• Genomics & Informatics
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• v.20 no.2
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• pp.17.1-17.11
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• 2022

Genetic associations have been quantified using a number of statistical measures. Entropy-based mutual information may be one of the more direct ways of estimating the association, in the sense that it does not depend on the parametrization. For this purpose, both the entropy and conditional entropy of the phenotype distribution should be obtained. Quantitative traits, however, do not usually allow an exact evaluation of entropy. The estimation of entropy needs a probability density function, which can be approximated by kernel density estimation. We have investigated the proper sequence of procedures for combining the kernel density estimation and entropy estimation with a probability density function in order to calculate mutual information. Genotypes and their interactions were constructed to set the conditions for conditional entropy. Extensive simulation data created using three types of generating functions were analyzed using two different kernels as well as two types of multifactor dimensionality reduction and another probability density approximation method called m-spacing. The statistical power in terms of correct detection rates was compared. Using kernels was found to be most useful when the trait distributions were more complex than simple normal or gamma distributions. A full-scale genomic dataset was explored to identify associations using the 2-h oral glucose tolerance test results and γ-glutamyl transpeptidase levels as phenotypes. Clearly distinguishable single-nucleotide polymorphisms (SNPs) and interacting SNP pairs associated with these phenotypes were found and listed with empirical p-values.

• Journal of Microbiology and Biotechnology
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• v.23 no.1
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• pp.15-21
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• 2013

We previously observed that Bacillus subtilis spores from sspE mutants presented a lower germination capacity in media containing high salt concentrations (0.9M NaCl). This deficiency was attributed to the absence of SASP-E (gamma-type small-acid-soluble protein), rich in osmocompatible amino acids released by degradation. Herein we observed that, in addition, this mutant spore presented a reduced capacity to use L-alanine as germinant (L-ala pathway), required longer times to germinate in calcium dipicolinate ($Ca^{2+}$-DPA), but germinated well in asparagine, glucose, fructose, and potassium chloride (AGFK pathway). Moreover, mild sonic treatment of mutant spores partially recovered their germination capacity in L-ala. Spore qualities were also altered, since sporulating colonies from the sspE mutant showed a pale brownish color, a higher adherence to agar plates, and lower autofluorescence, properties related to their spore coat content. Furthermore, biochemical analysis showed a reduced partition in hexadecane and a higher content of $Ca^{2+}$-DPA when compared with its isogenic wild-type control. Coat protein preparations showed a different electrophoretic pattern, in particular when detected with antibodies against CotG and CotE. The complementation with a wild-type sspE gene in a plasmid allowed for recovering the wild-type coat phenotype. This is the first report of a direct involvement of SASP-E in the spore coat assembly during the differentiation program of sporulation.

• KSBB Journal
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• v.24 no.5
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• pp.425-431
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• 2009

Hepatocyte growth factor (HGF) and its receptor play an important role in the formation and progression of glioma. In this study, I investigated the ability of HGF to recover of the PSA siRNA-suppressed cell proliferation, migration and invasion in U-251-MG cells. PSA siRNA-transfected U-251-MG cells showed the reduction of the proliferation, migration and invasion with compared to control. Treatment of HGF on the PSA siRNA-transfected U-251-MG cells recovered the ability of proliferation, migration and invasion. These data suggest that PSA and HGF may use unique and parallel signaling cascade leading to the proliferative, migrative and invasive phenotype of U-251-MG cells. I also showed that PSA cooperated with HGF to a migrative and invasive phenotype via the increased secretion of matrix metalloproteinase-2 (MMP-2) and MMP-9.

• Journal of Microbiology and Biotechnology
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• v.30 no.10
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• pp.1597-1606
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• 2020

Transcription factor engineering to regulate multiple genes has shown promise in the field of microalgae genetic engineering. Here, we report the first use of transcription factor engineering in Chlorella sp. HS2, thought to have potential for producing biofuels and bioproducts. We identified seven endogenous bZIP transcription factors in Chlorella sp. HS2 and named them HSbZIP1 through HSbZIP7. We overexpressed HSbZIP1, a C-type bZIP transcription factor, in Chlorella sp. HS2 with the goal of enhancing lipid production. Phenotype screening under heterotrophic conditions showed that all transformants exhibited increased fatty acid production. In particular, HSbZIP1 37 and 58 showed fatty acid methyl ester (FAME) yields of 859 and 1,052 mg/l, respectively, at day 10 of growth under heterotrophic conditions, and these yields were 74% and 113% higher, respectively, than that of WT. To elucidate the mechanism underlying the improved phenotypes, we identified candidate HSbZIP1-regulated genes via transcription factor binding site analysis. We then selected three genes involved in fatty acid synthesis and investigated mRNA expression levels of the genes by qRT-PCR. The result revealed that the possible HSbZIP1-regulated genes involved in fatty acid synthesis were upregulated in the HSbZIP1 transformants. Taken together, our results demonstrate that HSbZIP1 can be utilized to improve lipid production in Chlorella sp. HS2 under heterotrophic conditions.

• The Journal of Internal Korean Medicine
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• v.31 no.2
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• pp.189-200
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• 2010

Objectives : Regulatory T cells can reduce inflammation and allergic reactions through their inhibitory functions. Gardeniae Fructus(GF) is a Heat-clearing herb used in traditional Korean medicine, and a wide range of studies on its antiinflammatory effects are being carried out. The authors investigated the effect that Gardeniae Fructus has on regulatory T cells. Methods : The authors screened 14 herbs for their effects on regulatory T cells. 100mg of each herb were separately dissolved in 1ml of sterile saline and the supernatant was harvested after 10 minutes of centrifuge at 15,000 rpm. The supernatant was filtered through a 0.2 ${\mu}m$ syringe filter, and the resulting stock was refrigerated at $4^{\circ}C$. The stock was diluted before testing and used at a final concentration of $0.01{\mu}g/ml$. CD4+CD25+ T cells from healthy BALB/c spleens were used as natural regulatory T cells (nTreg), and CD4+CD25- T cells were used as reactive T cells. CD4+CD25+ and CD4+CD25- T cells were activated with anti-CD3e ($10{\mu}g/m{\ell}$)/anti-CD28 ($1{\mu}g/m{\ell}$) and cultured. IL-10 from supernatant of the culture medium was measured by IL-10 cytokine ELISA. The percentages, cell numbers, phenotype and function of CD4+CD25+ Treg cells were determined by flow cytometry. Results : Gardeniae Fructus was shown to be the most potent herb among the 14 herbs tested for suppressing CD4+CD25- reactive T cell proliferation by stimulating CD4+CD25+ natural regulatory T cells. Gardeniae Fructus induces IL-10 secretion increase by stimulating CD4+CD25+ natural regulatory T cells, and indirectly suppresses CD4+CD25- reactive T cell proliferation through increasing CD25 (IL-2 receptor $\alpha$) expression and thus promoting bonding with IL-2. Gardeniae Fructus did not directly affect CD4+CD25- reactive T cell proliferation. Conclusions : Gardeniae Fructus suppressed reactive T cell proliferation through inducing increases in IL-10 secretion and CD25 (IL-2 receptor $\alpha$) expression.

• 한국생물공학회:학술대회논문집
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• 2001.11a
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• pp.89-92
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• 2001

Aspergillus niger has been used as a host system to express many heterologous proteins. It has various advantages over other expression systems in that it is a small eukaryotic GRAS (Generally Recognized aS Safe) organism with a capacity of secreting large amount of foreign proteins. However, it has been known that the presence of an abundant protease is a limiting factor to express a heterologous protein. The proteases deficient mutants of A. niger were obtained using UV -mutagenesis. A total of 1 ${\times}$ $10^5$ spores were irradiated with 10-20% survival dose of UV, 600J/M2 at 280nm, and the resulting spores were screened on the casein -gelatin plates. Ten putative protease deficient mutants were further analyzed on the starch plates to differentiate the pro from the secretory mutant. An endogenous extracellular enzyme, glucose oxidase, was also examined to confirm that the mutant phenotype was due to the proteases deficiency rather than the mutation in the secretory pathway. The reduced proteolytic activity was measured using SDS-fibrin zymography gel, casein degradation assay, and bio-activity of a supplemented hGM -CSF (human Granulocyte-Macrophage Colony Stimulating Factor). Comparing with the wild type strain, less than 30 % of proteolytic activity was observed in the culture filtrate of the protease deficient mutant (pro -20) without any notable changes in cell growth and secretion.

• International Journal of Oral Biology
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• v.34 no.1
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• pp.21-28
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• 2009

Mutations in DLX3 are associated with both autosomal dominant hypoplastic hypomaturation amelogenesis imperfecta (ADHHAI) and tricho-dento-osseous (TDO) syndrome. ADHHAI is caused by a c.561_562delCT (2bp-del DLX3) mutation whereas TDO syndrome is associated with a c.571_574delGGGG (4bp-del DLX3) mutation. However, although the causal relationships between DLX3 and an enamel phenotype have been established, the pathophysiological role of DLX3 mutations in enamel development has not yet been clarified. In our current study, we prepared expression vectors for wild type and deletion mutant DLX3 products (4bp-del DLX3, 2bp-del DLX3) and examined the effects of their overexpression on the expression of the enamel matrix proteins and proteases. Wild type DLX3 enhanced the expression of matrix metalloprotease 20 (MMP20) mRNA and protein in murine ameloblast-like cells. However, neither a 4bp-del nor 2bp-del DLX3 increased MMP20 expression. Wild type DLX3, but not the above DLX3 mutants, also increased the activity of reporters containing 1.5 kb or 0.5 kb of the MMP20 promoter. An examination of protein stability showed that the half-life of wild type DLX3 protein was less than 12 h whilst that of both deletion mutants was longer than 24 h. Endogenous Dlx3 was also found to be continuously expressed during ameloblast differentiation. Since inactivating mutations in the gene encoding MMP20 are associated with amelogenesis imperfecta, the inability of 4bp-del or 2bp-del DLX3 to induce MMP20 expression suggests a possible involvement of such mutations in the enamel phenotype associated with TDO syndrome or ADHHAI.

• Journal of Ginseng Research
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• v.36 no.2
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• pp.161-168
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• 2012

The abnormal maturation and ossification of articular chondrocytes play a central role in the pathogenesis of osteoarthritis (OA). Inhibiting the enzymatic degradation of the extracellular matrix and maintaining the cellular phenotype are two of the major goals of interest in managing OA. Ginseng is frequently taken orally, as a crude substance, as a traditional medicine in Asian countries. Ginsenoside $Rb_1$, a major component of ginseng that contains an aglycone with a dammarane skeleton, has been reported to exhibit various biological activities, including anti-inflammatory and anti-tumor effects. However, a chondroprotective effect of ginsenoside $Rb_1$ related to OA has not yet been reported. The purpose of this study was to demonstrate the chondroprotective effect of ginsenoside $Rb_1$ on the regulation of pro-inflammatory factors and chondrogenic genes. Cultured rat articular chondrocytes were treated with 100 ${\mu}M$ ginsenoside $Rb_1$ and/or 500 ${\mu}M$ hydrogen peroxide ($H_2O_2$) and assessed for viability, reactive oxygen species production, nitric oxide (NO) release, and chondrogenic gene expression. Ginsenoside $Rb_1$ treatment resulted in reductions in the levels of pro-inflammatory cytokine and NO in $H_2O_2$-treated chondrocytes. The expression levels of chondrogenic genes, such as type II collagen and SOX9, were increased in the presence of ginsenoside $Rb_1$, whereas the expression levels of inflammatory genes related to chondrocytes, such as MMP1 and MMP13, were reduced by approximately 50%. These results suggest that ginsenoside $Rb_1$ has potential for use as a therapeutic agent in OA patients.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.4
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• pp.2185-2193
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• 2016

Background: The pathogenesis of sporadic colorectal cancer (CRC) is influenced by the patient genetic background and environmental factors. Based on prior understanding, these are classified in two major pathways of genetic instability. Microsatellite instability (MSI) and CPG island methylator phenotype (CIMP) are categorized as features of the hypermethylated prototype, and chromosomal instability (CIN) is known to be indicative of the non-hypermethylated category. Secreted frizzled related protein 2 (SFRP2), APC1A in WNT signaling pathway and the DNA repair gene, O6-methylguanine-DNA methyltransferase (MGMT), are frequently hypermethylated in colorectal cancer. Detection of methylated DNA as a biomarker by easy and inexpensive methods might improve the quality of life of patients with CRC via early detection of cancer or a precancerous condition. Aim: To evaluate the rate of SFRP2 and MGMT hypermethylation in both polyp tissue and serum of patients in south Iran as compared with matched control normal population corresponding samples. Materials and Methods: Methylation-specific PCR was used to detect hypermethylation in DNA extracted from 48 polypoid tissue samples and 25 healthy individuals. Results: Of total polyp samples, 89.5% had at least one promoter gene hypermethylation. The most frequent methylated locus was SFRP2 followed by MGMT-B (81.2 and 66.6 percent respectively). Serologic detection of hypermethylation was 95% sensitive as compared with polyp tissue. No hypermethylation was detected in normal tissue and serum and its detection in patients with polyps, especially of serrated type, was specific. Conclusions: Serologic investigation for detection of MGMT-B, SFRP2 hypermethylation could facilitate prioritization of high risk patients for colonoscopic polyp detection and excision.

• Korean Journal of Plant Resources
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• v.15 no.3
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• pp.177-187
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• 2002

In our experiment, selected mutants were used which showed not only the phenotype of a specific unpolished rice but also phenotypes of EM 40, LO 1050, and TAL 214. Reciprocal crosses between the mutants were conducted to select strains which would have more quantity of lipids than before. The constitution of fatty acid was also tested to figure out nutritional aspects of the mutants. In the crossing between EM 40 mutants and mutants (LO 1050) having a thick aleurone layer, the expression of EM 40 mutants has no relation with the thickness of the aleurone layer. And the lipid content of new F$_2$ strains through the crossing is 4.15 ％. The lipid content is larger than those of the parents including Kinmaze and in other crossings of this experiment. This is attributed to the fact that the new F$_2$ strains are the products of the crossing between genes responsible for the size of buds, where lipid is accumulated, and genes accountable for the thickness of the aleurone layer. In the crossing between EM 40 mutants and TAL 214 mutants, lipid content of the new F$_2$ strains is 3.8 ％, higher than 2.92 ％ of TAL 214 mutants. But the degree of lipid increase is smaller than in two other crossings. This is probably because genes expressing the phenotypes of TAL 214 affect the size of EM 40, which gets smaller. The aleurone layer of the new F$_2$ strains is 12 $\mu\textrm{m}$ thicker than the layer of TAL 214 mutants, but 6 $\mu\textrm{m}$ thinner than that of parents (LO 1050) having a thick aleurone layer. This seems to be affected by the size of a microscope. The phenotype of the new F$_2$ strains appears to be similar to that of TAL 214. The lipid content of the new F$_2$ strains is 3.85 ％, larger than 2.92 ％ of TAL 214 and 3.01 % of LO 1050. The increase may be due to the aleurone layer of LO 1050. And the size of the bud of the unpolished rice, though it is not big enough like that of LO 1050, seems to be affected by the accumulation of genes in the thick aleurone layer. The accumulation may contribute to the increase in the content of lipid. When it comes to the constitution of fatty acid, there is little difference between parents like Kinmaze and the new F$_2$ strains. But oleic acid increases while linoleic acid decreases. And the decrease in the linolenic acid seems to contribute to the increase in lipid content. This fact also raises the possibility that genes accountable for specific phenotypes could change the quality of rice if the genes are accumulated. Now, experiments on strains which have large lipid content in EM 40 type 1(ge-1, 3.68 ％), EM type 2(ge-2, 2.91 ％), thick aleurone layer(4.63 ％), and starch layer(3.44 ％) are under way to figure out the effects of gene accumulation. These experiments are likely to present the ways for increasing the lipid content.