• Korean Journal of Clinical Laboratory Science
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• v.39 no.1
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• pp.49-55
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• 2007

HCV is a single-stranded RNA virus and more than 1 million new cases are reported annually worldwide. The six major HCV genotypes and numerous subtypes vary in their geographic distribution. It is thought that genetic heterogeneity of HCV may account for some of the differences in disease outcome and response to treatment observed in HCV infected persons. In this study, we determined HCV genotypes among chronic Korean HCV patients and evaluated direct sequence PCR protocols developed. For the study, 232 chronic HCV patient sera were used. HCV RNA was extracted and two pairs of consensus PCR primers were selected in 5'UTR region for amplification of HCV RNA. Amplification products obtained from the HCV positive cases were subjected to automatic sequencing. Sequences were compared with those in GenBank by using the BLAST program. From this study, five HCV genotypes, 1b, 2a, 2b, 2c and 3a were found. HCV genotypes 4, 5 and 6 were not determined. HCV genotype 1b (53.9%, 125/232) and 2a (35.8%, 83/232) were most frequently found. This group was followed by 2b (3.9%, 9/232), 3a (3.4%, 8/232) and 2c (3.0%, 7/232). The data presented here suggest a complex distribution of HCV types and they were well correlated with other reports on Koreans and will be helpful for type-specific follow-up of Korean HCV patients. This study showed that 5'UTR direct sequence analysis is a sensitive and rapid method to identify HCV genotypes.

• Molecules and Cells
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• v.26 no.2
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• pp.212-215
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• 2008

The GC-rich discriminator sequence between the -10 region and the transcription start site of the rnpB promoter is responsible for stringent control of M1 RNA synthesis. The rnpB promoter also contains a G nucleotide at the previously identified transcription start site. In this study, we examined by mutagenesis of G to A whether this +1G nucleotide is involved in the stringent response. We found that the change did not alter the stringent response. Since the +1 mutation might alter transcription initiation, we compared the transcription start sites of the wt and mutant promoters by primer extension analysis. Surprisingly, we found that wild type rnpB transcription starts at both the +1G position (70%) and the -1C position (30%), and that the +1A mutation led to transcription initiation exclusively at the -1C position. We also generated two transversion mutations at the -1 position, both of which led to transcription starting exclusively at that position. The -1G mutant promoter gave a stringent signal similar to the wild-type, whereas the -1A mutant generated a significantly less stringent signal. Base on these results, we propose that a short sequence, up to 7 bp downstream of the -10 region, is involved in the stringent response of the rnpB promoter.

• The Plant Pathology Journal
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• v.31 no.3
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• pp.219-225
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• 2015

The primary step for efficient control of viral diseases is the development of simple, rapid, and sensitive virus detection. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has been used to detect viral RNA molecules because of its simplicity and high sensitivity for a number of viruses. RT-LAMP for the detection of Potato virus X (PVX) was developed and compared with conventional reverse transcription polymerase chain reaction (RT-PCR) to demonstrate its advantages over RT-PCR. RT-LAMP reactions were conducted with or without a set of loop primers since one out of six primers showed PVX specificity. Based on real-time monitoring, RT-LAMP detected PVX around 30 min, compared to 120 min for RT-PCR. By adding a fluorescent reagent during the reaction, the extra step of visualization by gel electrophoresis was not necessary. RT-LAMP was conducted using simple inexpensive instruments and a regular incubator to evaluate whether RNA could be amplified at a constant temperature instead of using an expensive thermal cycler. This study shows the potential of RT-LAMP for the diagnosis of viral diseases and PVX epidemiology because of its simplicity and rapidness compared to RT-PCR.

• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.333-340
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• 2011

Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P<0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.

• Applied Biological Chemistry
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• v.44 no.3
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• pp.153-161
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• 2001

In order to isolate genes involved in ecdysteroids biosynthesis in plants, total RNA was isolated from Achyranthes japonica Nakai, and RT-PCR was performed using degenerate primers selected based on the results of multi-alignment of four cytochrome P450 genes from plants and a putative ecdysone 20-hydroxylase gene from an insect. Fourteen partial cDNA clones showing unique base sequences were obtained, out of which six showed homologies at the levels of nucleotide and amino acid sequences to the other cytochrome P450 genes known to be involved in the ecdysteroid biosynthesis. Of the six clones, four showed relatively high homologies to a putative ecdysone 20-hydroxylase gene isolated from an insect.

• Journal of Dairy Science and Biotechnology
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• v.24 no.1
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• pp.19-28
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• 2006

This study was conducted to isolate antilisterial strains of the Bifidobacterium isolates from the infant feces. The bifidobacteria were isolated anaerobically on BL agar and screened for their inhibitory activity on the MRS-cysteine medium against three foodborne pathogens: Listeria monocytogenes, Bacillus cereus, and Staphylococcus aureus. Among the 52 bifidobacterial isolates, 5 strains(A24, Bl, B6, B10, and Bl2) were finally selected based on their stronger antilisterial activity against Listeria monocytogenes than other isolates tested. Morphologically, all the isolates were typically shown Y-and V-shaped under electron microscopic examination. Each isolate was primarily subjected to identification by a polymerase chain reaction(PCR) using a genus-specific primer designed for targeting the 16S rRNA gene sequence, and confirmed the primary identification data using an API-kit(Biomeriuex, France), commercially available product for identification based on biochemical and physiological traits. Of the isolates with antilisterial activity, strain A24 was finally confirmed as the Bifidobacterium longum A24.

• The Journal of Korean Medicine
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• v.21 no.4
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• pp.16-25
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• 2000

Objective : Acupuncture and Radix Astragali aqua-acupuncture stimuli have long been used to cure human diseases. However, the exact physiological and biochemical mechanisms involved remain undiscovered. Thus, many attempts have been made to show the scientific mechanisms involved. The effects of acupuncture and Radix Astragali aqua-acupuncture, which was known to date, as follow; effective circulation of body blood system and proliferation of leucocytes. Methods : In this study, we have applied acupuncture and Radix Astragali aqua-acupuncture stimuli to mouse on Sinsuhyul, a stimulative point of oriental medicine, to see effects on the expression of cytokine $IL-1{\beta}$. Mice were treated with lipopolysaccharide(LPS) for inflammation induction and then reverse transcriptase-polymerase chain reaction (RT-PCR) using each primer set were performed to trace the amounts of mRNA. Results : 1. $IL-1{\beta}$ was not expressed in LPS-nontreated mice at 15 to 60 min after acupuncture-stimuli. However, expression occurred after 3hrs. 2. $IL-1{\beta}$ was specifically expressed in LPS-treated mice at 30 min after acupuncture-stimuli. 3. $IL-1{\beta}$ was expressed in LPS-nontreated mice at 30 min after Radix Astragali aqua-acupuncture stimuli, however, not expressed at 60, 180 min. 4. $IL-1{\beta}$ was gradually expressed in LPS-treated mice at 15 to 180 min after Radix Astragali aqua-acupuncture stimuli. Conclusions : $IL-1{\beta}$ in LPS-treated mice was more effective than that of LPS-nontreated mice. We are now in the process of elucidating the immunological action mechanism of acupuncture and Radix Astragali aqua-acupuncture stimuli. And cytokine $IL-1{\beta}$ can be used not only as a basis of the effects of acupuncture and Radix Astragali aqua-acupuncture but also as a diagnosis guide through the immunological actions of those.

• Journal of Microbiology and Biotechnology
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• v.25 no.12
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• pp.2153-2159
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• 2015

Mycoplasma hyopneumoniae is known to cause porcine enzootic pneumonia (EP), an important disease in swine production. The objective of this study was to examine the effects of sonicated protein fractions of M. hyopneumoniae on inflammatory response and gene expression in the murine alveolar macrophage MH-S cell line. The effects of sonicated protein fractions and intact M. hyopneumoniae on the gene expression of cytokines and iNOS were assessed using RT-PCR. The Annealing Control Primer (ACP)-based PCR method was used to screen differentially expressed genes. Increased transcription of interleukin (IL)-1β, IL-6, tumor necrosis factor (TNF)-α, COX-2, and iNOS mRNA was observed after exposure to the supernatant (SPT), precipitant (PPT), and intact M. hyopneumoniae protein. A time-dependent analysis of the mRNA expression revealed an upregulation after 4 h for IL-6 and iNOS and after 12 h for IL-1β and TNF-α, for both SPT and PPT; the fold change in COX-2 expression was less. A dose- and time-dependent correlation was observed in nitrite (NO) production for both protein fractions; however, there was no significant difference between the effects of the two protein fractions. In a differential gene analysis, PCR revealed differential expression for nine gene bands after 3 h of stimulation — only one gene was downregulated, while the remaining eight were upregulated. The results of this study provide insights that help improve our understanding of the mechanisms underlying the pathogenesis of and macrophage defenses against M. hyopneumoniae assault, and suggest targets for future studies on therapeutic interventions for M. hyopneumoniae infections.

• Journal of fish pathology
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• v.18 no.2
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• pp.157-165
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• 2005

A new disease causing mass mortality of farmed snakehead (Channa arga) has emerged in Korea over the summer of 2005. The affected fish showed no specific external signs with the exception of a distended abdomen and hemorrhaging around the anus. After opening the abdomen, the visceral organs, liver, spleen and kidney, present numerous white nodular structures. Histopathological examination revealed these nodules to be evidence of granulomas in the visceral organs. A Gram-positive, filamentous bacterium was isolated from all of the affected fish. Development of primers for a genus-specific peR assay for Nocardia, following analysis of the sequences of the complete 16S rRNA genes from Nocardia spp. and non-Nocardia bacterial genes, allowed identification of the causative organism as Nocardia. This is the first report of a nocardial infection of fish in Korea.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.14 no.6
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• pp.3114-3119
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• 2013

The mangrove ecosystems have the capacity to act as a sink of heavy metals entering aquatic ecosystems. Despite their potential exposure to metal contaminated sediments, mangroves appear to be highly tolerant to heavy metals. In this study, we cloned metal tolerance gene from mangrove plant. Using CTAB method, RNA were isolated from leaves and root tissue of Rhizophora stylosa habitated at Weno island in Micronesia Chuuk lagoon using CTAB method and phytochelatin synthase 1 (PCS1) gene was cloned using gene specific primers. Expression of PCS1 gene was increased 1.91 fold and 2.72 fold in mangrove propagules exposed to 100 ppb Cd and 10 ppb Cu, respectively. These results indicate that expression of PCS1 gene are promising tools for health assessment of mangrove ecosystem.