• Korean Journal of Fisheries and Aquatic Sciences
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• v.42 no.2
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• pp.139-145
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• 2009

We cloned and sequenced the open reading frame (ORF) cDNA encoding myostatin from the muscle of abalone (Haliotis discus hannai). The ORF cDNA of the abalone myostatin is 1134 bp and encoded 377 amino acid residues that were 60-96% homologous with the amino acids of other organism myostatins. In addition, the ORF contained a conserved proteolytic cleavage site (RXRR) and nine conserved cysteine residues in the C-terminus. Semi-quantitative RT-PCR revealed the presence of myostatin mRNA in various tissues. The strongest expression was observed in the mantle of female abalone, and the gills and heart of male abalone.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.21-28
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• 2004

모든 생명체의 genetic information에는 보존적 염기서열과 다형적 염기서열이 존재한다. 다형적 염기서열과 보존적 염기서열은 하나의 종(species)을 감별하거나, 여러 종류의 종을 동시에 감별할 수 있는 genotyping의 표지자로 각각 이용될 수 있다. 본 논문은 병원성 감염질환 세균, 식중독 유발 세균, 생물의약품 오염 유발 세균 및 환경오염 세균 등 세균의 존재 유무와 속과 종 감별을 위해 대부분 세균 종의 보존적 염기서열과 다형적인 염기서열을 포함하고 있는 23S rDNA 유전자의 표적 염기 서열로부터 고안된 세균 특이적(bacterial-specific), 속 특이적(genus-specific), 종 특이적(species-specific) 올리고 뉴클레오티드프로브와 프라이머를 디자인하는 시스템을 소개한다. 시스템을 통해서 얻어진 프로브와 프라이머들은 PCR을 통한 검증단계를 거쳐서 디자인 결과의 정확성을 확인하였다. 본 시스템의 이용으로 프로브와 프라이머를 디자인하는데 몇 주가 소요되는 시간을 몇 일 내로 줄일 수 있었으며, 체계적인 데이터의 관리로 결과의 정확성을 높일 수 있었다.

• The Journal of the Korean Society for Microbiology
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• v.35 no.1
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• pp.49-60
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• 2000

ITSI-5.8S-ITSII rDNA region was amplified from the reference strains and clinical isolates with ITS1 and ITS4 primers. These primers amplified DNA fragments of 550 bp in Microsporum audouinii and Trichophyton violaceum, 700 bp in Microsporum gypseum, Trichophyton mentagrophytes, Trichophyton rubrum, and Trichophyton tonsurans, and 750 bp in Microsporum ferreugineum and Microsporum canis. The restriction enzyme patterns of PCR products digested with 13 restriction enzyme including PstI were distint among the genera, whereas identical in the same species. Examination of the ITS (Internal Transcribed Spacers)1 nucleotide sequence revealed that there was the genetic difference in each genera and species. Phylogenetic relationship among each species showed that the Trichophyton mentagrophytes was more closely related Trichophyton tonsurans than Trichophyton rubrum, and Microsporum gypseum was less related than Microsporum spp..

• Pediatric Infection and Vaccine
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• v.4 no.1
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• pp.97-105
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• 1997

Purpose : Aseptic meningitis mainly caused by enterovirus is common in pediatric population especially during summer & fall. Most of pediatric patients restore their health without any complications with proper management. Between May to August of 1996, Masan and surrounding areas of the Kyoungsangnamdo were epidemic areas for the aseptic meningitis. The purpose of this study was to determine causative virus and describe correlation between disease and clinical symptoms in aseptic meningitis patients and those with fever and characteristic rashes without apparent meningitis symptoms. Methods : Between May to August, 1996, 57 patients with high fever and characteristic feature of rashes were reviewed. From 22 cerebrospinal fluid & 57 stool obtained specimens, viral culture and detection of enterovirus RNA were conducted. Collected specimens were kept in $-30^{\circ}C$ environment until sending of specimens to labortory. The virus identified through indirect immunofluorescence. RT-PCR method was used to identify enterovirus RNA in cerebralspinal fluid. Results : 1) One hundred fifty five pediatric patients with viral infection required hospitalization. Disease occurred higher rate in male than female with ratio of 1.94:1. Examined patients' age ranged from 15days old to 15years old. But most of patients(74.8%) were under age of 5years old. The time of occurrence was between May to August of 1996. 2) All patients had high fever and physical symptoms in those patients include headache, vomiting, abdominal pain, diarrhea, and rashes. The rashes observed mainly in patients under age of 4 years and were predominantly commom patients under age of 18 months olds)<0.001). 3) Between sampled patients and non-sampled patients, clinical course was similar. Echovirus type 9 was cultivated in 41 out of 57 cases of collected stool specimens. RT-PCR that used on CSF showed positive results in 10 out of 22 cases. Three cases of positive cultivated of positive results in RT-PCR were echovirus type 9. Conclusions : Echovirus type 9 was thought to be the causative agent of aseptic meningitis that was prevalent throughout mid areas of Kyoungsangnamdo from May to August, 1996. Additionally causative agent that responsible for high fever with rashes without meningitis symptoms also thought to be the same echovirus type 9.

• Journal of the Korean Society of Food Science and Nutrition
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• v.37 no.10
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• pp.1343-1356
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• 2008

The evaluation of microbiological quality for school food samples collected from 19 selected middle and high schools located in Seoul was undertaken. Eighty-nine food samples consisting of 38 non-pretreated vegetables, 13 pre-washed and cut vegetables, 9 meats and poultry, 3 fish and shellfish, 7 dried fish, and shellfish and 20 processed foods were collected. Aerobic plate count, total coliforms, and Escherichia coli (E. coli ) were detected using $Petrifilm^{TM}$, and the food-borne pathogens were screened by multiplex PCR with species-specific primer sets. Sequentially, the quantitative and confirmative test of the food-borne pathogens were carried out with the selective media and biochemical kits. The contamination of coliform counts was observed on the pre-washed vegetables ($3.4{\sim}4.3\;log\;CFU/g$) and meats ($2.2{\sim}4.3\;log\;CFU/g$). Also, the cooked foods were heavily contaminated with coliform, ranging from 1.0 to $5.5\;log\;CFU/g$. E. coli counts were found in 16 raw and cooked food samples, exceeding the microbiological standards for the guideline of safety management for school foods. Through PCR detection, B acillus cereus was detected in 32 raw and cooked foods, and quantitatively found in pre-washed carrot, radish, and pan-broiled dried shrimp and filefish ranging from $2.3{\sim}3.6\;log\;CFU/g$, respectively. E. coli O157:H7 was detected on frozen pork sample and was confirmed with API kit. Campylobacter jejuni was found in 3 ready-to-eat type vegetables. Vibrio parahaemolyticus were found in 4 pre-washed vegetables and 2 cooked foods, indicating unsatisfactory quality based upon the microbiological standards of ready-to-eat vegetables and cooked foods by Korea Food and Drug Administration. Salmonella spp. was detected in frozen chicken sample and confirmed by API kit and latex antisera agglutination.

• Clinical and Experimental Reproductive Medicine
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• v.34 no.2
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• pp.95-106
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• 2007

Objective: We previously identified differentially expressed genes (DEGs) between germinal vesicle (GV) and metaphase II (MII) mouse oocyte. The present study was accomplished as a preliminary study to elucidate the role of ribose 5-phosphate isomerase A (Rpia), the essential enzyme of the pentose phosphate pathway (PPP), in oocyte maturation. We observed expression of Rpia in the mouse and porcine oocytes. Methods: Expression pattern of the 11 MII-selective DEGs in various tissues was evaluated using RT-PCR and selected 4 genes highly expressed in the ovary. According to the oocyte-selective expression profile, we selected Rpia as a target for this study. We identified the porcine Rpia sequence using EST clustering technique, since it is not yet registered in public databases. Results: The extended porcine Rpia nucleotide sequence was submitted and registered to GenBank (accession number EF213106). We prepared primers for porcine Rpia according to this sequence. In contrast to the oocyte-specific expression in the mouse, Rpia was expressed in porcine cumulus and granulosa cells as well as in oocytes. Conclusion: This is the first report on the characterization of the Rpia gene in the mouse and porcine ovarian cells. Results of the present study suggest that the mouse and porcine COCs employ different mechanism of glucose metabolism. Therefore, the different metabolic pathways during in vitro oocyte maturation (IVM) in different species may lead different maturation rates. It is required to study further regarding the role of Rpia in glucose metabolism of oocytes and follicular cell fore exploring the regulatory mechanism of oocyte maturation as well as for finding the finest culture conditions for in vitro maturation.

• Journal of Life Science
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• v.17 no.3 s.83
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• pp.386-395
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• 2007

A total of 27 strains of Vibrio parahaemolyticus (18 strains isolated from Korea and 9 strains from Japan) were serotyped and examined for biochemical characteristics, antimicrobial susceptibility patterns, cytotoxicity assay, thermostable direct hemolysin (TDH) production and molecular epidemiology. Using polymerase chain reaction (PCR) method and DNA probe hybridization method, the strains were tested for toxR, tdh, trh and ORF 8 genes. The V. parahaemolyticus isolated from patients were belonged to 8 different serotypes : O3:K6, O1:K38, O3:K57, O4:K9, O4:Kl2, O4:K68, O5:Kl5 and O6:K46. Urease-positive strain possessed the trh gene, and conversely, urease-negative strains lacked the gene, indicating that urease production by V. parahemolyticus strains strongly correlates with the possession of the trh gene. Most strains showed multiple resistant to more than three antibiotics and the antibiogram could be classified into 6 group (I to VI). All of the O3:K6 strains isolated in South Korea and Japan producted TDH at high levels. The TDH titers ranged between 256 and 2.048, and the average titer was 1009. To distinguish the new and increasingly common V. parahaemolyticus strains from clinical isolates, ORF 8 is a useful genetic marker. After Southern hybridization, the HindIII restriction fragment patterns of the tdh gene were grouped one type, respectively. One type showed two bands one of which was 4.3kb and the other was 11.5kb in size. Variation between the O3:K6 serotype are minor when compared to the differences seen with the non O3:K6 strains. The migration patterns of Not I -digested of the total DNA of the O3:K6 strains were similar, and only slight variations were observed between the serotypes. By contrast, the O3:K6 strains and non O3:K6 had markedly different profiles. In conclusion, Random amplified polymorphic DNA (RAPD) profile using appropriate primers was an effective epidemiological marker.

• Journal of Life Science
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• v.28 no.9
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• pp.1030-1041
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• 2018

Abiotic stresses limit the growth and productivity of plants. Cellular adaptation to abiotic stresses requires coordinated regulation in gene expression directed by complex mechanisms. This study used the activation tagging system to identify novel salt stress-responsive genes. The study selected 9 activation tagging lines that showed salt stress-tolerant phenotypes during their germination stages. Thermal asymmetric interlaced-PCR (TAIL-PCR) was used to identify the T-DNA tagging sites on the Arabidopsis genome in selected activation tagging lines, including AT7508, AT7512, AT7527, AT7544, AT7548, and AT7556. RT-PCR analysis showed that ClpC2/HSP93-III (At3g48870), plant thionin family (At2g20605), anti-muellerian hormone type-2 receptor (At3g50685), vacuolar iron transporter family protein (At4g27870), and microtubule-associated protein (At5g16730) were activated in AT7508, AT7512, AT7527, AT7544, and AT7556, respectively. Interestingly, in AT7548, both the genes adjacent to the T-DNA insertion site were activated: Arabinogalactan protein 13 (AGP13) (At4g26320) and F-box/RNI-like/FBD-like domains-containing protein (At4g26340). All of the seven genes were newly identified as salt stress-responsive genes from this study. Among them, the expression of ClpC2/HSP93-III, AGP13, F-box/RNI-like/FBD-like domains-containing protein gene, and microtubule-associated protein gene were increased under salt-stress condition. In addition, AT7508, AT7527, and AT7544 were more tolerant to salt stress than wild type at seedling development stage, functionally validating the screening results of the activation tagging lines. Taken together, our results demonstrate that the activation tagging system is useful for identifying novel stress-responsive genes.

• Korean Journal of Microbiology
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• v.42 no.4
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• pp.277-285
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• 2006

The most biofilm forming bacteria in catheter, Esctherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus were isolated and identified from a patient's catheter occuring catheter-associated urinary tract infection (CA-UTI). We examined mRNA expression and its quantification of AIs synthetic genes encoding signal substance of quorum sensing from each bacterial species in order to elucidated quorum sensing mechanism. Both pure cultures for each bacterial strains and a mixed cultures with three were grown for 24 hr and 30 days. Initial densities to be able to detect mRNA expression oil single strains culture were shown at $2.4{\times}10^5$ CFU/ml, $5.4{\times}10^6$ CFU/ml of E. coli for ygaG and S. aureus for luxS, and at $6.9{\times}10^4$ CFU/ml of P. aeruginosa for rhlI and lasI. Also, in mixed culture of three, initial cell densities of mRNA expression were appear to at $7.3{\times}10^5$ CFU/ml, $1.6{\times}10^7$ CFU/ml of E. coli for ygaG and S. aureus for luxS, and at $2.1{\times}10^5$ CFU/ml of P. aeruginosa for rhlI and lasI. Each AIs synthetic gene was expressed in initial cell density and the mRNA expression of the genes were detected continously during 30 days. And then, the quantification of mRNA expression level of ygaG, rhlI, last, and luxS which were related AIs synthesis was done each time point by real-time RT-PCR. Interestingly, the mRNA levels of ygaG, rhlI, lasI, and luxS from the mixed culture was higher than those from each single strain culture. In the case of E. coli ygaG, the amount of transcript from the mixed culture was at least 30 times for that from single culture. In the case of P. aeruginosa rhlI and lasI, the amount of transcript from the mixed culture was at least 40 times and 250 times for that from single strain culture. In the case of S. aureus luxS, the amount of transcript from the mixed culture was at least 5 times for that from single strain culture. And specially, the mRNA expression of rhlI and lasI of P. aeruginosa showed the highest efficency among four AIs synthetic genes.

• Journal of Food Hygiene and Safety
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• v.35 no.3
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• pp.234-242
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• 2020

In this study, we monitored the raw materials in home-meal replacement (HMR) products, which have shown more than 63% growth in market size for two years. A total of 89 HMR products were purchased and the DNA barcodes of 112 raw materials in the product samples were analyzed. In order to identify the raw material species, a primer set specific for the 16S ribosomal RNA region of each raw material species was amplified. The amplicon was purified and sequenced, and then used to perform a BLAST search provided by the National Institutes of Health (NIH). The species of the raw material was determined by comparing the nucleotide sequences of the species registered in GenBank with identity and match score. Twenty-four species and three genera were identified from 112 raw materials. Three genera were identified at the genus level because a large number of species belonging to the same genus exist within 98% of the identity criteria. The results of the determination were compared with the available raw materials suggested in the Korea Food Code to determine the Korean name and availability of the foods. Six non-listed species were determined to be edible according to information provided by influential domestic and foreign organizations.