• Journal of KIISE:Software and Applications
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• v.36 no.10
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• pp.851-860
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• 2009

Recently, among the computational methods of protein-protein interaction prediction, vast amounts of domain based methods originated from domain-domain relation consideration have been developed. However, it is true that multi domains collaboration is avowedly ignored because of computational complexity. In this paper, we implemented a protein interaction prediction system based the Interaction Significance matrix, which quantified an influence of domain combination pair on a protein interaction. Unlike conventional domain combination methods, IS matrix contains weighted domain combinations and domain combination pair power, which mean possibilities of domain collaboration and being the main body on a protein interaction. About 63% of sensitivity and 94% of specificity were measured when we use interaction data from DIP, IntAct and Pfam-A as a domain database. In addition, prediction accuracy gradually increased by growth of learning set size, The prediction software and learning data are currently available on the web site.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.3
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• pp.354-357
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• 2005

The in vitro degradability of yeast and the effect of yeast on the in vitro degradability of forage may differ in terms of the specific yeast strains or their incubation conditions. Thus in experiment 1, two strains of sake yeast (strainK7 and strainK9) and one strain of bakers' yeast (KY5649) were incubated in an aerobic condition. In experiment 2, aerobically or anaero bically incubated K7 was used for investigating the in vitro degradability of yeast, the effect of yeast on the in vitro degradability of forage, and the degradability of yeast by pepsin and pronase treatment. The in vitrodegradability of bakers' yeast was significantly (p<0.05) higher than those of sake yeasts. The in vitro degradability of anaerobically incubated yeast was significantly (p<0.01) higher than that of aerobically incubated yeast. The degradability of bakers' yeast by pepsin treatment was significantly (p<0.01) higher than that of the sake yeasts. The degradability of bakers' yeast by pronase treatment was slightly higher than that of the two sake yeasts, while the degradability of anaerobically incubated yeast by both enzymes, respectively, was significantly (p<0.01) higher than that of aerobically incubated yeast. The degradability of forages was increased significantly (p<0.05) by the addition of yeasts. The degradability of roughage by sake yeast tended to be higher than that by the bakers' yeast. The degradability of roughage was significantly (p<0.05) higher by anaerobically incubated yeast than by aerobically incubated yeast. Given the above results, it seems that in vitro degradability of yeast and the magnitude of the increment of roughage degradation differ among the yeast strains and their incubation conditions.

• Journal of Microbiology and Biotechnology
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• v.23 no.11
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• pp.1493-1499
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• 2013

A novel radiation-resistant Filobasidium sp. yeast strain was isolated from seawater. Along with this strain, a total of 656 yeast isolates were purified from seawater samples collected from three locations in the West Sea of Korea and assessed for their radiation tolerance. Among these isolates, five were found to survive a 5 kGy radiation dose. The most radiation-resistant strain was classified as Filobasidium sp. based on 18S rDNA sequence analysis and hence was named Filobasidium RRY1 (Radiation-Resistant Yeast 1). RRY1 differed from F. elegans, which is closely related to RRY1, in terms of the optimal growth temperature and radiation resistance, and was resistant to high doses of ${\gamma}$-ionizing radiation ($D_{10}$: 6-7 kGy). When exposed to a high dose of 3 kGy irradiation, the RRY1 cells remained intact and undistorted, with negligible cell death. When these irradiated cells were allowed to recover, the cells fully repaired their genomic DNA within 3 h of growth recovery. This is the first report in which a radiation-resistant response has been investigated at the physiological, morphological, and molecular levels in a strain of Filobasidium sp.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.138-149
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• 2004

In this study, we analyzed the gene expression data of Saccharomyces cerevisiae obtained from Holstege et al. 1998 to understand the relationship between expression level and nucleotide sequence of a gene. First, the correlation between gene expression and percent composition of each type of nucleotide was computed. It was observed that nucleotide 'G' and 'C' show positive correlation (r ${\geq}$ 0.15), 'A' shows negative correlation (r ${\approx}$ -0.21) and 'T' shows no correlation (r ${\approx}$ 0.00) with gene expression. It was also found that 'G+C' rich genes express more in comparison to 'A+T' rich genes. We observed the inverse correlation between composition of a nucleotide at genome level and level of gene expression. Then we computed the correlation between dinucleotides (e.g. AA, AT, GC) composition and gene expression and observed a wide variation in correlation (from r = -0.45 for AT to r = 0.35 for GT). The dinucleotides which contain 'T' have wide range of correlation with gene expression. For example, GT and CT have high positive correlation and AT have high negative correlation. We also computed the correlation between trinucleotides (or codon) composition and gene expression and again observed wide range of correlation (from r = -0.45 for ATA r = 0.45 for GGT). However, the major codons of a large number of amino acids show positive correlation with expression level, but there are a few amino acids whose major codons show negative correlation with expression level. These observations clearly indic ate the relationship between nucleotides composition and expression level. We also demonstrate that codon composition can be used to predict the expression of gene in a given condition. Software has been developed for calculating correlation between expression of gene and codon usage.

• The Korean Journal of Physiology
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• v.3 no.1
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• pp.45-49
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• 1969

The effects of water extracts and powder of Korean ginseng on the division of Saccharomyces cerevisiae were studied. 1. The addition of several doses of water extracts and powder of ginseng to the yeast medium of Moyer and Coghill showed various promoted division of Saccharomyces. 2. The optimal dose of ginseng on tile division of Saccharomyces (0.08% dry ginseng medium solution per $10\;cells/mm^3$) could be recognized. 3. On the culture for 24 hours at $18^{\circ}C$, the cell number of control group was $13.25{\times}10^3\;cells/mm^3$ and that of the optimal dose group of water extracts of ginseng was $23.20{\times}10^3\;cells/mm^3$. On the culture, for 24 hours at $25^{\circ}C$, the cell number of control group was $16.85{\times}10^3\;cells/mm^3$ and that of the optimal dose group was $30.20{\times}10^3\;cells/mm^3$. The increasing rate of cell divison by the ginseng was about twice than that of control group. The optimal dose treatment of ginseng at $18^{\circ}C$ was more effective than control group at $25^{\circ}C$. 4. On the culture for 24 hours at $18^{\circ}C$, the increasing rate of water extracts of ginseng was 75.1%, and the rate of ginseng powder was 7.6%. On the culture for 24 hours at $25^{\circ}C$, the rate of water extracts of ginseng was 79.8%, and the rate of ginseng powder was 57.2%. Therefore water extracts of ginseng was more effective than ginseng powder of same dry weight, and the promoted effect of ginseng powder at $25^{\circ}C$ was more effective than at $18^{\circ}C$.

• Journal of Microbiology and Biotechnology
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• v.28 no.10
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• pp.1589-1603
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• 2018

Twenty analogs of $[Orn^6,D-Ala^9]{\alpha}-factor$ were synthesized and assayed for their biological activities: seven analogs of $[Orn^6,X^9]{\alpha}-factor$, seven analogs of $[X^6,D-Ala^9]{\alpha}-factor$, five analogs of $[X^5,X^6,D-Ala^9]{\alpha}-factor$, and native ${\alpha}-factor$ (X = amino acids). Their biological activities (halo, gene induction, and affinity) were measured using S. cerevisiae Y7925 and LM102 and compared with those of native ${\alpha}-factor$ (100%). G protein-coupled receptor was expressed in strain LM102 containing pESC-LEU-STE2 vector. $[Dap^6,D-Ala^9]{\alpha}-factor$ with weak halo activity (10%) showed the highest receptor affinity (> 230%) and the highest gene induction activity (167%). $[Arg^6,D-Ala^9]{\alpha}-factor$ showed the highest halo activity (2,000%). The number of active binding sites per cell (about 20,000 for strain LM102) was determined using a newly-designed fluorescence-based detector, $[Arg^6,D-Ala^9]{\alpha}-factor-Edan$, with high sensitivity (12,500-fold higher than the absorption-based detector $[Orn^6]{\alpha}-factor-[Cys]_3$).

• The Korean Journal of Mycology
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• v.40 no.4
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• pp.204-209
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• 2012

In this study, a novel yeast, Y111-5 for Makgeolli manufacture was selected from Nuruk yeasts, and its optimal culture condition were investigated. The Y111-5 strain was identified as Saccharomyces cerevisiae by phylogenetic analysis of 18S RNA sequence. The maximal growth was obtained when the yeast was cultivated at $30^{\circ}C$ for 15 h in the medium containing sucrose 9% and yeast extract 5%.

• International Journal of Industrial Entomology and Biomaterials
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• v.5 no.1
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• pp.73-77
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• 2002

The Sec61 trimeric complex ($\alpha$,$\beta$, and ${\gamma}$ subunits) is one of the Sec-complex responsible for post-translational protein translocation across the endoplasmic reticulum membrane in diverse organisms. In this study, a cDNA encoding the Sec61p ${\gamma}$ subunit homologue was isolated from the cDNA library of the mole cricket, Gryllotalpa orientalis. Sequence analysis of a 442-bp cDNA clone showed it to contain an open reading frame of 68 amino acid residues consisted of 204-bp. The homologues of the gene were found in the GenBank database in a diverse organism including insect, mammals, fungi, and plants. The deduced amino acid sequence of Sec61p ${\gamma}$ subunit homologue of the mole cricket showed the highest homology to the gene of the singly known insect, Drosophila melanogester (93% identity), and the least homology to that of the baker's yeast, Saccharomyces cerevisiae (37.2%). Phylogenetic analysis also confirmed a close relationship between the insect Sec61p ${\gamma}$ subunit homologues of G. orientalis and D. melanogester. Hydropathy analysis of the cricket mole and published other data suggested that the hydrophobic segment close to C-terminus is predicted to be the putative membrane anchor, Multiple alignment of the Sec61p ${\gamma}$ subunit homologue among several organisms showed the presence of several conserved domains including the conserved proline at position 28.

• Korean Journal of Microbiology
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• v.6 no.2
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• pp.41-53
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• 1968

Studies on the carbohydrate metabolism of yeast as influenced by gamma-irradiation from cobalt-60 have been carried, then the mechanisms of radiation effect on respiration and fermentation were discussed under considerations of permeable changes of irradiated cell membrane. The cells of baker's yeast (Saccharomyces cerevisiae) which had been gamma-irradiated of 240 k.r. doses for an hour, then were put into aerobic oxidation and anaerobic fermentation without substrate. Total and fractionated carbohydrates of irradiated yeast cells were determined by calorimetric method with anthrone and orcinol reagents, the amounts of total carbohydrate, trehalose, RNA-ribose, PCA-soluble glycogen, alkali-soluble glycogen, acetic acid-soluble glycogen, mannan and glucan were determined according to the course of aerobic oxidation and anaerobic fermentation. It is found that the carbohydrates of irradiated cells leak out and amount of the losses teaches eleven times more than that of control, the volume of losses are seems to be replaced by water, it can be suggested the damage of gamma-irradiation occurs in the site of passive transport of cell membrane. The endogeneous aerobic respiration of irradiated cells are increased much more than control, the synthesis of reserve glycogen, glucan and RNA-ribose promoted much more than control. The anaerobic fermentation of irradiated cells are also increased than that of control, but the breakdown of carbohydrate is less than endogeneous respiration of irradiated cells. The synthetic rate is also less than that of aerobic oxidation. In irradiated yeast cells, trehalose is revealed to be primary substrate for endogeneous carbohydrate metabolism, so it is proved that the enzymic patterns are not changed but the activities of enzymes relating endogeneous respiration and autofermentation is activated. It is to be considerable to distiguish endogeneous respiration and autofermentation from exogeneous respiration and fermentation on irradiation, for membrane permeability changes and loses out carbohydrate by ionizing radiation.

• Journal of Microbiology and Biotechnology
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• v.20 no.12
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• pp.1702-1710
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• 2010

Korean traditional rice wines yakju and takju are generally brewed with nuruk as the source of the saccharogenic enzymes by natural fermentation. To improve the quality of Korean rice wine, the microorganisms in the nuruk need to be studied. The objective of this research was to improve the quality of Korean wine with the wild-type yeast strains isolated from the fermentation starter, nuruk. Only strain YA-6 showed high activity in 20% ethanol. Precipitation of Y89-5-3 was similar to that of very flocculent yeast (>80%) at 75.95%. Using 18S rRNA sequencing, all 10 strains were identified as Saccharomyces cerevisiae. Volatile compounds present in yakju were analyzed by gas chromatography-mass selective detector. The principal component analysis (PCA) of the volatile compounds grouped long-chain esters on the right side of the first principal component, PC1; these compounds were found in yakju that was made with strains YA-6, Y89-5-3, Y89-5-2, Y90-9, and Y89-1-1. On the other side of PC1 were short-chain esters; these compounds were found in wines that were brewed with strains Y183-2, Y268-3, Y54-3, Y98-4, and Y88-4. Overall, the results indicated that using different wild-type yeast strains in the fermentation process significantly affects the chemical characteristics of the glutinous rice wine.