• Journal of Life Science
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• v.14 no.1
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• pp.38-44
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• 2004

Two genes, SinIFS1 and SinIFS2 from Korean soybean cultivar, Sinpaldalkong known as one of isoflavonerich cultivars, were cloned with PCR and degenerate primers. The sequences of two genes were analyzed with previously reported IFS genes of leguminous plants and their expression pattern in various environmental conditions was surveyed. The genomic clone of SinIFS1 contained 1,828bp nucleotides and encoded a polypeptide of 521 amino acids, and 1912bp nucleotides and a polypeptide of 521 amino acids for SinIFS2. Both genes included several conserved motifs, oxygen binding and activation (A/G-G-X-E/D-T-T/S), ERR triad (E...R....R), and heme binding (F-X-X-G-X-R-X-C-X-G) domain, which are typical in any member of cytochrome P45O superfamily. Very high sequence homology (>98%) was observed in the comparison with other IFSs of legumes. In the northern blot analysis to check the expression and increase of SinIFS1 to various environmental renditions (low temperature, light, dark, UV, and fungal elicitor), the most significant induction, more than 6 times of transcript level compared to the dark treatment as a control, was observed from the fungal elicitor treatment. The next up-regulated expression was from UV treatment (4${\times}$), low temperature and light conditions.

• Proceedings of the Korean Society of Applied Pharmacology
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• 2002.07a
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• pp.113-113
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• 2002

Phylogenetically conserved Bcl-2 family proteins play a pivotal role in the regulation of apoptosis from virus to human. Members of the Bcl-2 family consist of antiapoptotic proteins such as Bcl-2, Bcl-xL, and Bcl-w, and proapoptotic proteins such as BAD, Bax, BOD, and Bok. It has been proposed that anti- and proapoptotic Bcl-2 proteins regulate cell death by binding to each other and forming heterodimers. A delicate balance between anti- and proapoptotic Bcl-2 family members exists in each cell and the relative concentration of these two groups of proteins determines whether the cell survives or undergoes apoptosis. Mcl-1 (Myeloid cell :leukemia-1) is a member of the Bcl-2 family proteins and was originally cloned as a differentiation-induced early gene that was activated in the human myeloblastic leukemia cell line, ML-1 . Mcl-1 is expressed in a wide variety of tissues and cells including neoplastic ones. We recently identified a short splicing variant of Mcl-1 short (Mcl-IS) and designated the known Mcl-1 as Mcl-1 long (Mcl-lL). Mcl-lL protein exhibits antiapoptotic activity and possesses the BH (Bcl-2 homology) 1, BH2, BH3, and transmembrane (TM) domains found in related Bcl-2 proteins. In contrast, Mcl-1 S is a BH3 domain-only proapoptotic protein that heterodimerizes with Mcl-lL. Although both Mc1-lL and Mcl-lS proteins contain BH domains fecund in other Bcl-2 family proteins, they are distinguished by their unusually long N-terminal sequences containing PEST (proline, glutamic acid, serine, and threonine) motifs, four pairs of arginine residues, and alanine- and glycine-rich regions. In addition, the expression pattern of Mcl-1 protein is different from that of Bcl-2 suggesting a unique role (or Mcl-1 in apoptosis regulation. Tankyrasel (TRF1-interacting, ankyrin-related ADP-related polymerasel) was originally isolated based on its binding to TRF 1 (telomeric repeat binding factor-1) and contains the sterile alpha motif (SAM) module, 24 ankyrin (ANK) repeats, and the catalytic domain of poly(adenosine diphosphate-ribose) polymerase (PARP). Previous studies showed that tankyrasel promotes telomere elongation in human cells presumably by inhibiting TRFI though its poly(ADP-ribosyl)action by tankyrasel . In addition, tankyrasel poly(ADP-ribosyl)ates Insulin-responsive amino peptidase (IRAP), a resident protein of GLUT4 vesicles, and insulin stimulates the PARP activity of tankyrase1 through its phosphorylation by mitogen-activated protein kinase (MAPK). ADP-ribosylation is a posttranslational modification that usually results in a loss of protein activity presumably by enhancing protein turnover. However, little information is available regarding the physiological function(s) of tankyrase1 other than as a PARP enzyme. In the present study, we found tankyrasel as a specific-binding protein of Mcl-1 Overexpression of tankyrasel led to the inhibition of both the apoptotic activity of Mel-lS and the survival action of Mcl-lL in mammalian cells. Unlike other known tankyrasel-interacting proteins, tankyrasel did not poly(ADP-ribosyl)ate either of the Mcl-1 proteins despite its ability to decrease Mcl-1 proteins expression following coexpression. Therefore, this study provides a novel mechanism to regulate Mcl-1-modulated apoptosis in which tankyrasel downregulates the expression of Mcl-1 proteins without the involvement of its ADP-ribosylation activity.

• Biomolecules & Therapeutics
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• v.23 no.5
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• pp.442-448
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• 2015

We evaluated the chondroprotective effects of wogonin by investigating its effects on the gene expression and production of matrix metalloproteinase-3 (MMP-3) in primary cultured rabbit articular chondrocytes, as well as on production of MMP-3 in the rat knee. Rabbit articular chondrocytes were cultured in a monolayer, and RT-PCR was used to measure interleukin-$1{\beta}$ (IL-$1{\beta}$)-induced expression of MMP-3, MMP-1, MMP-13, a disintegrin and metalloproteinase with thrombospondin motifs-4 (ADAMTS-4), and type II collagen. In rabbit articular chondrocytes, the effects of wogonin on IL-$1{\beta}$-induced production and proteolytic activity of MMP-3 were investigated using western blot analysis and casein zymography, respectively. The effect of wogonin on MMP-3 protein production was also examined in vivo. In rabbit articular chondrocytes, wogonin inhibited the expression of MMP-3, MMP-1, MMP-13, and ADAMTS-4, but increased expression of type II collagen. Furthermore, wogonin inhibited the production and proteolytic activity of MMP-3 in vitro, and inhibited production of MMP-3 protein in vivo. These results suggest that wogonin can regulate the gene expression and production of MMP-3, by directly acting on articular chondrocytes.

• Journal of Life Science
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• v.17 no.1 s.81
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• pp.6-11
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• 2007

[ $\beta$ ]-Fructofuranosidases, a family 32 of glycoside hydrolases (GH32), share three conserved domains including the W(L/M)(C/N)DP(Q/N), FRDPK, and ECP(D/G) motifs. The functional role of the conserved acidic residues within three domains of levan fructotransferase, one of the $\beta-fructofuranosidases$, from Microbacterium sp. AL-210 was studied by site-directed mutagenesis. Each mutant was overexpressed in E. coli BL21(DE3) and purified by using Hi-Trap chelating affinity chromatography and fast performance liquid chromatography. Substitution of Asp-63 by Ala, Asp-195 by Asn, and Glu-245 by Ala and Asp decreased the enzyme activity by approximately 100-fold compared to the wild-type enzyme. This result indicates that three acidic residues Asp-63, Asp-195, and Glu-245 play a major role in catalysis. Since the three acidic residues are present in a conserved position in inulinase, levanase, levanfructotransferase, and invertase, they are likely to have a common functional role as nucleophile, transition state stabilizer, and general acid in $\beta-fructofuranosidases$.

• Journal of Life Science
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• v.19 no.8
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• pp.1159-1163
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• 2009

It has been postulated that endoplasmic (ER) stress is involved in the development of several diseases. However, the detailed molecular mechanisms have not been fully understood. Therefore, we characterized a genetic network of genes induced by ER stress using cDNA microarray and gene set expression coherence analysis (GSECA), and identified gene function as well as several transcription regulators associated with ER stress. We analyzed time-dependent gene expression profiles in thapsigargin-treated Sk-Hep1 using an oligonucleotide expression chip, and then selected functional gene sets with significantly high expression coherence which was processed into functional clusters according to the expression similarities. The functions related to sugar binding, lysosome, ribosomal protein, ER lumen, and ER to golgi transport increased, whereas the functions with mRNA processing, DNA replication, DNA repair, cell cycle, electron transport chain and helicase activity decreased. Furthermore, functional clusters were investigated for the enrichment of regulatory motifs using GSECA, and several transcriptional regulators associated with regulation of ER-induced gene expression were found.

• Journal of Microbiology and Biotechnology
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• v.20 no.12
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• pp.1735-1743
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• 2010

The full-length genes gyrB (2,415 bp), parC (2,277 bp), and parE (1,896 bp) in Edwardsiella tarda were cloned by PCR with degenerate primers based on the sequence of the respective quinolone resistance-determining region (QRDR), followed by elongation of 5' and 3' ends using cassette ligation-mediated PCR (CLMP). Analysis of the cloned genes revealed open reading frames (ORFs) encoding proteins of 804 (GyrB), 758 (ParC), and 631 (ParE) amino acids with conserved gyrase/topoisomerase features and motifs important for enzymatic function. The ORFs were preceded by putative promoters, ribosome binding sites, and inverted repeats with the potential to form cruciform structures for binding of DNA-binding proteins. When comparing the deduced amino acid sequences of E. tarda GyrB, ParC, and ParE with those of the corresponding proteins in other bacteria, they were found to be most closely related to Escherichia coli GyrB (87.6% identity), Klebsiella pneumoniae ParC (78.8% identity), and Salmonella Typhimurium ParE (89.5% identity), respectively. The two topoisomerase genes, parC and parE, were found to be contiguous on the E. tarda chromosome. All 18 quinolone-resistant isolates obtained from Korea thus far did not contain subunit alternations apart from a substitution in GyrA (Ser83$\rightarrow$Arg). However, an alteration in the QRDR of ParC (Ser84$\rightarrow$Ile) following an amino acid substitution in GyrA (Asp87$\rightarrow$Gly) was detected in E. tarda mutants selected in vitro at $8{\mu}g/ml$ ciprofloxacin (CIP). A mutant with a GyrB (Ser464$\rightarrow$Leu) and GyrA (Asp87$\rightarrow$Gly) substitution did not show a significant increase in the minimum inhibitory concentration (MIC) of CIP. None of the in vitro mutants exhibited mutations in parE. Thus, gyrA and parC should be considered to be the primary and secondary targets, respectively, of quinolones in E. tarda.

• Korean Journal of Plant Taxonomy
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• v.41 no.4
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• pp.299-314
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• 2011

The choice of molecular markers is the first step when selecting experimental plans in the field of population genetics. The popular molecular markers in population genetic studies are mainly allozyme, RAPD, RFLP, AFLP, microsatellite, SNP and ISSR. Among these, microsatellites are frequently found in nuclear, chloroplast and mitochondrial genome, showing a high level of polymorphism and nuclear microsatellites are codominant. Thus, it is a favorable molecular marker for population structure analyses and genetic diversity studies. Microsatellites are composed of tandem repeated 1~6 base pair nucleotide motifs and can be easily amplified by PCR reactions using locus specific primers. Because microsatellites have low cross-species transferability, however, they are only applicable between phylogenetically close species. In wild plants, the lack of genomic information and the high development cost of the microsatellite obstruct the wider use of microsatellites in plant population genetics research. In this review, we introduce the basis for microsatellite markers, the development process, and analytical methods as well as evolutionary models and their applications. In addition, possible genotyping errors which lead to erroneous conclusions are discussed.

• Journal of the Korean Institute of Landscape Architecture
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• v.38 no.3
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• pp.115-125
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• 2010

A theme park is not just a recreational space for leisure activities, but also a place of storytelling as collected around abstract boundaries called themes. These stories are 'a space that tells the meaning' that the visitor is looking for and the Robot Land space offers robots, humans, and nature. This study is a description of the design strategy and content of the work which was elected as a subject of the subsequent rank negotiation of the Masan Robot Land design contest for the selection of a private contractor. The focus of the plan is, first, the organizational power of each space and the delivery power of a theme for the history of revisits, which might be considered depending on whether or not the theme park has been successful in the visitor's mind. Second, it is to actively use the potential of Masan, which is not only the key hub of the mechanical industry but also has beautiful coastal resources. First, they created a space that can flexibly react depending on the user's desire and the change of form, minimizing environmental damage by using a linear metabolism that can provide an amalgam of the elemental characteristics of robots, humans, and nature as motifs. They introduced a planting plan for the admissions square, an existing forest, slope, vacation spot, the inside of a complex, and Eco Island, etc. by utilizing symbolic meaning and adjusting to the spatial characteristics of each space. In addition, they sought a detailed space by setting up zones tailored to the use and character of the subject area, having exhibitions and education about robots, vacation facilities for lodgers, various recreational and commercial facilities, and space for utopian gardens as themes. They planned Masan Robot Land to be a true cultural space that creates mental richness on the basis of not only the economical effects but also local emotion.

• Journal of KIISE:Databases
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• v.30 no.5
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• pp.507-520
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• 2003

In this paper, an automatic construction method of theme melody index for large music database and an associative content-based music retrieval mechanism in which the constructed theme melody index is mainly used to improve the users' response time are proposed. First, the system automatically extracted the theme melody from a music file by the graphical clustering algorithm based on the similarities between motifs of the music. To place an extracted theme melody into the metric space of M-tree, we chose the average length variation and the average pitch variation of the theme melody as the major features. Moreover, we added the pitch signature and length signature which summarize the pitch variation pattern and the length variation pattern of a theme melody, respectively, to increase the precision of retrieval results. We also proposed the associative content-based music retrieval mechanism in which the k-nearest neighborhood searching and the range searching algorithms of M-tree are used to select the similar melodies to user's query melody from the theme melody index. To improve the users' satisfaction, the proposed retrieval mechanism includes ranking and user's relevance feedback functions. Also, we implemented the proposed mechanisms as the essential components of content-based music retrieval systems to verify the usefulness.

• Korean Journal of Microbiology
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• v.41 no.4
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• pp.246-254
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• 2005

Analysis of the complete genome of Neurospora crassa reveals that at least 19 proteins contain tetratricopeptide repeat (TPR) motifs. One of them shows over $60\%$ homology to Ssn6 of Saccharomyces cerevisiae, a universal repressor that mediates repression of genes involved in various cellular processes. Mutant strains generated by RIP (repeat-induced point mutation) process showed four distinctive vegetative growth patterns and slow growth in various rates. Firstly, a mutant showed denser mycelial growth, yellow, csp, and looked like ropy mutant. Secondly, slower growth, dense mycelial, and conidial phenotype. Thirdly, extremely slower growth and aconidial. And finally, flat, tittle aerial hyphae, acon, and similar with a rco-1 RIP mutant. They are all male-fertile, yet female-sterile and produced little or no perithecium. It seems that various phenotypes were occurred depending upon mostly likely, the degree of RIP. These results indicate that this gene may be involved in several cellular possess during vegetative growth, and asexual and sexual development. Therefore it is pleiotropic. Sequence analysis of cDNA shows that it encodes a putative 102 kDa protein composed of 917 amino acids, and has six introns. It is designated rcm-1 (regulation of conidiation and morphology).