• Genomics & Informatics
• /
• v.9 no.4
• /
• pp.181-188
• /
• 2011

In planning a model-based phylogenic study for highly related ethnic data, the SNP marker number is an important factor to determine for relationship inferences. Genotype frequency data, utilizing a sub sampling method, from 63 Pan Asian ethnic groups was used for determining the minimum SNP number required to establish such relationships. Bootstrap random sub-samplings were done from 5.6K PASNPi SNP data. DA distance was calculated and neighbour-joining trees were drawn with every re-sampling data set. Consensus trees were made with the same 100 sub-samples and bootstrap proportions were calculated. The tree consistency to the one obtained from the whole marker set, improved with increasing marker numbers. The bootstrap proportions became reliable when more than 7,000 SNPs were used at a time. Within highly related ethnic groups, the minimum SNPs number for a robust neighbor-joining tree inference was about 7,000 for a 95% bootstrap support.

• Genomics & Informatics
• /
• v.17 no.3
• /
• pp.28.1-28.9
• /
• 2019

Bar-code (tag) microarrays of yeast gene-deletion collections facilitate the systematic identification of genes required for growth in any condition of interest. Anti-sense strands of amplified bar-codes hybridize with ~10,000 (5,000 each for up-and down-tags) different kinds of sense-strand probes on an array. In this study, we optimized the hybridization processes of an array for fission yeast. Compared to the first version of the array (11 ㎛, 100K) consisting of three sectors with probe pairs (perfect match and mismatch), the second version (11 ㎛, 48K) could represent ~10,000 up-/ down-tags in quadruplicate along with 1,508 negative controls in quadruplicate and a single set of 1,000 unique negative controls at random dispersed positions without mismatch pairs. For PCR, the optimal annealing temperature (maximizing yield and minimizing extra bands) was 58℃ for both tags. Intriguingly, up-tags required 3× higher amounts of blocking oligonucleotides than down-tags. A 1:1 mix ratio between up- and down-tags was satisfactory. A lower temperature (25℃) was optimal for cultivation instead of a normal temperature (30℃) because of extra temperature-sensitive mutants in a subset of the deletion library. Activation of frozen pooled cells for >1 day showed better resolution of intensity than no activation. A tag intensity analysis showed that tag(s) of 4,316 of the 4,526 strains tested were represented at least once; 3,706 strains were represented by both tags, 4,072 strains by up-tags only, and 3,950 strains by down-tags only. The results indicate that this microarray will be a powerful analytical platform for elucidating currently unknown gene functions.

• Journal of Microbiology and Biotechnology
• /
• v.24 no.1
• /
• pp.1-7
• /
• 2014

The possibility of using hyphomycete fungi as suitable biocontrol agents against greenhouse whitefly has led to the isolation of various insect pathogenic fungi. Among them is Beauveria bassiana, one of the most studied entomopathogenic fungi. The objective of this study was to use B. bassiana M130 as an insecticidal agent against the greenhouse whitefly. M130 isolated from infected insects is known to be a biocontrol agent against greenhouse whitefly. Phylogenetic classification of M130 was determined according to its morphological features and 18S rRNA sequence analysis. M130 was identified as B. bassiana M130 and showed chitinase (342.28 units/ml) and protease (461.70 units/ml) activities, which were involved in the invasion of the host through the outer cuticle layer, thus killing them. The insecticidal activity was 55.2% in petri-dish test, 84.6% in pot test, and 45.3% in field test. The results of this study indicate that B. bassiana has potential as a biological agent for the control of greenhouse whitefly to replace chemical pesticides.

• Journal of Plant Biotechnology
• /
• v.32 no.2
• /
• pp.135-138
• /
• 2005

Embryogenic callus was obtained from cotyledonary explants of Codonopsis lanceloata on Murashige & Skoog's medium supplemented with 1 mg/L 2,4-D. Suspension cultures of the embryogenic calli were grown on a shaker at 100 strokes/min, and then the calli were subcultured for 2 weeks in 2,4-D-free medium to produce somatic embryo. In somatic embryos at the globular stage, cotyledon initials began to differentiate themselves in the near distal end of the procambial strand. Dicotyledons, tricotyledon, tetracotyledon and fused cotyledon were differentiated from the distal ends of two, three, four and circular procambial strands, respectively. Nearly circular procambial strand in lower hypocotyls were independently differentiated into two, three, four procambial tissues at cotyledonary node and cotyledons to form somatic embryos with dicotyledon, tricotyledon, tetracotyledon. If the distal subepidermal cells of globular embryo exclusively became cotyledon initials, the torpedo or cotyledonary embryo was characterized by somatic embryos with fused cotyledon.

• Journal of Plant Biotechnology
• /
• v.32 no.2
• /
• pp.91-95
• /
• 2005

Agrobacterium tumefaciens-mediated immature embryo transformation was used to produce transgenic maize. Immature embryo of Hi II genotype were co-cultivated with strains Agrobacterium tumefaciens (C58C1) containing the binary vectors (pPTN290) carrying with Ubiquitin promoter-GUS gene as reporter gene and NOS promoter-nptll gene conferring resistance to paromomycin as selective agent. Seven embryogenic callus lines transformed showed the resistance in paromomycin antibiotics. Histochemical GUS assay showed that 7 individual lines transformed with the GUS gene were positive response among the transformants. Southern blot analysis revealed that the nptll gene segregated and expressed in their progeny.

• Archives of Pharmacal Research
• /
• v.23 no.5
• /
• pp.525-530
• /
• 2000

mST3GaIV synthesizes ganglioside GM3, the precursor for simple and complex a- and b- series gangliosides, and the expression and regulation of mST3GaIV (CMP-NeuAc: lactosylceramide $\alpha$2,3-sialyltransferase) activity is central to the production of almost all gangliosides, a class of glycosphingolipids implicated in variety of cellular processes such as transmembrane signaling, synaptic transmission, specialized membrane domain formation and cell-cell interactions. To understand the developmental expression of mST3GaIV in mice, we investigated the spatial and temporal expression of mST3GaIV mRNA during the mouse embryogenesis [embryonic (E) days; 19, E11, E13, E15] by in situ hybridization with digoxigenin-labeled RNA probes. All tissues from 19 and E11 were positive for mST3GaIV mRNA. On E13, mST3GaIV mRNA was expressed in various neural and non-neural tissues. In contrast to these, on E15, the telencephalon and liver produced a strong expression of mST3GaIV which was a quite similar to that of E13. In this stage, mST3GaIV mRNA was also expressed in some non-neural tissues. These data indicate that mST3GaIV is differently expressed at developmental stages of embryo, and this may be importantly related with regulation of organogenesis in mice.

• Genomics & Informatics
• /
• v.7 no.1
• /
• pp.38-40
• /
• 2009

The EST Knowledge Integrated System, EKIS (http://ekis.kribb.re.kr), was established as a part of Korea's Ministry of Education, Science and Technology initiative for genome sequencing and application research of the biological model organisms (GEAR) project. The goals of the EKIS are to collect EST information from GEAR projects and make an integrated database to provide transcriptomic and metabolomic information for biological scientists. The EKIS constitutes five independent categories and several retrieval systems in each category for incorporating massive EST data from high-throughput sequencing of 65 different species. Through the EKIS database, scientists can freely access information including BLAST functional annotation as well as Genechip and pathway information for KEGG. By integrating complex data into a framework of existing EST knowledge information, the EKIS provides new insights into specialized metabolic pathway information for an applied industrial material.

• Bulletin of the Korean Chemical Society
• /
• v.28 no.5
• /
• pp.783-790
• /
• 2007

The immobilization of proteins and their molecular interactions on various polymer-modified glass substrates [i.e. 3-aminopropyltriethoxysilane (APTS), 3-glycidoxypropyltrimethoxysilane (GPTS), poly (ethylene glycol) diacrylate (PEG-DA), chitosan (CHI), glutaraldehyde (GA), 3-(trichlorosilyl)propyl methacrylate (TPM), 3'-mercaptopropyltrimethoxysilane (MPTMS), glycidyl methacrylate (GMA) and poly-l-lysine (PL).] for potential applications in a nanoarray protein chip at the single-molecule level was evaluated using prismtype dual-color total internal reflection fluorescence microscopy (dual-color TIRFM). A dual-color TIRF microscope, which contained two individual laser beams and a single high-sensitivity camera, was used for the rapid and simultaneous dual-color detection of the interactions and colocalization of different proteins labeled with different fluorescent dyes such as Alexa Fluor® 488, Qdot® 525 and Alexa Fluor® 633. Most of the polymer-modified glass substrates showed good stability and a relative high signal-to-noise (S/N) ratio over a 40-day period after making the substrates. The GPTS/CHI/GA-modified glass substrate showed a 13.5-56.3% higher relative S/N ratio than the other substrates. 1% Top-Block in 10 mM phosphate buffered saline (pH 7.4) showed a 99.2% increase in the blocking effect of non-specific adsorption. These results show that dual-color TIRFM is a powerful methodology for detecting proteins at the single-molecule level with potential applications in nanoarray chips or nano-biosensors.

• Bulletin of the Korean Chemical Society
• /
• v.30 no.4
• /
• pp.917-923
• /
• 2009

The maize lipoxgyenase-1 is a non-traditional dual positional specific enzyme and the reaction proceeds via enzyme-initiated catalysis. Bioinformatic analysis indicated that the maize lipoxygenase-1 is structurally more similar to soybean LOX1 than pea LOXN2 in that it has an additional external loop (residues 318-351) in the carboxy-terminal catalytic domain. We analyzed the dependence of product distribution on concentration of linoleic acid and monitored the formation of hydroperoxyoctadecadienoic acid as a function of enzyme concentration. Product distribution was strongly influenced by substrate concentration, such that kinetically-controlled regioisomers were enriched and thermodynamically-controlled regioisomers were depleted at high substrate concentration. Kinetic studies indicated that the formation of hydroperoxyoctadecadienoic acid saturated rapidly in an enzyme concentration-dependent manner, which implied that reactivation by reoxidation of inactive Fe(II) failed to occur. Our results support the previously proposed enzyme-initiated catalytic mechanism of the maize lipoxgyenase-1 and reveals that a substrate molecule serves as a hydrogen atom donor in its enzyme-initiated catalysis.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.11 no.6
• /
• pp.510-515
• /
• 2006

The putative EPA synthesis gene cluster was mined from the entire genome sequence of Shewanella oneidensis MR-1. The gene cluster encodes a PKS-like pathway that consists of six open reading frames (ORFs): ORFSO1602 (multi-domain beta-ketoacyl synthase, KS-MAT-4ACPs-KR), ORFSO1600 (acyl transferase, AT), ORFSO1599 (multi-domain beta-ketoacyl synthase, KS-CLF-DH-DH), ORFSO1597 (enoyl reductase, ER), ORFSO1604 (phosphopentetheine transferase, PPT), and ORFSO1603 (transcriptional regulator). In order to prove involvement of the PKS-like machinery in EPA synthesis, a 20.195-kb DNA fragment containing the genes was amplified from S. oneidensis MR-1 by the long-PCR method. Its identity was confirmed by the methods of restriction enzyme site mapping and nested PCR of internal genes orfSO1597 and orfSO1604. The DNA fragment was cloned into Escherichia coli using cosmid vector SuperCos1 to form pCosEPA. Synthesis of EPA was observed in four E. coli clones harboring pCosEPA, of which the maximum yield was 0.689% of the total fatty acids in a clone designated 9704-23. The production yield of EPA in the E. coli clone was affected by cultivation temperature, showing maximum yield at $20^{\circ}C$ and no production at $30^{\circ}C$ or higher. In addition, production yield was inversely proportional to glucose concentration of the cultivation medium. From the above results, it was concluded that the PKS-like modules catalyze the synthesis of EPA. The synthetic process appears to be subject to regulatory mechanisms triggered by various environmental factors. This most likely occurs via the control of gene expression, protein stability, or enzyme activity.