• 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.

• Journal of Microbiology and Biotechnology
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• v.27 no.4
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• pp.808-815
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• 2017

We demonstrated the quantitative detection of a toxin-producing Microcystis aeruginosa (M. aeruginosa) strain with the laboratory protocol of the NanoGene assay. The NanoGene assay was selected because its laboratory protocol is in the process of being transplanted into a portable system. The mcyD gene of M. aeruginosa was targeted and, as expected, its corresponding fluorescence signal was linearly proportional to the mcyD gene copy number. The sensitivity of the NanoGene assay for this purpose was validated using both dsDNA mcyD gene amplicons and genomic DNAs (gDNA). The limit of detection was determined to be 38 mcyD gene copies per reaction and 9 algal cells/ml water. The specificity of the assay was also demonstrated by the addition of gDNA extracted from environmental algae into the hybridization reaction. Detection of M. aeruginosa was performed in the environmental samples with environmentally relevant sensitivity (${\sim}10^5$ algal cells/ml) and specificity. As expected, M. aeruginosa were not detected in nonspecific environmental algal gDNA over the range of $2{\times}10^0$ to $2{\times}10^7$ algal cells/ml.

• Journal of Microbiology and Biotechnology
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• v.11 no.3
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• pp.482-490
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• 2001

The gene for glycoprotein B (gB2) of HSV-2-strain G was subcloned, sequenced, recombinated into the lacZ-HcNPV, expressed in insect cells, and compared with the homologous gene of other HSV-2 strains. The ORF of the gB2 gene was 2,715 bp. The overall nucleotide sequence homology of te gB2 gene compared ith that of the two previously reported HSV-2 strains appeared to be over 98%. A recombinant virus named Baculo-gB2 protein in insect cells. The recombination was confirmed by a PCR and the expression was demonstrated by radio immunoprecipitation. Insect cells infected with the Baculo-gB2 virus synthesized and processed gB2 with approximately 120 kDa in the cells, and then secreted it into the culture media, where it reacted with a nomoclonal antibody to gB2. The gB2 polypeptide contained two main hydrophobic regions (a signal sequence from 1 to 23 amino acid residues, and a membrane anchor sequence from aa 745 to 798), eight N-glycosylation sites evenly distributed, and was rich in alanine (11.2%). Antibodies to this recombinant protein that were raised in mice recognized the viral gB2 and neutralized the infectivity of the HSV-2 in vitro. There results show that the gB2 protein was successfully porduced in insect cells and could be used to raise a protective neutralizing antibody. Accordingly, this particular recombinant protein may be useful in the development of a subunit vaccine.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.29 no.2
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• pp.128-135
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• 1984

Gamadi, a native rice cultivar from Nepal in which the panicle remains enclosed within its flag leaf sheath upto maturity, was crossed with different genetic marker testers of 12 linkage groups in order to analyze its linkage relationship. The results obtained from the experiment were summarized as follows: Normal segregations of all the genetic marker genes used in this experiment viz Cl, wx and Pla of linkage group I, Pn, Rd and Pub of linkage group III, and lg, g, Ps, gh, Hla, la, nl, bl, be and gl of linkage groups II, IV, V, VI, VII, VIII, IX, X, XI, and XII respectively confirmed the previous results, and also strongly indicated that the genetic constituent of the Gamadi and marker testers is same. 'Gamadiness' (the panicle enclosing character) was controlled by two complementary dominant genes with the segregation ratio of 9 Gamadi to 7 normal panicle-exserting types. These genes have been temporarily proposed as G-a and G-b for gamadiness. G-a gene was found to be linked with the neckleaf gene (nl) of linkage group Ⅸ with the crossover value of 0.3733$\pm$0.027. G-b gene appeared to be associated with the brittle culm gene (bc) of the linkage group XI with the crossover value of 0.2725$\pm$0.061.TEX>0.061.

• Journal of Microbiology and Biotechnology
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• v.10 no.3
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• pp.355-362
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• 2000

The Herpes simplex virus type 1 (HSV-1) glycoprotein B (gB) gene in the pHLA-21 plasmid was inserted into a baculovirus (Hyphantria cunea nuclear polyhedrosis virus) expression vector (lacZ-HcNPV) to construct a recombinant virus gB-HcNPV expressing gB. Spodoptera frugiperda cells infected with this recombinant virus synthesized and processed gB of approximately 120 kDa, which cross-reacted with the monoclonal antibody to gB. The recombinant gB was identified on the membrane of the insect cells using an immunofluorescence assay. Antibodies to this recombinant raised in mice recognize the viral gB and neutralized the infectivity of the HSV-1 in vitro. These results show that the gB gene has the potential to be expressed in insect cells. They also demonstrate that it is possible to produce a mature protein by gene transfer in eukaryotic cells, and indicate the utility of the lacZ-HcNPV-insect cell system for producing and characterizing eukaryotic proteins. Furthermore, the neutralizing antibodies would appear to protect mice against HSV. Accordingly, this particular recombinant protein may be useful in the development of a subunit vaccine.

• Korean Journal of Animal Reproduction
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• v.25 no.2
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• pp.171-180
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• 2001

Compared to other gene transfer system, the advantages of retrovirus-mediated gene transfer are technical ease, efficient expression and genetic stability. Despite the high potency of the retrovirus vector system in gene transfer, one of the drawbacks is a difficulty in concentration of virus stock. To overcome this problem, we tested a new retrovirus vector system producing the progeny retrovirus particles encapsidated with VSV-G (vesicular stomatitis virus G glycoprotein). The infectivity of this virus was not sacrificed by ultracentrifugal concentration and the host cell range extended from all mammalian to fish embryos. Virus titer after 1,000 x concentration was more than 10$^{8}$ CFU/ $m\ell$ on most of the target cell lines. We applied this pantropic viruses in transgenic chicken production by injecting the concentrated (100$\times$) stock into subgerminal cavity of stage X chicken embryos. The survival rate of chicken embryos after injection was about 20% and gene integration rate in surviving embryos was scored almost 100%. Analyses of RT-PCR and fluorescence microscopy, however, showed no evidence of the transgene expression.

• Korean Journal of Biological Psychiatry
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• v.11 no.2
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• pp.110-116
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• 2004

Objectives:Recently, polymorphisms of several serotonin genes have been suggested to be associated with suicide, but the results are still unclear. We examined whether the T102C polymorphisms of the serotonin 2A receptor gene and the G861C polymorphisms of the serotonin 1B receptor gene were associated with suicidal behavior using drug intoxication. Methods:The subjects were 52 patients who visited emergency room with suicidal behaviors. Fifty controls were selected from healthy volunteers matched for sex and age to the suicide subjects. The polymorphisms were analyzed with TaqMan$^{(R)}$ assay using primers based on previous studies. Results:The T102C polymorphism of the serotonin 2A receptor gene showed no significant difference between the suicidal attempters and controls in both genotype and allele frequency analyses(p=0.179 and p=0.422, respectively). There was no statistically significant difference between the suicidal attempters and the controls in the G861C polymorphism of the serotonin 1B receptor gene and any significant effect of the genotype distributions or the allele frequencies was not observed(p=0.092 and p=0.987, respectively). Conclusion:These findings suggest that the T102C polymorphism in serotonin 2A receptor gene and the G861C polymorphism in serotonin 1B receptor gene are not related to the susceptibility to suicide attempts using drugs. To clarify the genetic influences of the serotonergic system on suicidal behavior, the polymorphisms of other candidate genes in the serotonergic system should be studied with larger numbers of subjects.

• The Korean Journal of Food And Nutrition
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• v.23 no.1
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• pp.118-123
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• 2010

To estimate the regulatory effects of Scutellaria baicalensis extracts on melanin biosynthesis, we evaluated the regulatory effects of the tyrosinase gene on B16 melanoma cells. The results revealed that methanolic extracts of Scutellaria baicalensis resulted in a high increase in the expression of the tyrosinase gene. Specifically, treatment with extracts at concentrations of $10\;{\mu}g/m{\ell}$ and $100\;{\mu}g/m{\ell}$ resulted in increases in tyrosinase gene expression rates of approximately 231% and 256%, respectively, when compared to the control. Moreover, the solvent fraction layers(methylene chloride, ethyl acetate, butyl alcohol, water) improved the expression of the tyrosinase gene, but to a lesser degree than the methanolic extracts. An MTT assay revealed, that the methanolic extract exhibited very low cytotoxicities at $10\;{\mu}g/m{\ell}$ and $100\;{\mu}g/m{\ell}$. Taken together, the results of this study indicated that the methanolic extracts of Scutellaria baicalensis was a very effective positive regulator of tyrosinase gene expression.

• Fisheries and Aquatic Sciences
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• v.19 no.7
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• pp.31.1-31.6
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• 2016

Background: The objective of this study was to develop an efficient selectable marker for transgenic Dunaliella salina. Results: Tests of the sensitivity of D. salina to the antibiotic chloramphenicol and the herbicide Basta$^{(R)}$ showed that cells ($1.0{\times}10^6cells/ml$) treated with 1000 or $1500{\mu}g/ml$ chloramphenicol died in 8 or 6 days, respectively, whereas D. salina cells ($1.0{\times}10^6cells/ml$) treated with 5, 10, 20, or $40{\mu}g/ml$ Basta$^{(R)}$ died in 2 days. Therefore, D. salina is more sensitive to Basta$^{(R)}$ than to chloramphenicol. To examine the possibility of using the phosphinothricin N-acetyltransferase (pat) gene as a selectable marker gene, we introduced the pat genes into D. salina with particle bombardment system under the condition of helium pressure of 900 psi from a distance of 3 cm. PCR analysis confirmed that the gene was stably inserted into the cells and that the cells survived in $5{\mu}g/ml$ Basta$^{(R)}$, the medium used to select the transformed cells. Conclusions: The findings of this study suggest that the pat gene can be used as an efficient selectable marker when producing transgenic D. salina.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.7
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• pp.863-866
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• 2010

Myostatin, which is also known as growth and differentiation factor 8 (GDF8), has been reported to act as a negative regulator of skeletal muscle development. Variation in the myostatin gene (MSTN) has been associated with variation in muscularity in certain "meaty" sheep breeds. Polymerase Chain Reaction-Single Strand Conformational Polymorphism (PCR-SSCP) analysis was used to investigate allelic variation in the previously described g+6223G>A single-nucleotide polymorphism (SNP) in the 3' untranslated region (3' UTR) of MSTN. The sheep studied were 79 New Zealand (NZ) Romney lambs derived from a single sire heterozyous for g+6223G>A, which is in itself notable as this polymorphism has not been described previously in this breed. Allelic variation was observed to be associated with an abnormal gender ratio (p = 0.046) in the progeny. The presence of allele A was observed to have an effect (p<0.05) on birth weight, mean loin yield, proportion yield loin and total muscle yield. Allelic variation did not significantly affect mean shoulder yield, leg yield, proportion yield shoulder and proportion yield leg. This preliminary result suggests that while the A allele at MSTN g+6223 appears to improve some valuable traits in NZ Romney sheep, further research is required to understand if and how it may affect other traits.