• International Journal of Oral Biology
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• 제45권3호
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• pp.77-83
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• 2020

In the oral cavity, complex microbial community is shaped by various host and environmental factors. Extensive literature describing the oral microbiome in the context of oral health and disease is available. Advances in DNA sequencing technologies and data analysis have drastically improved the analysis of the oral microbiome. For microbiome study, bacterial 16S ribosomal RNA gene amplification and sequencing is often employed owing to the cost-effective and fast nature of the method. In this review, practical considerations for performing a microbiome study, including experimental design, molecular analysis technology, and general data analysis, will be discussed.

• 한국소음진동공학회:학술대회논문집
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• 한국소음진동공학회 2002년도 추계학술대회논문초록집
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• pp.360.1-360
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• 2002

Current information storage devices, such as HDD, CD/DVD-ROM/RW, probe-based memory and cabon nano tubes, are compared with biological information storage mechanisms in DNA and brain memory. Various biological components in living cells are analyzed based on "irreducible complexity" of intelligent design concept. Linear and arel density of information stored in the biological and mechanical storages are compared for the applications and developments of new storage devices.

• Journal of Microbiology and Biotechnology
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• 제7권2호
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• pp.138-143
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• 1997

We have designed and constructed a gene encoding novel high essential amino acid encoding protein(HEAAE). The resultant DNA fragment was tested for in vitro and in vivo expression and then cloned into plant expression vector pBI121, under the control of the cauliflower mosaic virus 35S promoter. Agrobacterium tumefaciens, strain LBA4404, was subsequently transformed with this new construct and Nicotiana tabacum var. Xanthi transgenic plants were obtained. DNA analysis by Southern procedure confirmed the presence of the multi-copy number of genes in the transformed plants. Analysis of RNA and protein synthesized in these transgenic plants demonstrated the stable expression of this gene.

• 생약학회지
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• 제28권1호
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• pp.1-8
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• 1997

Bangpoong (防風) is a popular crude drug used to expel wind from the body surface (祛風解表) to remove dampness (勝濕). And to relieve pain (正痛) and spasm (正痙). In China and Japan, roots of Saposhnikovia divaricata (Turcz.) Schischk. Is used as Bangpoong. However, the roots of Peucedanum japonicum Thunb. Or Glehnia littoralis (A. Gray) Fr. Schmidt ex Miquel, being called Sikbangpoong (植防風) and Wonbangpoong (元防風) respectively are used instead of Bangpoong in Korea. The ITS regions of nuclear ribosomal DNA were analyzed to determine original plants and to design a molecular identification method for the crude drugs used as Bangpoong in Korea and China. It is demonstrated that RFLP analysis via PCR has the great potential as a novel tool to test crude drugs for the quality control and standardization.

• Genomics & Informatics
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• 제9권4호
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• pp.189-193
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• 2011

Simple sequence repeats (SSRs) are ubiquitous short tandem duplications found within eukaryotic genomes. Their length variability and abundance throughout the genome has led them to be widely used as molecular markers for crop-breeding programs, facilitating the use of marker-assisted selection as well as estimation of genetic population structure. Here, we report a software application, "SSR-Primer Generator " for SSR discovery, SSR-primer design, and homology-based search of in silico amplicons from a DNA sequence dataset. On submission of multiple FASTA-format DNA sequences, those analyses are batch processed in a Java runtime environment (JRE) platform, in a pipeline, and the resulting data are visualized in HTML tabular format. This application will be a useful tool for reducing the time and costs associated with the development and application of SSR markers.

• Genomics & Informatics
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• 제3권3호
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• pp.80-85
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• 2005

HExDB is a database for analyzing exon and splicing pattern information in Homo sapiens. HExDB is useful for specific purposes: 1) to design primers for exon amplification from cDNA and 2) to understand the change of ORFs by alternative splicing. HExDB was constructed by integrating data from AltExtron which is the computationally predicted exon database, Ensemble cDNA annotation, and Affymetrix genome tile published recently. Although it may contain false positive data, HExDB is good starting point due to its sensitivity. At present, there areas many as 2,046,519 exons stored in the HExDB. We found that $16.8\%$ of the exons in the database was constitutive exons and $83.1\%$ were novel gene exons.

• Parasites, Hosts and Diseases
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• 제61권3호
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• pp.231-239
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• 2023

Toxoplasma gondii is an intracellular parasitic organism affecting all warm-blooded vertebrates. Due to the unavailability of commercialized human T. gondii vaccine, many studies have been reported investigating the protective efficacy of pre-clinical T. gondii vaccines expressing diverse antigens. Careful antigen selection and implementing multifarious immunization strategies could enhance protection against toxoplasmosis in animal models. Although none of the available vaccines could remove the tissue-dwelling parasites from the host organism, findings from these pre-clinical toxoplasmosis vaccine studies highlighted their developmental potential and provided insights into rational vaccine design. We herein explored the progress of T. gondii vaccine development using DNA, protein subunit, and virus-like particle vaccine platforms. Specifically, we summarized the findings from the pre-clinical toxoplasmosis vaccine studies involving T. gondii challenge infection in mice published in the past 5 years.

• Biotechnology and Bioprocess Engineering:BBE
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• 제9권2호
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• pp.93-99
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• 2004

Pathogens pose a significant threat to humans, animals, and plants. Consequently, a considerable effort has been devoted to developing rapid, convenient, and accurate assays for the detection of these unfavorable organisms. Recently, DNA-microarray based technology is receiving much attention as a powerful tool for pathogen detection. After the target gene is first selected for the unique identification of microorganisms, species-specific probes are designed through bioinformatic analysis of the sequences, which uses the info rmation present in the databases. DNA samples, which were obtained from reference and/or clinical isolates, are properly processed and hybridized with species-specific probes that are immobilized on the surface of the microarray for fluorescent detection. In this study, we review the methods and strategies for the development of DNA microarray for pathogen detection, with the focus on probe design.

• 미생물학회지
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• 제41권2호
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• pp.117-124
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• 2005

Rotifer와 병든 넙치 자어로부터 분리된 2개의 균주는 표현형적인 특성 확인 결과 Vibrio ichthyoenteri로 확인이 되었다. V. ichthyoenteri를 검출하기 위래 고감도 PCR 방법 개발을 하기 위래 V. ichthyoenteri 16S-23S rRNA intergenic spacer region(ISR)을 분석하였고, V. ichthyoenteri중 특이적 primer를 개발하였다. V. ichthyoenteri 의 ISR를 분석한 결과 1개의 다형성 ISR type서열을 포함하고 있었다. ISR서열은 길이는 348bp이며 tRNA gene을 가지고 있지 않았다. 이 서열을 가지고 이미 알려진 다른 Vibrio 종의 ISR 서열과 mutiple alignment를 수행한 결과 여러 영역에서 높은 가변성을 나타내어 가변 부위를 표적으로 하여 V. ichthyoenteri를 검출하기 위한 종 특이적 primer를 제작하였다. 제작된 primer의 특이성을 확인하기 위해 Vibrio 표준균주 19종의 genomic DNA와 분리균주 18 group에 genomic DNA 그리고 V. ichthyoenteri와 가장 유사한 서열을 가지고 있다고 알려진 Vibrio 종의 genomic DNA를 가지고 시험하였다. 그 결과 본 연구에서 제작된 종 특이적 primer를가지고 PCR 반응을 하면 V. ichthyoenteri를 검출 할 수가 있다.

• Asian Pacific Journal of Cancer Prevention
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• 제13권7호
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• pp.3455-3460
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• 2012

Objectives: To report the prevalence of atypical squamous cells of undetermined significance and atypical squamous cells-cannot exclude high squamous intraepithelial lesions and to determine the possible association of Pap test results with high-risk human papillomavirus and high squamous intraepithelial lesions in women from Duhok, Iraq. Design: A prospective, observational study was conducted between January 2005 and December 2011. Overall, 596 women with a cervicovaginal Pap test showing atypical squamous cells of undetermined significance and 93 atypical squamous cells-cannot exclude high squamous intraepithelial lesion for whom pathologic follow-up was available were studied. Follow-up consisted of repeat cytology, colposcopy and histology. High risk human papillomavirus DNA testing was performed on exfoliated cervical cells from 106 women, using conventional PCR after at least 36 months from the initial Pap smear. Results: Significantly high proportions of both atypical squamous cells of undetermined significance (87.9%) and atypical squamous cells-cannot exclude high squamous intraepithelial lesion (62.4%) demonstrated no significant lesion on subsequent follow up. Low squamous intraepithelial lesions were observed in 1.7% of cases of atypical squamous cells of undetermined significance and in 5.4% of atypical squamous cells-cannot exclude high squamous intraepithelial lesion. High squamous intraepithelial lesion was demonstrated in 0.8% and 16.1% respectively. In the latter there was also one case of invasive carcinoma. High-risk HPV DNA was demonstrated in 40% of atypical squamous cells of undetermined significance and 57.1% of atypical squamous cells-cannot exclude high squamous intraepithelial lesions. Conclusions: Since both atypical squamous cells of undetermined significance and atypical squamous cells-cannot exclude high squamous intraepithelial lesion identify patients who are at an increased risk for the development of high squamous intraepithelial lesions and a considerable percentage harbor high risk-HPV, both should be retained as diagnostic categories and patients warrant a diligent follow up and testing for high risk-HPV DNA. Colposcopic evaluation and biopsy, when indicated, are a must.