• Journal of Life Science
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• v.13 no.3
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• pp.291-297
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• 2003

A human endogenous retroviral family (HERV-W) has recently been described that is related to multiple sclerosis-associated retrovirus (MSRV) sequences that have been identified in particles recovered from monocyte cultures from patients with multiple sclerosis. Two pol fragments (HWP-FB10 and HWP-FBl2) of HERV-W family were identified and analysed by the PCR approach with cDNA library of human fetal brain. They showed 89 percent nucleotide sequence similarity with that of the HERV-W (accession no. AF009668). Deletion/insertion or point mutation in the coding region of the pol fragments from human fetal brain resulted in amino acid frameshift that induced a mutated protein. Phylogenetic analysis of the HERV-W family from GenBank database indicates that the HWP-FB10 is very closely related to the AC000064 derived from human chromosome 7q21-q22. Further studies on the genetic relationship with neighbouring genes and functional role of these new HERV-W pol sequences are indicated.

• Journal of Life Science
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• v.13 no.6
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• pp.879-888
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• 2003

In order to measure the enzyme activity of 5-epi-aristolochene hydroxylase, one of cytochrome P450 (P450) enzymes in eicitor-treated pepper cell, we used in vivo assay method and demonstrated a dramatic suppression of the activity by P450-inhibitors, ancymidol and ketocornazole. Using RT-PCR method with degenerate primer of the well conserved domains found within most P450-enzymes, and using cDNA library screening method, one distinct cDNA, being designated P450Hy01, was successfully isolated from elicitor-treated pepper cells. P450Hy01 mRNA was all induced in elicitor-treated cells whereas never induced in control cells. Moreover, levels of P450Hy01 expression were highly correlated with the levels of extracellular capsidiol production by different elicitors in cell cultures. P450Hy01 transcript was also induced by several other elicitors such as, cellulase, arachidonic acid, jasmonic acid, yeast extract as well as UV stress. P450Hy01 sequence contained high probability amino acid matches to known Plant P450 genes and ORF with a conserved FxxGxRxCxG heme-binding domain. P450Hy01 cDNA showed 98% of homology in sequence of nucleotide as well as amino acid to 5-epi-aristolochene-1, 3-hydroxylase (5EAl, 3H) which has been isolated in tobacco cells, suggesting that P450Hy01 is prominent candidate gene for P450-enzyme encoding 5EAl, 3H in pepper cell.

• Journal of Life Science
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• v.26 no.6
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• pp.705-710
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• 2016

Colorectal cancer (CRC) is the third most common cancer and a leading cause of cancer-related death worldwide. Although several diagnostic and therapeutic tools have been available, CRC remains difficult to complete cure because of insufficient understanding of the molecular mechanisms underlying this disease progression. MicroRNAs (miRNAs) are small non-coding RNA molecules that strongly regulate gene expression via transcriptional and translational control mechanisms. Many crucial cellular pathways are frequently disrupted in cancer development process due to dysregulation of several miRNAs. Mir-31 functions as an oncogene that modulate expression of multiple cancer related genes. Thus, we aimed to demonstrate clinical relevance of miR-31 in human CRC. Quantitative RT-PCR analysis of miR-31 expression was performed in 175 CRC tissues and 16 normal colonic mucosa (NM). Next, we investigated clinical significances of miR-31 expression in various clinicopathologic features in CRC patients cohort. Mir-31 was significantly up-regulated in CRC tissues compared to NM. In CRC tissues, miR-31 expression level was significantly elevated in a stage-dependent manner, which was associated with poor survival in patients with CRC. High miR-31 levels in CRC tissues significantly correlated with poor prognosis (hazard ratio [HR]=2.4) as well as distant metastasis (odds ratio [OR]=2.3). In conclusion, we identified clinical significance of miR-31 expression in CRC. High miR-31 expression may be clinically able to use as a biomarker for CRC prognosis and predicting metastasis.

• Journal of Life Science
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• v.21 no.1
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• pp.96-101
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• 2011

S-Adenosyl-L-methionine synthtase (SAM-s) catalyzes the biosynthesis of SAM from ATP and L-methionine. SAM plays important roles in the primary and secondary metabolism of cells. A metK encoding a SAM-s was searched from Streptomyces natalensis producing natamycin, a predominantly a strong antifungal agent, inhibiting the growth of both yeasts and molds and preventing the formation of aflatoxin in filamentous fungi. To obtain the metK of S. natalensis, PCR using primers designed from the two highly conserved regions for metK genes of Streptomyces strains was carried out, and an intact 1.2-kb metK gene of S. natalensis was cloned by genomic Southern hybridization with PCR product as a probe. To identify the function of the cloned metK gene, it was inserted into pSET152ET for its high expression in the Streptomyces strain, and then introduced into S. lividans TK24 as a host by transconjugation using E. coli ET12567(pUZ8002). The high expression of metK in S. lividans TK24 induced actinorhodin production on R5 solid medium, and its amount in R4 liquid medium was 10-fold higher than that by exconjugant including only pSET152ET.

• Korean Journal of Microbiology
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• v.54 no.3
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• pp.289-292
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• 2018

Using pyrene as the enrichment nutrient, a bacterial strain 10PY1A, was isolated by enrichment culture from oil-contaminated sea sand of Arabian Gulf in Saudi Arabia, and this strain belongs to the species Idiomarina piscisalsi, based on 16S RNA gene sequence analysis. The genome of I. piscisalsi strain 10PY1A contains 2,346 protein-coding sequences and an average GC content of 47.4% in its chromosome (2.59 Mbp). Genes encoding proteins related to the degradation of pyrene were existed in the strain 10PY1A genome, indicating that this strain can be used to degrade polycyclic aromatic hydrocarbons in oil-contaminated marine flora and soil.

• Korean Journal of Environmental Biology
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• v.37 no.1
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• pp.72-81
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• 2019

Bisphenol A (BPA), a representative endocrine disrupting chemicals, has adverse effects on growth, development and reproduction in aquatic organisms. The object of this study was to investigate the modulation of antioxidant enzyme-coding genes using quantitative real time RT-PCR (qRT-PCR), enzyme activity and total protein content, to understand oxidative stress responses after exposure to BPA for 48 h in brackish water flea Diaphanosoma celebensis. The BPA ($3mg\;L^{-1}$) significantly upregulated the expression of Cu/Zn-SOD, Mn-SOD, and catalase (CAT) mRNA. Three GST isoforms (GST-kappa, GST-mu, and GST-theta) mRNA levels significantly increased at the rate of $0.12mg\;L^{-1}$ of BPA. In particular, GST-mu showed the highest expression level, indicating its key role in antioxidant response to BPA. SOD activity was induced with a concentration-dependent manner, and total protein contents was reduced. These findings indicate that BPA can induce oxidative stress in this species, and these antioxidants may be involved in cellular protection against BPA exposure. This study will provide a better understanding of molecular mode of action of BPA toxicity in aquatic organisms.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.10a
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• pp.84-84
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• 2003

DNA methylation is involved in epigenetic processes such as X-chromosome inactivation, imprinting and silencing of transposons. DNA methylation is a highly plastic and critical component of mammalian development The DNA methyltransferases (Dnmts) are responsible for the generation of genomic methylation patterns, which lead to transcriptional silencing. The maintenance DNA methyltransferase enzyme, Dnmt 1, and the de novo methyltransferase, Dnmt3a and Dnmt3b, are indispensable for development because mice homozygous for the targeted disruption of any of these genes are not viable. The occurrence of DNA methylation is not random, and it can result in gene silencing The mechanisms underlying these processes are poorly understood. It is well established that DNA methylation and histone deacetylation operate along a common mechanistic pathway to repress transcription through the action of methyl-binding domain proteins (MBDs), which are components of, or recruit, histone deacetylase (HDAC) complexes to methylated DNA. As a basis for future studies on the role of the DNA-methyl-transferase in porcine development, we have isolated and characterized a partial cDNA coding for the porcine Dnmt1. Total RNA of testis, lung and ovary was isolated with TRlzol according to the manufacture's specifications. 5 ug of total RNA was reverse transcribed with Super Script II in the presence of porcine Dnmt 1 specific primers. Standard PCRs were performed in a total volume of 50 ul with cDNA as template. Two DNA fragmenets in different position were produced about 700bp, 1500bp and were cloned into pCR II-TOPO according to the manufacture's specification. Assembly of all sequences resulted in a cDNA from 158bp of 5'to 4861bp of 3'compare with the known human maintenance methyltransferase. Now, we are cloning the unknown Dnmt 1 region by 5'-RACE method and expression of Dnmt 1 in tissues from adult porcine animals.

• Journal of Animal Science and Technology
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• v.50 no.6
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• pp.753-762
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• 2008

The primers for RT-PCR and RACE-PCR were designed by aligning the pig genomic sequence and the human complement factor B(CFB) coding sequence(CDS) from the GenBank. Each PCR product was amplified in pig cDNA and sequencing was carried out. The CDS length of pig CFB gene was determined to be 2298 bp. In addition, the pig CDS was more longer than human and mouse orthologs because of insertion and deletion. The identities of porcine nucleotide sequences with those of human and mice were 84% and 80%, and the identities of amino acids were 79% to 77%, respectively. Three complement control protein(CCP) domains, one Von Willebrand factor A(VWFA) domain and a serine protease domain, that are revealed typically in mammals, were found in the pig CFB gene. Based on the CDSs determined, the primers were designed in intron regions for amplification of entire length of exons. In amplification and direct sequencing with genomic DNAs of six pig breeds, three cSNPs(coding single nucleotide polymorphisms) were identified and verified as missense mutations. Using the Multiplex-ARMS method, we genotyped and verified the mutations identified from direct sequencing. To demonstrate recrudescence, we performed both direct sequencing and Multiplex-ARMS with two randomly selected DNA samples. The genotype of each sample exhibited the same results using both methods. Therefore, three cSNPs were identified from pig CFB gene and that can be used for haplotype analysis of the swine leukocyte antigen(SLA) class III region. Moreover, the results indicate that the Multiplex-ARMS method should be powerful for genotyping of genes in the SLA region.

• Korean Journal of Microbiology
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• v.41 no.1
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• pp.67-73
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• 2005

Photoautotrophic bacteria are promising candidates for the production of poly(3-hydroxybutyrate) (PHB) since they can address the critical problem of substrate costs. In this study, we isolated 25 Tn5-inserted mutants of the Synechocystis sp. PCC 6803 which showed enhanced PHB accumulation compared to the wild-type strain. After 5-days cultivation under nitrogen-limited mixotrophic conditions, the intracellular levels of PHB content in these mutants reached up to $10-30\%$ of dry cell weight (DCW) comparable to $4\%$ of DCW in the wild-type strain. Using the method of inverse PCR, the affected genes of the mutants were mapped on the completely known genome sequence of Synechocystis sp. PCC 6803. As a result, the increased PHB accumulation in 5 mutants were found to be resulted from defects of genes coding for NADH-ubiquinone oxidoreductase, O-succinylbenzoic-CoA ligase, photosystem II PsbT protein or histidine kinase, which are involved in photosystem in thylakoid inner membrane of the cell. The values of $NAD(P)H/NAD(P)^+$ ratio in the cells of these mutants were much higher than that of the wild-type strain as measured by using pulse-amplitude modulated fluorometer, suggesting that PHB synthesis could be enhanced by increasing the level of cellular NAD(P)H which is a limiting substrate for NADPH-dependent acetoacetyl-CoA reductase. From these results, it is likely that NAD(P)H would be a limiting factor for PHB synthesis in Synechocystis sp. PCC 6803.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.289-292
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• 2019

Lachnospiraceae bacterium KGMB03038 (=KCTC 15821) belonging to the class Clostridia in phylum Firmicutes, was isolated from a stool sample of a healthy Korean. Herein, we report the complete genome sequence of strain KGMB03038 analyzed using the PacBio Sequel platform. The genome comprises of 3,334,474 bp with G + C content of 47.8%, which includes 3,099 predicted protein-coding genes, 12 ribosomal RNAs, 54 transfer RNAs, and 4 ncRNAs. Genome analysis revealed that strain KGMB03038 possesses a number of genes involved in hydrolysis of carbohydrates, including mono-, di-, and oligo-saccharides, and biosynthesis of various amino acids.