• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.4 no.2
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• pp.155-160
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• 2001

Purpose: Helicobacter pylori has been known to have diverse vacA allelic types. The purpose of the study was to identify vacA diversity in Korea and design new primers for signal sequence alleles indigenous to Korea. Methods: Fifty antral biopsy specimens, which had been proven to be H. pylori-positive, were examined for vacA status; signal sequence and mid-region. After PCR amplification and DNA sequencing, vacA alleles of Korean H. pylori strains were compared with those from other countries. Results: Among Korean H. pylori strains vacA alleles with all combinations of signal sequence and mid-region were found, with the exception of s1b or s2. vacA genotype s1c/m1 was predominant in Korea. We found that GGGAGCGTTR in s1a and GGGGYTATTG in s1c were the indigenous sequences to Korea and constructed the new Korean specific primers for the vacA signal sequence; VASK-F, VASK-R, S1AK-F, and S1CK-F. Conclusion: This study showed that s1c/m1 is the predominant type of vacA allele in Korea. We designed new primers for the vacA signal sequence.

• Journal of Veterinary Clinics
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• v.27 no.5
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• pp.508-513
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• 2010

Cytokines are important mediators of the immune response, and quantitating cytokine mRNA is a highly sensitive and attractive method for measuring cytokine production. The objective of the current study was to develop and validate a SYBR green quantitative real-time reverse transcriptase PCR (qRT-PCR) assay for measuring canine cytokine mRNA. The optimal annealing temperatures ($T_a$) of the designed primers were $62^{\circ}C$ for interleukin (IL)-$1{\beta}$, IL-6 and IL-10; $60^{\circ}C$ for glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and tumor necrosis factor (TNF)-${\alpha}$; and $58^{\circ}C$ for high mobility group box 1 (HMGB1). Primer efficiencies of all primers calculated for standard curve samples were between 97.1% and 102.6%. No evidence of secondary structure or primer-dimer formation was seen via melt-curve analysis or gel electrophoresis. The developed qRT-PCR assays are highly specific and sensitive and can be used to quantify gene expression levels of canine cytokines.

• Parasites, Hosts and Diseases
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• v.34 no.1
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• pp.15-20
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• 1996

Cysts of Entamoebn histoIMtica are still found from humans in Korea, but notall of the cysts are known as pathogenic. The non-pathogenic strain is regarded as a differenL species, E. nispnr. In this study, Korean isolates of conventional E. histolvticn were subjected for the differentiation by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Human stools were screened by routine microscopic examination, and cyst or trophozoite positive stools were inoculated into Robinson media. The cultivated trophozoites were prepared for DNA extraction, and the DNAs were used for PCR with common primers of Pl gene. The PCR products were divested with 3 restriction enzymes and RFLP was observed. Also anti-sense primers containing the cleavage site of each restriction eWe were designed for differentiation only by PCR. The PCR products of Korean isolates 59,512, YS-6, and YS-27 were spliced by Taq I and Xmnl but not byAccl, and the isolates S1, S3, S11, S15, S16, S17, S20, YS- l7, and YS-44 were spliced by Acc I but not by Taq I and Xmn I. These RFLP pattern correlated well with PCR products by the species specific primers. The findings confirm that the Korean isolates 59,512, YS-6, and YS-27 are E. histolwtico and others are E. dispar. In Korea, most of the asymptomatic cyst carriers are infected by E. dispar, not by E. histolytica. Key words: Entcmoebc histolytica, Entcmoebn dispar Korean isolates, polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP)

• Journal of Oral Medicine and Pain
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• v.26 no.1
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• pp.87-93
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• 2001

SOX9과 SRY 유전자는 척추동물에서 남성고환의 형성을 유도하는 요소로 알려졌다. SOX9 유전자는 SRY related HMG box gene중 하나로 유전질환의 XY성전환 및 성을 결정하는 데에 관여하며 성결정시기에 그 양에 따른 성전환 발생등 연구가 진행되고 있다. 그러나 이 유전자가 성별판정에 유용할 지는 확실치 않다. 반면 SRY 유전자는 포유동물에서의 배형성시기 고환형성을 결정하는 Y염색체 유전자로 남성에만 존재하고 여성에는 존재 않는다. 현재까지 이을 이용하여 법의학적 검체에서 남성판별에 유용하게 사용되고 있다. 본 실험에서는 X, Y와 같은 성염색체가 아닌 상동염색체상에 있으면서 SRY 유전자와 더불어 남성고환을 결정하는 또다른 요소로서의 기능을 가진 SOX9 유전자를 치아에서 검출하여 법의학적 성별판정에 유용할 수 있는지 알아보고자 본 연구를 수행하였다. 남녀각각 5개의 치아에서 치수와 상아질을 분리한 후 DNA를 추출하여 SOX9과 SRY 유전자의 특이적인 시발체를 제작하고 중합효소연쇄반응을 시행하여 증폭하고 전기영동을 시행하였다. 그 결과 SOX9 유전자는 남녀모두에서 유전자가 검출되었고, SOX9 유전자산물과 SRY 유전자를 혼합하여 사용시 남자에서만 유전자가 검출되었다. 이는 법의치과학적 성별판정에 있어 SOX9 유전자는 사람의 치아에서는 남녀 모두 존재하며 남녀 구별을 위한 성별판정에는 이용할 수 없으며 SRY 유전자와 함께 적용시 남성 특이적 SRY 유전자 검사중 발생할 수 있는 가성 음성 반응여부를 확인하는 데 유용할 것으로 사료된다.

• The Korean Journal of Malacology
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• v.26 no.2
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• pp.185-188
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• 2010

The Web-based the genus Haliotis SNP database was constructed on the basis of Intel Server Platform ZSS130 dual Xeon 3.2 GHz cpu and Linux-based (Cent OS) operating system. Haliotis related sequences (2,830 nucleotide sequences, 9,102 EST sequences) were downloaded through NCBI taxonomy browser. In order to eliminate vector sequences, we conducted vector masking step using cross match software with vector sequence database. In addition, poly-A tails were removed using Trimmest software from EMBOSS package. The processed sequences were clustered and assembled by TGICL package (TIGR tools) equipped with CAP3 software. A web-based interface (Haliotis SNP Database, http://www.haliotis.or.kr) was developed to enable optimal use of the clustered assemblies. The Clustering Res. menu shows the contig sequences from the clustering, the alignment results and sequences from each cluster. And also we can compare any sequences with Haliotis related sequences in BLAST menu. The search menu is equipped with its own search engine so that it is possible to search all of the information in the database using the name of a gene, accession number and/or species name. Taken together, the Web-based SNP database for Haliotis will be valuable to develop SNPs of Haliotis in the future.

• The Journal of Korean Academy of Prosthodontics
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• v.47 no.4
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• pp.424-434
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• 2009

Statement of problem: Problems such as loosening and fractures of retained screws and fracture of implant fixture have been frequently reported in implant prosthesis. Purpose: Implant has weak mechanical properties against lateral loading compared to vertical occlusal loading, and therefore, stress analysis of implant fixture depending on its material and geometric features is needed. Material and methods: Total 28 of external hexed implants were divided into 7 of 4 groups; Group A (3i, FULL $OSSEOTITE^{(R)}$Implant), Group B (Nobelbiocare, $Br{\aa}nemark$ $System^{(R)}$Mk III Groovy RP), Group C (Neobiotec, $SinusQuick^{TM}$ EB), Group D (Osstem, US-II). The type III gold alloy prostheses were fabricated using adequate UCLA gold abutments. Fixture, abutment screw, and abutment were connected and cross-sectioned vertically. Hardness test was conducted using MXT-$\alpha$. For fatigue fracture test, with MTS 810, the specimens were loaded to the extent of 60-600 N until fracture occurred. The fracture pattern of abutment screw and fixture was observed under scanning electron microscope. A comparative study of stress distribution and fracture area of abutment screw and fixture was carried out through finite element analysis Results: 1. In Vicker's hardness test of abutment screw, the highest value was measured in group A and lowest value was measured in group D. 2. In all implant groups, implant fixture fractures occurred mainly at the 3-4th fixture thread valley where tensile stress was concentrated. When the fatigue life was compared, significant difference was found between the group A, B, C and D (P<.05). 3. The fracture patterns of group B and group D showed complex failure type, a fracture behavior including transverse and longitudinal failure patterns in both fixture and abutment screw. In Group A and C, however, the transverse failure of fixture was only observed. 4. The finite element analysis infers that a fatigue crack started at the fixture surface. Conclusion: The maximum tensile stress was found in the implant fixture at the level of cortical bone. The fatigue fracture occurred when the dead space of implant fixture coincides with jig surface where the maximum tensile stress was generated. To increase implant durability, prevention of surrounding bone resorption is important. However, if the bone resorption progresses to the level of dead space, the frequency of implant fracture would increase. Thus, proper management is needed.

• Pediatric Infection and Vaccine
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• v.5 no.1
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• pp.79-87
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• 1998

Purpose : The P1 protein of Mycoplasma pneumoniae mediates the attachment of the pathogen to its host cell and elicits a strong humoral immune response during infection with this organism. Mycoplasma pneumoniae strains can be classified into two groups(I and II) by PCR method of P1 cytadhesin gene. In this study, we evaluated the prevalence, epidemiological and clinical characteristics of each group. Methods : From 155 patients with Mycoplasma pneumoniae, who admitted to the Department of Pediatrics, Sung-Ae and Kwangmyung Sung-Ae Hospital between November 1996 and October 1997, we collected their throat swabs or nasopharyngeal aspirates for DNA extraction and serum for indirect hemagglutination test of Mycoplasma pneumoniae. The group specific PCR amplification were performed using specific oligonucleotide primers designed for P1 gene genotyping. Results : Group I(137 patients, 88.4%) occurred frequently than group II(18 patients, 11.6%). In both group, the most prevalent season was winter in 1996(Nov. to Dec.) and fall in 1997(Aug. to Oct.) The prevalent age was four to six years old. The number of male was more than female in both group; Group 1(1.2:1), Goup 2(1.6:1). No significant relationship were found between two groups in duration of fever and hospital days(P>0.05). The rate of high antibody titers(>1:5120) was lower in group I(6/137, 4.4%) than group II(2/18, 11.1%). Conclusion : Group I was much more prevalent than group II during 1996~1997 in Korea. There was no difference between two groups in epidemiological and clinical parameters except the rate of high antibody titers. Further follow-up survey will be needed for the epidemiologic and clinical studies of Mycoplasma pneumoniae in Korea.

• Journal of Life Science
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• v.20 no.3
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• pp.411-415
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• 2010

Anisakis simplex is one of the parasitic nematodes, and has a complex life cycle in crustaceans, fish, squid or whale. When people eat under-processed or raw fish, it causes anisakidosis and also plays a critical role in inducing serious allergic reactions in humans. However, no web-based database on A. simplex at the level of DNA or protein has been so far reported. In this context, we constructed a web-based database for Anisakis research. To build up the web-based database for Anisakis research, we proceeded with the following measures: First, sequences of order Ascaridida were downloaded and translated into the multifasta format which was stored as database for stand-alone BLAST. Second, all of the nucleotide and EST sequences were clustered and assembled. And EST sequences were translated into amino acid sequences for Nuclear Localization Signal prediction. In addition, we added the vector, E. coli, and repeat sequences into the database to confirm a potential contamination. The web-based database gave us several advantages. Only data that agrees with the nucleotide sequences directly related with the order Ascaridida can be found and retrieved when searching BLAST. It is also very convenient to confirm contamination when making the cDNA or genomic library from Anisakis. Furthermore, BLAST results on the Anisakis sequence information can be quickly accessed. Taken together, the Web-based database on A. simplex will be valuable in developing species specific PCR markers and in studying SNP in A. simplex-related researches in the future.