• Genomics & Informatics
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• 제3권1호
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• pp.1-7
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• 2005

Case-control studies are widely used for disease gene mapping using individual genotyping data. However, analyses of large samples are often impractical due to the expense of individual genotyping. The use of DNA pooling can significantly reduce the number of genotyping reactions required; hence reducing the cost of large-scale case-control association studies. Here, we discuss the design and analysis of DNA pooling genetic association studies.

• Asian-Australasian Journal of Animal Sciences
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• 제15권10호
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• pp.1412-1421
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• 2002

To examine the feasibility of using a sperm vector system for gene transfer, we have investigated the binding and the uptaking of foreign DNA into the sperm nucleus by PCR, in situ hybridization and LSC. We have also examined the transportation of exogenous DNA into oocytes by immunofluorescene via PCR. Sperm cells were incubated with DNA/liposome complexes (1:4 ratio) in fertilization medium with BSA or without BSA. In situ hybridization demonstrated that the transfection rate of sperm cells with and without BSA was 41 and 68% respectively, when the cells were treated with liposome/DNA complexes and 13% for DNA alone. LSC analysis showed that the binding of exogenous DNA was greatly reduced by DNase I treatment which digests DNA bound onto spermatozoa, suggesting that some of the DNA was internalized into the sperm membrane. To find out whether transfected DNA was internalized into sperm intracytomembrane, sperm DNA was amplified by inverse PCR. No PCR products were detected from sperm cells, indicating that the foreign DNA was simply bound onto the sperm membrane. To investigate transfer rates of exogenous DNA into oocytes via sperm cells, we used immunofluorescene method to follow the distribution of foreign DNA via spermatozoa: a few exogenous DNA was located in the cytoplasm of early embryos (13/60, 21.7% for DNA+/liposome+/BSA) and was not located in the pronucleus and/or nucleus. These results suggest that most of the transfected sperm cells could carry the foreign DNA into the egg by in vitro fertilization, but that the transferred DNA is degraded in the developing embryos without stable integration into the zygote genome. Therefore, we have directly injected with transfected sperm cell into oocyte cytoplasm and observed that some of the exogenous DNA was detected in preimplantation embryonic cytoplasm and expressed at preimplantation stages, suggesting that exogenous DNA in early zygote has their integrity. In this study, we have not identified a noble mechanism that interfering transportation of foreign DNA into zygote genome via spermatozoa. Our data, however, demonstrated that inverse PCR and immunofluorescene methods would be used as a new tool for follow-up of gene distribution in oocyte via sperm cells.

• Clinical and Experimental Reproductive Medicine
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• 제37권3호
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• pp.245-251
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• 2010

목 적: 인간 정자 핵 내의 DNA integrity는 배아의 발달 및 임신 유지에 중요한 역할을 하여 DNA integrity가 손상된 경우 불임과 유산의 원인이 된다고 하며, 정계정맥류는 DNA 손상을 일으키는 대표적인 원인 중 하나이다. 본 연구에서는 미세술기를 이용한 정계정맥류절제술로 정계정맥류를 교정을 하였을 때 정자 핵 내 DNA integrity가 어떠한 영향을 받는지에 대하여 알아보았다. 연구방법: 2006년 4월부터 2007년 4월까지 불임을 주소로 미세술기를 이용한 정계정맥류절제술을 받았던 18명의 환자에서 수술 전 후에 정액검사의 다른 지표들과 함께 정자 핵 내 DNA integrity가 어떻게 변화하였는지 조사하였다. 정자 핵 내 DNA integrity를 측정하는 방법으로 comet assay를 시행하였고, comet assay를 통한 DNA 손상 정도는 DNA fragmentation index (DFI)로 나타내었다. 결 과: 수술 후 4개월에 모든 환자에서 재발의 소견은 보이지 않았으며, DNA 손상 정도를 나타내는 평균 DFI는 수술 전에 19.3%, 수술 후에 13.7%로 유의한 변화를 보였다. 수술 전 DFI가 10 이상으로 비정상인 14명의 환자들 중 12명 (85%)에서 개선 소견을 보였으나, 수술 전 DFI가 10 미만인 정상 환자 4명에서는 1명 (25%)만이 개선 소견을 보였다. 수술 후 정자의 밀도, 운동성, 생존성에서 호전 양상을 보였으나 유의한 차이는 없었다. 결 론: 미세술기를 이용한 정계정맥류절제술을 통한 수술적 교정은 정액검사상의 다른 지표의 개선 뿐 아니라, 정자 핵 내 DNA 손상을 감소시킬 수 있다. 이상에서 정계정맥류의 수술적 교정으로 정자 핵 내 DNA integrity의 개선을 기대할 수 있으며, 이는 보다 양호한 정자를 많이 얻을 수 있어 자연임신이나 보조 생식술의 성공 가능성을 높일 수 있다는 점을 제시한다.

• Journal of Microbiology and Biotechnology
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• 제10권5호
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• pp.651-655
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• 2000

Polymerase chain reaction (PCR) was used to specifically detect Phytophthora infestans by analyzing the sequences of the ribosomal internal transcribed spacer regions (ITS) in the rDNA of the Phytophthora species. Based on the sequence data, PISP-1 together with the ITS3 primer were used to detect p. infestans. A single ca. 450 bp segment was observed in P. infestans, but not in the other fungal or bacterial isolates. Two factors, the annealing temperature and template DNA quantity, were investigated to determine the optimal conditions. Using these species-specific primers, a unique band was obtained within annealing temperatures of $55^{\circ}C$-$61^{\circ}C$ and template DNA levels of 10 pg-100 ng.

• Journal of Microbiology
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• 제35권2호
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• pp.79-86
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• 1997

For the phylogenetic study of the genus Trichaptum, nuclear ribosomal DNA sequences from eight strains of four Trichaptium species were examined. Phylogenetic trees were constructed using molecular data on 18 rDNA and 5.8S rDNA and thei ITSs. Parsimony analyses of the Trichaptum species showed that T. biforme and T. laricinum made a monophyletic group respectively, suggesting that each species is phylogenetically independent. However, T. abietum represented a polyphyletic group and T. fusco-violaceum formed a polytomous group, suggesting that these species could be in the process of evolutionary differentiation. Examination of base substitutions of the 18S rRNA gene reveals that the C-T transition is most predominant and that there is a stronger transition bias between closely related organisms rather than between distantly related ones.

• Biotechnology and Bioprocess Engineering:BBE
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• 제11권3호
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• pp.179-186
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• 2006

End-Labeled Free-Solution Electrophoresis (ELFSE) is a new technique that is a promising bioconjugate method for DNA sequencing (or separation) and genotyping by both capillary and microfluidic device electrophoresis. Because ELFSE enables high-resolution electrophoretic separation in aqueous buffer alone (i.e., without a polymer matrix), it eliminates the need to load viscous polymer networks into electrophoresis microchannels. To achieve microchannel DNA separations with high performance, ELFSE requires monodisperse perturbing entities (i.e., drag-tags), which create a large amount of frictional drag when pulled behind DNA during free-solution electrophoresis, and which have other properties suitable for microchannel electrophoresis. In this article, the theoretical concepts of ELFSE and the required characteristics of the drag-tag molecules for the ultimate performance of ELFSE are reviewed. Additionally, the merits and limitations of current drag-tags are also discussed in the context of recent experimental data of ELFSE separation (or sequencing).

• International journal of advanced smart convergence
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• 제5권3호
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• pp.8-15
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• 2016

In recent years, one of deep learning models called Deep Belief Network (DBN) which formed by stacking restricted Boltzman machine in a greedy fashion has beed widely used for classification and recognition. With an ability to extracting features of high-level abstraction and deal with higher dimensional data structure, this model has ouperformed outstanding result on image and speech recognition. In this research, we assess the applicability of deep learning in dna classification level. Since the training phase of DBN is costly expensive, specially if deals with DNA sequence with thousand of variables, we introduce a new encoding method, using decimal-binary vector to represent the sequence as input to the model, thereafter compare with one-hot-vector encoding in two datasets. We evaluated our proposed model with different contrastive algorithms which achieved significant improvement for the training speed with comparable classification result. This result has shown a potential of using decimal-binary vector on DBN for DNA sequence to solve other sequence problem in bioinformatics.

• 한국자기공명학회논문지
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• 제5권2호
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• pp.118-129
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• 2001

Binding interactions of cationic porphyrins, T4MPyP and TMAP with DNA oligomer d(CGCGAATTCGCG), were studied with NMR spectroscopy, W and CD spectroscopic method. Two porphyrins showed significant differences in NMR, UV and CD data upon binding to DNA. T4MPyP was considered to position more closely to DNA bases through partial intercalation as well as ionic intercalation between the positive charges of porphyrin and phosphate group of DNA at 5’-GC-3’steps. Contrast to this, TMAP was thought to bind to phosphate of DNA more or less outside of the groove.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2002년도 생물공학의 동향 (X)
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• pp.539-542
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• 2002

We propose new encoding method for numerical data in DNA using temperature gradient. To represent numerical values in DNA sequences, we introduce melting temperature. Since DNA strands representing smaller values have a lower Tm, they tend to denature with ease and also easily amplified by denaturation temperature gradient PCR. We also implement a local search molecular algorithm using temperature gradient, which is contrasted to conventional exhaustive search molecular algorithms. The proposed methods are verified by solving an instance of the travelling salesman problem. We could effectively amplify the correct solutions and the use of temperature gradient made the detection of solutions easier.

• 대한수의학회지
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• 제39권1호
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• pp.90-95
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• 1999

A species-specific 760 base pair(bp) BamHI to EcoRI DNA fragment(fMG-2) of lipoprotein gene was isolated from a Mycoplasma gallisepticum(M gallisepticum) genomic library. Based on the DNA sequence data of fMG-2, a pair of 25bp primers was synthesized. When used in the polymerase chain reaction(PCR), 732bp DNA products were amplified from 6 standard strains and 10 field isolates of M gallisepticum, but not from 2 Mycoplasma synoviae and 7 other Mycoplasma species. The lower detection limit was 100fg of the genomic DNA. Identity of the PCR products was confirmed by comparison of patterns of restriction endonuclease analysis with AseI, DraI, EcoRV and SspI.