many product that class components, Class Diagram, form, object, and design pattern. So this Paper suggests Index/XML Sequence Relation information system for product abstraction and classification, the system of design product Sequence Relation abstraction which can store, reuse design patterns in the meta modeling database with pattern Relation information. This is Index/XML Sequence Relation system which can easily change various relation information of product for product abstraction and classification. This system designed to extract and classify design pattern efficiently and then functional indexing, sequence base indexing for standard pattern, code indexing to change pattern into code and grouping by Index-ID code, and its role information can apply by structural extraction and design pattern indexing process. and it has managed various products, class item, diagram, forms, components and design pattern.

• Journal of Microbiology
• /
• v.41 no.2
• /
• pp.129-136
• /
• 2003

The Epstein-Barr virus (EBV)-encoded latent membrane protein 1 (LMPI) exhibits considerable sequence heterogeneity among EBV isolates. Seven distinct EBV strains have been defined based on sequence polymorphisms in the LMPI gene, which are designated China 1, China 2, China 3, Alaskan, Mediterranean, NC, and the B95-8 strains. In this study, we analyzed a 30-bp deletion and sequence variations in the carboxy-terminal region of the LMPl gene in 12 EBV isolates from spontaneous lym-phoblastoid cell lines derived from individuals with non-EBV associated cancers in Korea. Eleven of the 12 isolates showed a 30-bp deletion spanning LMPI amino acids 342 to 353, suggesting a high prevalence of the LMPI 30-bp deletion variant among EBV isolates in Korea. In addition, all 12 isolates had a 15-bp common deletion in the 33-bp repeat region and multiple base-pair changes relative to the prototype B95-8 EBV strain along with variations in the number of the 33-bp repeats. The bp changes at positions 168746, 168694, 168687, 168395, 168357, 168355, 168631, 168320, 168308, 168295, and 168225 were highly conserved among the isolates. Comparative analysis of sequence change patterns in the LMPI carboxy-terminal coding region identified nine 30-bp deletion variants as China 1, two deletion variants as a possible interstrain between the Alaskan and China 1 strains, and a single undeleted variant as a possible variant of the Alaskan strain. These results suggest the predominance of the China 1 EBV strain in the Korean population.