• Korean Journal of Veterinary Research
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• v.38 no.4
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• pp.777-783
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• 1998

Antigenic types of 114 Salmonella pullorum and 152 Salmonella gallinarum field isolates were evaluated. All 3 antigenic types were identified among field isolates of S pullorum by factor-serum analysis but the majority of them were standard type(90.4%). Of the 114 S pullorum isolates, only eight(7.0%) were intermediate type and 3(2.6%) were variant type. Using the ammonium sulfate precipitation(ASP) test, one-hundred and three(90.4%) S pullorum isolates were standard type, while intermediate and variant types were 8.4% and 1.4%, respectively. One-hundred and fifty-two S gallinarum isolates were identified as standard type by ASP test and serological analysis. According to the random amplified polymorphisms of DNA(RAPD) patterns, most of S pullorum isolates were differentiated with 3 types in their fragment-patterns. No correlations were found between SDS-PAGE profiles and antigenic types of S pullorum isolates.

• The Plant Pathology Journal
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• v.28 no.1
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• pp.93-100
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• 2012

The rhizobacterium NJ134, showing strong $in$ $vitro$ antifungal activity against $Fusarium$ $oxysporum$, was isolated from field grown tomato plants and identified as $Pseudomonas$ sp. based on 16S ribosomal DNA sequence and biochemical analyses. The antifungal compound purified by gas chromatography-mass spectrometry, infrared, and nuclear magnetic resonance analyses from NJ134 cultures was polyketide 2,4-diacetylphloroglucinol (DAPG). Analysis of the sequence of part of one of the genes associated with DAPG synthesis, $phlD$, indicated that the DAPG producer NJ134 was a novel genotype or variant of existing genotype termed O that have been categorized based on isolates from Europe and North America. A greenhouse study indicated that about $10^8$ CFU/g of soil NJ134 culture application was required for effective biocontrol of Fusarium wilt in tomato. These results suggest that a new variant genotype of a DAPG-producing strain of $Pseudomonas$ has the potential to control Fusarium wilt under the low disease pressure conditions.

• Genomics & Informatics
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• v.15 no.1
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• pp.48-50
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• 2017

Tumor tissues from biopsies or surgery are major sources for the next generation sequencing (NGS) study, but these procedures are invasive and have limitation to overcome intratumor heterogeneity. Recent studies have shown that driver alterations in tumor tissues can be detected by liquid biopsy which is a less invasive technique capable of both capturing the tumor heterogeneity and overcoming the difficulty in tissue sampling. However, it is still unclear whether the driver alterations in liquid biopsy can be detected by targeted NGS and how those related to the tissue biopsy. In this study, we performed whole-exome sequencing for a breast cancer tissue and identified PTEN p.H259fs*7 frameshift mutation. In the plasma DNA (liquid biopsy) analysis by targeted NGS, the same variant initially identified in the tumor tissue was also detected with low variant allele frequency. This mutation was subsequently validated by digital polymerase chain reaction in liquid biopsy. Our result confirm that driver alterations identified in the tumor tissue were detected in liquid biopsy by targeted NGS as well, and suggest that a higher depth of sequencing coverage is needed for detection of genomic alterations in a liquid biopsy.

• Proceedings of the Korean Society of Toxicology Conference
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• 2002.05a
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• pp.75-75
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• 2002

Two types of normal human breast epithelial cells (HBECs) have already been established and characterized. Type I HBECs are deficient in gap junctional intercellular communication and are capable of anchorage-independent growth and of expressing luminal epithelial cell markers, a variant estrogen receptor (ER), and stem cell characteristics.(omitted)

• BMB Reports
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• v.31 no.3
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• pp.245-248
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• 1998

Human epidermoid carcinoma A431 cells have an extraordinarily large number of epidermal growth factor (EGF) receptors, and their growth is inhibited by EGF, which results in growth arrest at the Gl phase. In order to investigate the EGF-mediated inhibition mechanism, the expression level of DNA topoisomerase (topo) II was analyzed after EGF treatment. As a result, it was shown that EGF treatment lowered the amount of 170 kDa topo II (topo $II{\alpha}$) but not 180 kDa (topo $II{\beta}$). However, the A431 cell variant resistant to EGF was not sensitive to EGF treatment. These results suggest that EGF-induced growth arrest of A431 cells may be closely related to the depletion of topo $II{\alpha}$.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.8
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• pp.1091-1101
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• 2009

In an attempt to understand the biochemical mechanism for the synthesis of the anabolic steroid, 19-nortestosterone, produced by prepubertal boar testes and its physiological role, normalized complementary DNA (cDNA) from boar testes was generated. DNA sequencing of 2,016 randomly selected clones yielded 794,116 base pairs of high quality nucleotide sequence. Computer-assisted assembly of the nucleotide sequence of each clone resulted in 423 contigs and 403 singletons including several genes for steroidogenic enzymes and molecules related to steroid metabolism. Analysis of gene expression pattern by use of the presently-fabricated cDNA microarray identified a number of genes that were differentially expressed during the postnatal development period in boar testes. Two genes of unknown function were identified to be highly expressed in the testis of 2-weeks-old neonatal boar. In addition, the sequencing of open reading frames of these genes revealed their homology with human alpha hemoglobin and Homo sapiens hypothetical LOC643669, transcript variant 1. Moreover, the transcripts of these genes were also detected in porcine muscle and adipocytes, in addition to Leydig cells of pigs.

• Animal cells and systems
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• v.3 no.4
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• pp.393-397
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• 1999

Length variations in human mitochondrial DNA (mtDNA) offer useful markers in the study of female aspects of human population history. One such length variation is a 9-bp deletion in the small noncoding segment located between the COII and Iysine tRNA genes (COII/tRNA/$^{Lys}$ intergenic region) which usually contain two tandemly arranged copies of a 9-bp sequence (ccccctcta) in human mtDNA. The mtDNA 9-bp deletion and polymorphic variants of expanded 9-bp repeat motif in the intergenic COII/tRNA$^{Lys}$ region have been found at varying frequencies among different human ethnic groups. We have examined the length variation of the mtDNA COII/tRNA$^{Lys}$ intergenic region from a total of 813 individuals in east Asian populations. The occurrence of the 9-bp deletion was found to be relatively homogeneous in northeast Asian populations (Chinese, 14.2%; Japanese, 14.3%: Koreans, 15.5%), with the exception of Mongolians (5.1%). In contrast, Indonesians (25.0%) and Vietnamese (23.2%) of the southeast Asian populations appeared to have relatively high frequencies of the 9-bp deletion. We identified the existence of a new expanded 9-bp repeat motif which likely resulted from a slipped mispairing insertion of six more cytosines in the intergenic COII$^{Lys}$ region. It was present at low frequencies in the Korean (2/349) and Japanese populations (2/147). Based on the results of this study, the Korean population may reflect a close genetic affinity with the Japanese and Chinese populations than the others surveyed east Asian populations.

• Journal of Microbiology and Biotechnology
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• v.14 no.1
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• pp.153-157
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• 2004

Tyrosine phenol-lyase (TPL) is a useful enzyme for the synthesis of pharmaceutical aromatic amino acids. In the current study, sequential DNA shuffling and screening were used to enhance the stability of TPL. Twenty-thousand mutants were screened, and several improved variants were isolated. One variant named A13V, in which the $13^{th}$ amino acid alanine was substituted by valine, exhibited a higher temperature and denaturant stability than the wild-type TPL. The purified mutant TPL, A13V, retained about 60% of its activity at $76^\circ{C}$, whereas the activity of the wild-type TPL decreased to less than 20% at the same temperature. Plus, A13V exhibited about 50% activity with 3 M urea, while the wild-type TPL lost almost all its catalytic activity, indicating an increased denaturant tolerance in the mutant A13V. It is speculated that the substitution of Val for the Ala in the $\beta$-strand of the N-terminal arm was responsible for the heightened stabilization, and that the current results will contribute to further research on the structural stability of TPL.

• Fisheries and Aquatic Sciences
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• v.9 no.1
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• pp.22-29
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• 2006

We determined the partial cDNA of Type II procollagen ${\alpha}1$[pro-${\alpha}1$(II)] chain (1802 bp) of the skate Raja kenojei, which codes 581 amino acid residues. The partial structure of the pro-${\alpha}1$(II) chain consisted of a part of triple helical region (309 residues) and a C-domain (272 residues). Comparing the chain to other vertebrates showed relatively low homology (about 50%) at the amino acid level. However, eight Cys residues in the C-domain of the skate pro-${\alpha}1$(II) chain were conserved in common with those of other vertebrates. The skate pro-${\alpha}1$ (II) chain mRNA was detected by RT-PCR of various tissues, but was undetected in tissues containing Type II collagen. The low homology and unexpected expression pattern suggest the presence of another mRNA variant of the skate pro-${\alpha}1$(II) chain. The present study is the first report of the primary structure of pro-${\alpha}1$(II) chain in an elasmobranch.

• Genomics & Informatics
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• v.17 no.4
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• pp.42.1-42.6
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• 2019

Robust identification of genetic alterations is important for the diagnosis and subsequent treatment of tumors. Screening for genetic alterations using tumor tissue samples may lead to biased interpretations because of the heterogeneous nature of the tumor mass. Liquid biopsy has been suggested as an attractive tool for the non-invasive follow-up of cancer treatment outcomes. In this study, we aimed to verify whether the mutations identified in primary tumor tissue samples could be consistently detected in plasma cell-free DNA (cfDNA) by digital polymerase chain reaction (dPCR). We first examined the genetic alteration profiles of three colorectal cancer (CRC) tissue samples by targeted next-generation sequencing (NGS) and identified 11 non-silent amino acid changes across six cancer-related genes (APC, KRAS, TP53, TERT, ARIDIA, and BRCA1). All three samples had KRAS mutations (G12V, G12C, and G13D), which were well-known driver events. Therefore, we examined the KRAS mutations by dPCR. When we examined the three KRAS mutations by dPCR using tumor tissue samples, all of them were consistently detected and the variant allele frequencies (VAFs) of the mutations were almost identical between targeted NGS and dPCR. When we examined the KRAS mutations using the plasma cfDNA of the three CRC patients by dPCR, all three mutations were consistently identified. However, the VAFs were lower (range, 0.166% to 2.638%) than those obtained using the CRC tissue samples. In conclusion, we confirmed that the KRAS mutations identified from CRC tumor tissue samples were consistently detected in the plasma cfDNA of the three CRC patients by dPCR.