• Korean Journal of Microbiology
• /
• v.29 no.1
• /
• pp.16-24
• /
• 1991

The yeast gene THR1 encodes the homoserine kinase (EC 2.7.1.39: HKase) which catalyses the first step of the threonine specific arm at the end of the common pathway for methionine and threonine biosynthesis. A recombinant plasmid pMC3 (12.6 kilobase pairs, vector YCp50) has been cloned into E. coli HB101 from a yeast genomic library through its complementing activity of a thr1 mutation in a yeast recipient strain M39-1D. When subcloned into pMC32 (8.6kbp, vector YRp7) and pMC35 (8.3 kbp, vector YIp5), the HindIII fragment (2.7 kbp) of pMC3 insery was positive in the thrI complementing activity in both yeast and E. coli auxotrophic strains. The linearized pMC35 was introduced into the original recipient yeast strain and the mitotically stable chromosomal integrant was identified among the transformants. Through the tetrad analysis, the integration site of the pMC35 was localized to the region of THR1 structural gene at an expected genetic distance of approximately 11.1 cM from the ARG4 locus on the right arm of the yeast chromosome VIII. When episomically introduced into the auxotrophic cells and cultured in Thr omission liquid medium, the cloned gene overexpressed the HKase in the order of thirteen to fifteenfold, as compared with a wildtype. HKase levels are repressed by addition of threonine at the amount of 300 mg/l and 1, 190 mg/l for pMC32 and pMC3, respectively. Data from genetic analysis and HKase response thus support that the cloned HindIII yeast DNA fragment contains the yeast thr1 structural gene, along with necessary regulatory components for control of its proper expression.

• The Journal of Korean Institute of Communications and Information Sciences
• /
• v.34 no.10A
• /
• pp.769-775
• /
• 2009

This paper proposes the optimal transmission parameter selection method for an energy efficient Wireless Personal Area Network (WPAN) system which is applicable to the Maritime Telematics targeting for various ship models. Since the transmission parameter selection is an important factor for WPAN system to decide its energy efficiency, we propose an energy consumption model for ship area network (SAN) employing IEEE 802.15.3 based TDMA HR-WPAN model and analyzes the effect of transmission parameter selection on the performance of energy consumption. In particular, the main performance decision parameter of the SAN applying HR-WPAN is path loss, since it is very varied according to the material of shipbuilding such as steel (large ship), FRP (medium size ship) and compound wood (small ship). Thus, we analyzed and demonstrated that the proper transmission parameter selection among transmit power, PHY data rate and fragment size for each ship model guarantee the energy efficiency.

• Journal of Crop Science and Biotechnology
• /
• v.10 no.2
• /
• pp.98-105
• /
• 2007

Phylogenetic relationships in Korean watermelons were evaluated by genetic similarity coefficients using 15 SSR(simple sequence repeat), 14 SCAR(sequence characterized amplified region) and 14 CAPS(sequence characterized amplified region) markers. The SSR markers were selected from previously reported melon and watermelon SSRs through testing polymorphisms within a set of commercial $F_1$ varieties. The SCAR and CAPS markers were developed from polymorphic AFLP(amplified fragment length polymorphism) markers between inbred lines 'BN4001' and 'BN4002'. From the AFLP analysis, 105 polymorphic fragments were identified between the inbred lines using 1,440 primer combinations of EcoRI+CNNN and XbaI+ANNN. Based on the sequencing data of these polymorphic fragments, we synthesized sequence specific primer pairs and detected clear and reliable polymorphisms in 27 primer pairs by indels(insertion/deletion) or RFLP(restriction fragment length polymorphism). A total of 43 sequence-based PCR markers were obtained and polymorphic information content(PIC) was analyzed to measure the informativeness of each marker in watermelon varieties. The average PIC value of SCAR markers was 0.41, which was similar to that of SSR markers. Genetic diversity was also estimated by using these markers to assess the phylogenetic relationships among commercial varieties of watermelon. These markers differentiated 26 Korean watermelon varieties into two major phylogenetic groups, but this grouping was not significantly correlated with their morphological and physiological characteristics. The mean genetic similarity was 66% within the complete set of 26 commercial varieties. In addition, these sequence-based PCR markers were reliable and useful to identify cultivars and genotypes of watermelon.

• Korean Journal of Microbiology
• /
• v.55 no.1
• /
• pp.1-8
• /
• 2019

Due to the major role played by several species of Streptococcus in the etiology of periodontitis, it is important to assess the pattern of Streptococcus pathogenic pathways within the infected subgingival pockets using a bacterial specific 16S rRNA fragment. From the total of 50 patients with periodontitis included in the study, only 23 Streptococcal isolates were considered for further analyses, in which their 16S rRNA fragments were amplified and sequenced. Then, a comprehensive phylogenetic tree was constructed and in silico prediction was performed for the observed Streptococcal species. The phylogenetic analysis of the subgingival Streptococcal species revealed a high discrimination power of the 16S rRNA fragment to accurately identify three groups of Streptococcus on the species level, including S. salivarius (14 isolates), S. anginosus (5 isolates), and S. gordonii (4 isolates). The employment of state-of-art in silico tools indicated that each Streptococcal species group was characterized with particular transcription factors that bound exclusively with a different 16S rRNA-based secondary structure. In conclusion, the observed data of the present study provided in-depth insights into the mechanism of each Streptococcal species in its pathogenesis, which differ in each observed group, according to the differences in the 16S rRNA secondary structure it takes, and the consequent binding with its corresponding transcription factors. This study paves the way for further interventions of the in silico prediction, with the main conventional in vitro microbiota identification to present an interesting insight in terms of the gene expression pattern and the signaling pathway that each pathogenic species follows in the infected subgingival site.

• BMB Reports
• /
• v.52 no.6
• /
• pp.373-378
• /
• 2019

The nucleotide-binding and oligomerization domain (NOD) is an innate pattern recognition receptor that recognizes pathogen- and damage-associated molecular patterns. The 29-kDa amino-terminal fibronectin fragment (29-kDa FN-f) is a matrix degradation product found in the synovial fluids of patients with osteoarthritis (OA). We investigated whether NOD2 was involved in 29-kDa FN-f-induced pro-catabolic gene expression in human chondrocytes. The expression of mRNA and protein was measured using quantitative real-time polymerase chain reaction (qrt-PCR) and Western blot analysis. Small interfering RNAs were used for knockdown of NOD2 and toll-like receptor 2 (TLR-2). An immunoprecipitation assay was performed to examine protein interactions. The NOD2 levels in human OA cartilage were much higher than in normal cartilage. NOD1 and NOD2 expression, as well as pro-inflammatory cytokines, including interleukin-1beta (IL-$1{\beta}$) and tumor necrosis factor-alpha (TNF-${\alpha}$), were upregulated by 29-kDa FN-f in human chondrocytes. NOD2 silencing showed that NOD2 was involved in the 29-kDa FN-f-induced expression of TLR-2. Expressions of IL-6, IL-8, matrix metalloproteinase (MMP)-1, -3, and -13 were also suppressed by TLR-2 knockdown. Furthermore, NOD2 and TLR-2 knockdown data demonstrated that both NOD2 and TLR-2 modulated the expressions of their adaptors, receptorinteracting protein 2 (RIP2) and myeloid differentiation 88, in 29-kDa FN-f-treated chondrocytes. 29-kDa FN-f enhanced the interaction of NOD2, RIP2 and transforming growth factor beta-activated kinase 1 (TAK1), an indispensable signaling intermediate in the TLR-2 signaling pathway, and activated nuclear factor-${\kappa}B$ (NF-${\kappa}B$), subsequently leading to increased expressions of pro-inflammatory cytokines and cartilage-degrading enzymes. These results demonstrate that 29-kDa FN-f modulated pro-catabolic responses via cross-regulation of NOD2 and TLR-2 signaling pathways.

• Korean Journal of Plant Taxonomy
• /
• v.34 no.1
• /
• pp.43-61
• /
• 2004

Molecular taxonomic studies were conducted to evaluate interspecific relationships in Korean Viola 34 taxa including two Japanese populations using RAPD(randornly amplified polymorphic DNA), ISSR(inter simple sequence repeat) and PCR-RFLP(restriction fragment length polymorphism) analysis. Only six and four primers out of 40 arbitrary and 12 ISSR primers were screened for 34 taxa, and were revealed 70 (98.6%) and 28 (96.6%) polymorphic bands, respectively. Fifteen restriction endonucleases produced 80 restriction sites and size variations from the large single copy region of cpDNA, 16 (20%) of which were polymorphic. The separate analyses from the RAPD, ISSR and PCR-RFLP data were incongruent in the relationships among 34 taxa, but combined data was in accordance with previous infrageneric classification system based on morphological characters, especially the subsection and series level. Section Chamaemelanium placed between subsect. Patellares and Vagimtae of section Nomimium was not formed as a distinct group. Viola alb ida complex including three very closely related taxa was recognized independent group within subsect. Patellares in combined data tree. This result strongly suggested that they should be treated to series Pinmtae. RAPD analysis was very useful to clarify the interspecific relationships among the species of Korean Viola than ISSH and PCR-RFLP analyses.

• Molecules and Cells
• /
• v.27 no.5
• /
• pp.547-556
• /
• 2009

Parathyroid hormone is the most important endocrine regulator of calcium concentration. Its N-terminal fragment (1-34) has sufficient activity for biological function. Recently, site-directed mutagenesis studies demonstrated that substitutions at several positions within shorter analogues (1-14) can enhance the bioactivity to greater than that of PTH (1-34). However, designing the optimal sequence combination is not simple due to complex combinatorial problems. In this study, support vector machines were introduced to predict the biological activity of modified PTH (1-14) analogues using mono-substituted experimental data and to analyze the key physicochemical properties at each position that correlated with bioactivity. This systematic approach can reduce the time and effort needed to obtain desirable molecules by bench experiments and provide useful information in the design of simpler activating molecules.

• Proceedings of the Korean Society of Plant Pathology Conference
• /
• 2003.10a
• /
• pp.115.1-115
• /
• 2003

Post-harvest decay, caused by Penicillium spp. is a serious problem of fruits worldwide. Morphological characteristics and molecular markers were used to characterize 22 Penicillium isolates from apples, 18 isolates from pears, 60 from oranges and 18 from grapes and 23reference isolates representing related Penicillium spp. to assess their diversity and resolve their taxonomy. Based on morphological and physiological characteristics, the isolates were grouped as identical or very similar to P. digitatum, P. italicum, P. ulaiense or very similar to P. crustosum, P. expansum, P. solitum and unidentified Penicillium spp. Based on sequence comparisons of ITS region, variable site were presented within and among the species, but there variation were not correlated with the species. Cluster analyses of AP-PCR fragment patterns using UP and L45 primer and the -tubulin gene sequence, the Penicillium species were segregated into distinct groups. Particularly. the -tubulin partial sequence data provided support for species concepts based on morphological and physiological characteristics.

• Proceedings of the Korea Database Society Conference
• /
• 1997.10a
• /
• pp.504-514
• /
• 1997

관계형 데이터베이스의 성능을 향상시키는데 중요한 요소 중의 하나는 트랜잭션을 처리하기 위해 데이터를 디스크에서 주기억장치로 옮기는데 필요한 디스크 액세스(access) 횟수이다. 본 연구는 관계형 데이터베이스에서 트랜잭션을 처리할 때, 릴레이션(relation)을 수직분할하여 디스크에 단편(fragment)으로 저장하므로써 필요한 단편만 액세스하여 액세스 횟수를 감소시키는데 목적이 있다. 단편에 속성을 중복할당하여 수직분할하므로써 트랜잭션을 만족시키는 단편의 수를 감소시켜 중복할당을 고려하지 않은 방법보다 디스크 액세스 횟수를 감소시킬 수 있다. 갱신트랜잭션의 경우 하나의 속성이 갱신되면 중복된 속성을 모두 갱신하여야 하므로 액세스 횟수가 증가하지만, 조회트랜잭션의 경우 각 단편에 속성을 중복할당하여 액세스 횟수를 감소시킬 수 있다. 본 연구에서는 속성의 중복을 허용하여 단편을 구성하는 경우에 중복을 고려하지 않은 경우를 포함하므로 효과적으로 디스크 액세스 횟수를 감소시킬 수 있다. 본 연구에서는 중복할당을 고려하여 디스크의 액세스 횟수를 최소화시킬 수 있는 수직분할문제의 0-1 정수계획모형을 개발하고, 모형에 대한 최적해법으로 분지한계법을 제안한다.

• Journal of Microbiology
• /
• v.40 no.1
• /
• pp.38-42
• /
• 2002

The strain KKI isolated from soil contaminated with polycyclic aromatic hydrocarbons was identified as Pseundomonas sp. based on analyses by MIDI and Biolog Identification System. Cellular and physiological responses of strain KKI to two-ring polycyclic aromatic hydrocarbon, naphthalene were evaluated using radiorespirometry, PLFAs and sequence analysis of Rieske-type iron sulfur center of dioxygenase. KKI was found to be able to rapidly mineralize naphthalene. Notably, KKI cells pregrown on phenanthrene were able to mineralize naphthalene much more rapidly than naphthalenepregrown cells. The total cellular fatty acids of KKI were comprised of eleven C-even and two C-odd fatty acids (fatty acids < 0.2% in abundance were not considered in this calculation). Lipids 12:0 2OH, 12:03 OH, 16:0, 18:1 6c, 18:0 increased for naphthalene-exposed cells, while lipids 18:1 7c1/15:0 ism 2OH, 17:0 cyclo, 18:1 7c, 19:0 cyclo decreased. Data from Northern hybridization using a naphthalene dixoygenase gene fragment cloned out from KKI as a probe provided the information that naphthalene dioxygenase gene was more highly expressed in cells grown on phenanthrene than naphthalene.