• Genomics & Informatics
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• 제15권4호
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• pp.123-127
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• 2017

Synonymous sites are generally considered to be functionally neutral. However, there are recent contradictory findings suggesting that synonymous alleles might have functional roles in various molecular aspects. For instance, a recent study demonstrated that synonymous single nucleotide polymorphisms have a similar effect size as nonsynonymous single nucleotide polymorphisms in human disease association studies. Researchers have recognized synonymous codon usage bias (SCUB) in the genomes of almost all species and have investigated whether SCUB is due to random nucleotide compositional bias or to natural selection of any functional exposure generated by synonymous mutations. One of the most prominent observations on the non-neutrality of synonymous codons is the correlation between SCUB and levels of gene expression, such that highly expressed genes tend to have a higher preference toward so-called optimal codons than lowly expressed genes. In relation, it is known that amounts of cognate tRNAs that bind to optimal codons are significantly higher than the amounts of cognate tRNAs that bind to non-optimal codons in genomes. In the present paper, we review various functions that synonymous codons might have other than regulating expression levels.

• BMB Reports
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• 제29권2호
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• pp.180-182
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• 1996

One of the essential functions of virus surface proteins is the recognition of specific receptors on target cell membranes, and cellular receptors play an important role in viral pathogenesis. But the earliest steps of hepatitis B virus (HBV) infection, such as hepatocyte receptor interaction with the virus, are poorly understood. Previous work has suggested an important role of the preS1 region of HBV envelope protein in mediating viral binding to hepatocytes. Although hepatitis B virus (HBV) infection appears to be initiated by specific binding of virions to cell membrane structures via one or potentially several viral surface proteins, data showing the identification or isolation of the HBV receptor (s) are not yet available. The receptor-like proteins on the plasma membrane surface of HepG2 cells that bind to PreS1 were separated and identified using affinity chromatography, and the amino-terminal amino acid sequences of the receptor-like proteins were determined.

• Toxicological Research
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• 제17권
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• pp.299-304
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• 2001

Xenobiotics and their reactive intermediates bind to cellular macromolecules and/or generate oxidative stress. which provoke deleterious effects on the cell function. Induction of xenobiotic-biotrans-forming enzymes and antioxidant molecules is an important defense mechanism against such insults. A group of genes involved in the defense mechanism. e.g. genes encoding glutathione S-transferases. NAD(P)H: quinone oxidoreductase, UDP-glucuronosyltransferase (UDP-GT) and ${\gamma}$-glutamylcysteine synthetase (GGCS). have a common regulatory sequence, Antioxidant or Electrophile Responsive Element (ARE/EpRE). Recently. Nrf2. discovered as a homologue of erythroid transcription factor p45 NF-E2, was shown to bind ARE/EpRE and induce the expression of these defense genes. Mice that lack Nrf2 show low basal levels of expression and/or impaired induction of these genes. which makes the animals highly sensitive to xenobiotic toxicity. Indeed. we show here that nrf2-deficient mice had a higher mortality than did the wild-type mice when exposed to acetaminophen (APAP). Detailed analyses of APAP hepatotoxicity in the nrf2 knockout mice indicate that a large amount of reactive APAP metabolites was generated in the livers due to the impaired basal expression of two detoxifying enzyme genes, UDP-GT (Ugt1a6) and GGCS. while the cytochrome P450 content was unchanged. Thus. the studies using the nrf2 knockout mice clearly demonstrate significance of the expression of Nrf2-regulated enzymes in protection against xenobiotic toxicity.

• Journal of Microbiology and Biotechnology
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• 제20권8호
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• pp.1179-1184
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• 2010

We report the generation of the first monoclonal antibody that specifically binds to the polysaccharide chitosan. Mice were immunized with a mixture of chitosans, and hybridoma clones were screened for specific binders, resulting in the isolation of a single clone secreting a chitosan-specific IgM, mAbG7. In ELISAs, the antibody could bind to chitosans of varying composition, but demonstrated the highest affinity for chitosans with lower degrees of acetylation (DA) and very poor binding to chitin. We tested the ability of the antibody to bind to chitosan in situ, using preparations of fungal cell walls. Immunofluorescence microscopy confirmed that the antibody bound strongly to the cell walls of fungi with high levels of chitosan, whereas poor staining was observed in those species with cell walls of predominantly chitin or cellulose. The potential use of this antibody for the detection of fungal contamination and the protection of plants against fungal pathogens is discussed.

• Journal of Microbiology and Biotechnology
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• 제17권7호
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• pp.1120-1126
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• 2007

This study was performed to screen probiotic bifidobacteria for their ability to bind and neutralize lipopolysaccharides (LPS) from Escherichia coli and to verify the relationship between LPS-binding ability, cell surface hydrophobicity (CSH), and inhibition of LPS-induced interleukin-8 (IL-8) secretion by HT-29 cells of the various bifidobacterial strains. Ninety bifidobacteria isolates from human feces were assessed for their ability to bind fluorescein isothiocyanate (FITC)-labeled LPS from E. coli. Isolates showing 30-60% binding were designated LPS-high binding (LPS-H) and those with less than 15% binding were designated LPS-low binding (LPS-L). The CSH, autoaggregation (AA), and inhibition of LPS-induced IL-8 release from HT-29 cells of the LPS-H and LPS-L groups were evaluated. Five bifidobacteria strains showed high levels of LPS binding, CSH, AA, and inhibition of IL-8 release. However, statistically significant correlations between LPS binding, CSH, AA, and reduction of IL-8 release were not found. Although we could isolate bifidobacteria with high LPS-binding ability, CSH, AA, and inhibition of IL-8 release, each characteristic should be considered as strain dependent. Bifidobacteria with high LPS binding and inhibition of IL-8 release may be good agents for preventing inflammation by neutralizing Gram-negative endotoxins and improving intestinal health.

• 약학회지
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• 제40권4호
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• pp.422-427
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• 1996

The anti-Ex-A IgG was specifically labeled with stable isotopes, DL-His-2,4-$d_2$, L-Phe-$d_5$, L-Trp-$d_5$, L-Tyr-2,6-$d_2$ and L-[1-$^{13}C$]Trp, by growing hybridoma cell in serum-free medium. By use of NMR spectroscopy with selectively labeled Fab fragment, we applied a paratope mapping on antigen-antibody complex. Assignments of the observed carbonyl carbon resonances have been determined by using $^{13}C$-$^{15}N$ double labeling method in order to assign the Trp resonances. Photo CIDNP was also applied to investigate the antigen-binding site(s) on the surface residues of antibody. We found that Trp 36, which is located at the $V_H$ domain, is an important residue to bind to Ex-A, however, two Tyr on the surface of anti-Ex-A IgG plays no crucial role to bind to antigen. On the basis of these results, we demonstrate that stable isotope-aided NMR strategy can be extended to molecular structural analyses of the complex of an Fab fragment and a protein antigen.

• 한국식품영양과학회지
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• 제28권5호
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• pp.984-989
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• 1999

This study was carried out to investigate the effects of ethanol extracts on lipid oxidation of oil emulsion. The results are as follows; The scavenging ability of plant extracts for hydroxyl radical was found, and plant extracts played an important role as a strong chelating agents to bind iron if Fe2+ ion exists in oil emulsion. Pinus densiflora(PD), Lithospermum erythrorhizon(LE) and PD＋LE acted as strong chelating agents to bind iron to reduce lipid oxidation in oil emulsion. The content of Fe2+ ion in ethanol extracts from LE and PD＋LE were significantly higher(p<0.05) than that of ethanol extracts from PD. The content of total iron has same tendency. The ascorbic acid content of PD(16.36ppm) was slightly higher than those of LE(13.08ppm). Electron donating ability of PD was significantly higher(p<0.05) than those of LE. However, the superoxide(SOD) like ability of LE showed a little higher than those of LE and PD＋LE, which means the strong antioxidant activity of LE. The nitrite scavenging effects were dependent on pH value, however, they decreased as pH value increased. Especially, they almost didn't show the nitrite scavenging effect in pH 6.0. In conclusion, the PD and LE extracts may be used as natural antioxidant sources to reduce lipid oxidation in oil emulsion.

• BMB Reports
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• 제41권2호
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• pp.132-138
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• 2008

AtbZIP16 and AtbZIP68 are two putative G group bZIP transcription factors in Arabidopsis thaliana, the other three members of G group bZIPs are GBF1-3 which can bind G-box. Members of G group have conservative protein structure: highly homological basic region and a proline-rich domain in the N-terminal region. Here, we report that AtbZIP16 and AtbZIP68 could bind cis elements with ACGT core, such as G-box, Hex, C-box and As-1, but with different binding affinities which from high to low were G-box > Hex > C-box > As-1; AtbZIP16 and AtbZIP68 could form homodimer and form heterodimer with other members of G group; N-terminal proline rich domain of AtbZIP16 had transactivation activity in yeast cells while that of AtbZIP68 did not; AtbZIP16 and AtbZIP68 GFP fusion protein localized in the nucleus of onion epidermal cells. These results indicated that AtbZIP16 and AtbZIP68 were two new members of GBFs. In Arabidopsis, AtbZIP16 and AtbZIP68 may also participate in light-responsive process in which GBF1-3 are involved.

• 한국미생물·생명공학회지
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• 제22권3호
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• pp.233-239
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• 1994

The characteristics of the bacteriophage resistant Lactococcus lactis subsp. cremoris ATCC 11602-A1, the phage-resistant mutant of Lactococcus lactis subsp. cremoris ATCC 11602, was examined. Electron microscopic study of phage adsorption to A1 revealed that after 10 min. incubation of the host-phage mixture, A1 did not show phage adsorption, and after 60 min. did not show a real burst and the release of new phage particles which could be detected in the mixture of its parent strain and phage. However, the phage adsorption rate of A1 after SDS treatment increased to 98%. Moreover, when the cell walls from A1 and parent strain, and the polysaccharide(PS) and peptidoglycan(PG) of their cell wall were mixed with phage and incubated for 15 min., PS and PG from A1 did not bind phage, but only SD-treated cell wall bound phage, and the cell wall and PS of parent strain bound phage. Both A1 and parent strain treated with 0.2 N HCl-and 5% TCA(100$$C) did not bind phage. The results suggest that the phage receptor is still present in the cell wall of the A1, but a cell wall constituent hydrolyzed by SDS blocks phage adsorption by masking the phage receptor. It also suggests that the phage receptor of parent strain is associated with PS of the cell wall.

• Molecules and Cells
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• 제28권2호
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• pp.87-92
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• 2009

Human SIRT3 gene contains an intronic VNTR enhancer. A T > C transition occurring in the second repeat of each VNTR allele implies the presence/absence of a putative GATA binding motif. A partially overlapping AP-1 site, not affected by the transition, was also identified. Aims of the present study were: 1) to verify if GATA and AP-1 sites could bind GATA2 and c-Jun/c-Fos factors, respectively; 2) to investigate whether such sites modulate the enhancer activity of the SIRT3-VNTR alleles. DAPA assay proved that GATA2 and c-Jun/c-Fos factors are able to bind the corresponding sites. Moreover, co-transfection experiments showed that the over-expression of GATA2 and c-Jun/c-Fos factors boosts the VNTR enhancer activity in an allelic-specific way. Furthermore, we established that GATA2 and c-Jun/c-Fos act additively in modulating the SIRT3-VNTR enhancer function. Therefore, GATA2 and AP-1 are functional sites and the T > C transition of the second VNTR repeat affects their activity.