• Proceedings of the Microbiological Society of Korea Conference
• /
• 2002.10a
• /
• pp.162-172
• /
• 2002

Schizosaccharomyces pombe is suited for the study of cytokinesis as it divides by forming a septum in the middle of the cell at the end of mitosis. To enhance our understanding of the cytokinesis, we have carried out a genetic screen for temperature-sensitive S. pombe mutants that show defects in septum formation and cell division. Here we present the isolation and characterization of a new temperature-sensitive mutant, sun1(septum uncontrolled), which undergoes uncontrolled septation during cell division cycle at restrictive temperature $(37^{\circ}C)$. In sun1 mutant, actin ring and septum are positioned at random locations and angles, and nuclear division cycle continues. These observations suggest that the sun] gene product is required for the proper placement of the actin ring as well as precise septation. The sun] mutant is monogenic recessive mutation unlinked to previously known various cdc genes of S. pombe. In a screen for $sunl^+$ gene to complement the sun] mutant, we have cloned a gene, $susl^+$(suppressor of sun1 mutant), that encodes a protein of 689 amino acids. The predicted amino acid sequence of $susl^+$ gene is similar to the human hMadlp and Saccharomyces cerevisiae Mad1p, a component of the spindle checkpoint in eukaryotic cells. The null mutant of $susl^+$ gene grows normally at various temperatures and has the increased sensitivity to anti-microtubule drug, while $susl^+$ mutant shows no sensitivity to microtubule destabilizing drugs. The putative S. pombe Sus1p directly interacts with S. pombe Mad2p in yeast two-hybrid assays. These data suggest that the newly isolated susr gene encodes S. pombe Mad1p and suppresses sun] mutant defective in controlled septation in a cell division cycle.

• Journal of KIISE:Databases
• /
• v.41 no.4
• /
• pp.249-255
• /
• 2014

Copy number variations(CNVs) are a recently recognized class of human structural variations and are associated with a variety of human diseases, including cancer. To find important cancer genes, researchers identify novel CNVs in patients with a particular cancer and analyze large amounts of genomic and clinical data. We present a tool called CNVDAT which is able to detect CNVs from NGS data and systematically analyze the genomic and clinical data associated with variations. CNVDAT consists of two modules, CNV Detection Engine and Sequence Analyser. CNV Detection Engine extracts CNVs by using the multi-resolution system of scale-space filtering, enabling the detection of the types and the exact locations of CNVs of all sizes even when the coverage level of read data is low. Sequence Analyser is a user-friendly program to view and compare variation regions between tumor and matched normal samples. It also provides a complete analysis function of refGene and OMIM data and makes it possible to discover CNV-gene-phenotype relationships. CNVDAT source code is freely available from http://dblab.hallym.ac.kr/CNVDAT/.

• The Journal of Korean Society of Virology
• /
• v.30 no.2
• /
• pp.101-112
• /
• 2000

Rotaviruses are the most common cause of severe vomiting and diarrhea in children worldwide and classified as a genus in the family Reoviridae. Rotavirus has eleven segmented dsRNAs and the virion consists of three shells. Outer capsid VP7 and VP4 induce neutralizing antibodies and are classified into G types (glycoprotein VP7) and P types (protease-sensitive VP4). Characterization of VP7 gene of Korean isolates of human rotavirus was performed using multiplex PCR and nucleotide sequence analysis. After RT-PCR amplification of full length (1,062 bp) of VP7 genes, the amplified PCR products were G typed by multiplex PCR and the nucleotide sequences were compared with those of reference rotavirus from GenBank. The G type analysis revealed that 25% (2/8) belong to G1, whereas 37.5% (3/8) benong to G2 and G4, respectively. The Korean isolates within the same serotypes showed high homology of nucleotide sequences and could be discriminated from foreign isolates exception with two strains (CAU009 and CAU022). But Korean isolates CAU009 and CAU022 were close related into japanease isolates 417 (99.2%) and indian isolates (97.6%) than Korean isolatese. Our results showed that these two strains were supposed to be originated from abroad. As a results, The G typing and nucleotide sequence analysis of VP7 gene of rotavirus isolated from infants in Korea could be used for identification, serotying and determination of novel or unusual strains of rotaviruses.

• Journal of Plant Biotechnology
• /
• v.29 no.2
• /
• pp.139-144
• /
• 2002

Sterols play two major roles in plants: a bulk component in biological membranes and precursors of plant steroid hormones. Physiological effects of plant steroids, brassinosteroids (BRs), include cell elongation, cell division, stress tolerance, and senescence acceleration. Arabidopsis mutants that carry genetic defects in BR biosynthesis or its signaling display characteristic phenotypes, such as short robust inflorescences, dark-green round leaves, and sterility. Currently there are more than 100 dwarf mutants representing 7 genetic loci in Arabidopsis. Mutants of 6 loci, dwf1/dim1/cbb1, cpd/dwf3, dwf4, dwf5, det2/dwf6, dwf7 are rescued by exogenous application of BRs, whereas bri1/dwf2 shares phenotypes with the above 6 loci but are resistant to BRs. These suggest that the 6 loci are defective in BR biosynthesis, and the one locus is in BR signaling. Biochemical analyses, such as intermediate feeding tests, examining the levels of endogenous BR, and molecular cloning of the genes revealed that dwf7, dwf5, and dwf1 are defective in the three consecutive steps of sterol biosynthesis, from episterol to campesterol via 5-dehydroepisterol. Similarly, det2/dwf6, dwf4, and cpd /dwf3 were shown to be blocked in D$^4$reduction, 22a-hydroxylation, and 23 a-hydroxylation, respectively. A signaling mutant bril/dwf2 carries mutations in a Leucine-rich repeat receptor kinase. Interestingly, the bri1 mutant was shown to accumulate significant amount of BRs, suggesting that signaling and biosynthesis are dynamically coupled in Arabidopsis. Thus it is likely that transgenic plants over-expressing the rate-limiting step enzyme DWF4 as well as blocking its use by BRIl could dramatically increase the biosynthetic yield of BRs. When applied industrially, BRs will boost new sector of plant biotechnology because of its potential use as a precursor of human steroid hormones, a novel lead compound for cholesterol-lowering effects, and a various application in plant protection.

• Journal of Life Science
• /
• v.22 no.8
• /
• pp.1024-1033
• /
• 2012

A gene encoding a novel geranylgeranyl pyrophosphate (GGPP) synthase from Kocuria gwangalliensis has been cloned and expressed in Escherichia coli. The deduced amino acid sequence showed 59.6% identity with a putative GGPP synthase (CrtE) from K. rhizophila. An expression plasmid containing the crtE gene was constructed, and E. coli cells containing this plasmid produced a recombinant protein with a theoretical molecular mass of 41 kDa, corresponding to the molecular weight of GGPP synthase. Due to the lack of crtE, crtB, and crtI in E. coli, the biosynthesis of lycopene was only obtained when the plasmid pCcrtE was co-transformed into E. coli expressing the pRScrtBI-carrying carotenoid biosynthesis crtB and crtI genes, which were sub-cloned from Paracoccus haeundaensis. The biochemical studies on the expressed proteins were performed via HPLC. The results obtained from this study will provide a wider base of knowledge regarding the primary structure of CrtE cloned from K. gwangalliensis at the molecular level.

• Journal of Life Science
• /
• v.26 no.12
• /
• pp.1487-1497
• /
• 2016

Bacterial cell to cell communication strategies called quorum sensing (QS) using small diffusible signaling molecules (auto-inducers) govern the expression of various genes dependent on their population density manner. As a consequence of synthesis and response to the signaling molecules, individual planktonic cells synchronized group behaviors to control a diverse array of phenotypes such as maturation of biofilm, production of extra-polymeric substances (EPS), virulence, bioluminescence and antibiotic production. Many studies indicated that biofilm formations are associated with QS signaling molecules such as acyl-homoserine lactones (AHLs) mainly used by several Gram negative bacteria. The biofilm maturation causes undesirable biomass accumulation in various surface environments anywhere water is present called biofouling, which results in serious eco-technological problems. Numerous molecules that interfere the bacterial QS called quorum quenching (QQ), have been discovered from various microorganisms, and their functions and mechanisms associated with QS have also been elucidated. To resolve biofouling problems related to various industries, the novel approach based on QS interference has been emerged attenuating multi-drug resisting bacteria appearance and environmental toxicities, which may provide potential advantages over the conventional anti-biofouling approaches. Therefore this paper presents recent information related to bacterial quorum sensing system, quorum quenching enzymes that can control the QS signaling, and lastly discuss the anti-biofouling approaches using the quorum quenching.

• Journal of Life Science
• /
• v.30 no.2
• /
• pp.122-128
• /
• 2020

Although Candida albicans is the major fungal pathogen of candidemia, severe infections by non-albicans Candida (NAC) spp. have been increasing in recent years. Among NAC spp., C. glabrata has emerged as the second most common pathogen. However, few studies have been conducted to investigate its structure, epidemiology, and basic biology. In the present study, multi-locus sequence typing (MLST) was performed with a total of 102 C. glabrata clinical isolates that were isolated from various types of clinical specimen. For MLST, six housekeeping genes-FKS, LEU2, NMT1, TRP1, UGP1, and URA3-were amplified and sequenced. The results were analyzed using the C. glabrata database. Out of a total of 3,345 base-pair DNA sequences, 49 variable nucleotide sites were found, and the results showed that 12 different sequence types (ST) were identified from the 102 clinical isolates. The data also demonstrated that the undetermined ST1 was the most predominant ST in Korea. Further, seven undetermined STs (UST) containing UST2-8 were classified at specific loci. The data from this study may provide a fundamental database for further studies on C. glabrata, including its epidemiology and evolution. The data may also contribute to the development of novel antifungal agents and diagnostic tests.

• Molecules and Cells
• /
• v.25 no.4
• /
• pp.559-565
• /
• 2008

Members of the TGA family of basic domain/leucine zipper transcription factors regulate defense genes through physical interaction with NON-EXPRESSOR OF PR1 (NPR1). Of the seven TGA family members, TGA4/octopine synthase (ocs)-element-binding factor 4 (OBF4) is the least understood. Here we present evidence for a novel function of OBF4 as a regulator of flowering. We identified CONSTANS (CO), a positive regulator of floral induction, as an OBF4-interacting protein, in a yeast two-hybrid library screen. OBF4 interacts with the B-box region of CO. The abundance of OBF4 mRNA cycles with a 24 h rhythm under both long-day (LD) and short-day (SD) conditions, with significantly higher levels during the night than during the day. Electrophoretic mobility shift assays revealed that OBF4 binds to the promoter of the FLOWERING LOCUS T (FT) gene, a direct target of CO. We also found that, like CO and FT, an OBF4:GUS construct was prominently expressed in the vascular tissues of leaf, indicating that OBF4 can regulate FT expression through the formation of a protein complex with CO. Taken together, our results suggest that OBF4 may act as a link between defense responses and flowering.

• Molecules and Cells
• /
• v.39 no.2
• /
• pp.103-110
• /
• 2016

As a degenerative joint disease, osteoarthritis (OA) constitutes a major cause of disability that seriously affects the quality of life of a large population of people worldwide. However, effective treatment that can successfully reverse OA progression is lacking until now. The present study aimed to determine whether two small non-coding RNAs miR-29a and miR-140, which are significantly down-regulated in OA, can be applied together as potential therapeutic targets for OA treatment. MiRNA synergy score was used to screen the miRNA pairs that potentially synergistically regulate OA. An in vitro model of OA was established by treating murine chondrocytes with IL-$1{\beta}$. Transfection of miR-29a and miR-140 via plasmids was investigated on chondrocyte proliferation and expression of nine genes such as ADAMTS4, ADAMTS5, ACAN, COL2A1, COL10A1, MMP1, MMP3, MMP13 and TIMP metallopeptidase inhibitor 1 (TIMP1). Western blotting was used to determine the protein expression level of MMP13 and TIMP1, and ELISA was used to detect the content of type II collagen. Combined use of miR-29a and miR-140 successfully reversed the destructive effect of IL-$1{\beta}$ on chondrocyte proliferation, and notably affected the MMP13 and TIMP1 gene expression that regulates extracellular matrix. Although co-transfection of miR-29a and miR-140 did not show a synergistic effect on MMP13 protein expression and type II collagen release, but both of them can significantly suppress the protein abundance of MMP13 and restore the type II collagen release in IL-$1{\beta}$ treated chondrocytes. Compared with single miRNA transfection, cotransfection of both miRNAs exceedingly abrogated the suppressed the protein production of TIMP1 caused by IL-$1{\beta}$, thereby suggesting potent synergistic action. These results provided1novel insights into the important function of miRNAs' collaboration in OA pathological development. The reduced MMP13, and enhanced TIMP1 protein production and type II collagen release also implies that miR-29a and miR-140 combination treatment may be a possible treatment for OA.

• Plant Biotechnology Reports
• /
• v.3 no.2
• /
• pp.147-155
• /
• 2009

Oryza grandiglumis Chitinase IVa (OgChitIVa) cDNA encoding a class IV chitinase was cloned from wild rice (Oryza grandiglumis). OgChitIVa cDNA contains an open reading frame of 867 nucleotides encoding 288 amino acid residues with a predicted molecular weight of 30.4 kDa and isoelectric point of 8.48. Deduced amino acid sequences of OgChitIVa include the signal peptide and chitin-binding domain in the N-terminal domain and conserved catalytic domain. OgChitIVa showed significant similarity at the amino acid level with related monocotyledonous rice and maize chitinase, but low similarity with dicotyledoneous chitinase. Southern blot analysis showed that OgChitIVa genes are present as two copies in the wild rice genome. It was shown that RNA expression of OgChitIVa was induced by defense/stress signaling chemicals, such as jasmonic acid, salicylic acid, and ethephon or cantharidin and endothall or wounding, and yeast extract. It was demonstrated that overexpression of OgChitIVa in Arabidopsis resulted in mild resistance against the fungal pathogen, Botrytis cinerea, by lowering disease rate and necrosis size. RT-PCR analysis showed that PR-1 and PR-2 RNA expression was induced in the transgenic lines. Here, we suggest that a novel OgChitIVa gene may play a role in signal transduction process in defense response against B. cinerea in plants.