• Journal of Genetic Medicine
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• 제3권1호
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• pp.15-19
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• 1999

We have investigated the genetic variation in the human apo B mRNA editing protein (apobec-1) gene. Exon 3 of the apobec-1 gene was amplified by polymerase chain reaction. After detection of an additional band by single strand conformational polymorphism (SSCP) analysis, sequencing of the SSCP-shift sample revealed a single-base mutation. The mutation was a CGG transversion at codon 80 resulting in a lleRMet substitution. This substitution was confirmed by restriction fragment length polymorphism analysis since a Pvull site is abolished by the substitution. Population and family studies confirmed that the inheritance of the genotypes for apobec-1 gene polymorphism is controlled by two codominant alleles (P1 and P2). A significant difference in plasma triglyceride was detected among the different apobec-1 genotypes in the CAD patients (P<0.05). Our study could provide the basis for elucidating the interaction between genetic variation of the apobec-1 gene and disorders related to lipid metabolism.

• BMB Reports
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• 제46권2호
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• pp.65-72
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• 2013

In situ detection of RNAs is becoming increasingly important for analysis of gene expression within and between intact cells in tissues. International genomics efforts are now cataloging patterns of RNA transcription that play roles in cell function, differentiation, and disease formation, and they are demon-strating the importance of coding and noncoding RNA transcripts in these processes. However, these techniques typically provide ensemble averages of transcription across many cells. In situ hybridization-based analysis methods complement these studies by providing information about how expression levels change between cells within normal and diseased tissues, and they provide information about the localization of transcripts within cells, which is important in understanding mechanisms of gene regulation. Multi-color, single-molecule fluorescence in situ hybridization (smFISH) is particularly useful since it enables analysis of several different transcripts simultaneously. Combining smFISH with immunofluorescent protein detection provides additional information about the association between transcription level, cellular localization, and protein expression in individual cells.

• Toxicological Research
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• 제22권4호
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• pp.323-328
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• 2006

Global gene expression profile was analyzed by microarray analysis of rat liver RNA after acute acetaminophen (APAP) administration. A single dose of 1g/kg body weight of APAP was given orally, and the liver samples were obtained after 24, 48 h, and 2 weeks. Histopathologic and biochemical studies enabled the classification of the APAP effect into injury (24 and 48 h) and regeneration (2 weeks) stages. The expression levels of 4900 clones on a custom rat gene microarray were analyzed and 484 clones were differentially expressed with more than a 1.625-fold difference(which equals 0.7 in log2 scale) at one or more time points. Two hundred ninety seven clones were classified as injury-specific clones, while 149 clones as regeneration-specific ones. Characteristic gene expression profiles could be associated with APAP-induced gene expression changes in lipid metabolism, stress response, and protein metabolism. We established a global gene expression profile utilizing microarray analysis in rat liver upon acute APAP administration with a full chronological profile that not only covers injury stage but also later point of regeneration stage.

• 응용통계연구
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• 제24권2호
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• pp.315-321
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• 2011

Gene expression microarray data often include multiple missing values. Most gene expression analysis (including gene clustering analysis); however, require a complete data matric as an input. In ordinary clustering methods, just a single missing value makes one abandon the whole data of a gene even if the rest of data for that gene was intact. The quality of analysis may decrease seriously as the missing rate is increased. In the opposite aspect, the imputation of missing value may result in an artifact that reduces the reliability of the analysis. To clarify this contradiction in microarray clustering analysis, this paper compared the accuracy of clustering with and without imputation over several microarray data having different missing rates. This paper also tested the clustering efficiency of several imputation methods including our propose algorithm. The results showed it is worthwhile to check the clustering result in this alternative way without any imputed data for the imperfect microarray data.

• Clinical and Experimental Reproductive Medicine
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• 제24권1호
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• pp.51-56
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• 1997

Recently, through the development of the primer extension preamplification(PEP) method which amplifies the whole genome, simultaneous multiple DNA analysis has become possible. Whole genome from each single cell can be amplified using 15 base oligonucleotide random primer. The greatest advantage of PEP-PCR is the ability to investigate several loci simultaneously and confirm results by analysing multiple aliquots for each locus. This technique led to the development of preimplantation genetic disease diagnosis using blastomere from early embryo, sperm, polar body and oocyte. In this study, we applied PEP-PCR in 20 cases of single amniocyte and 20 cases of single chorionic villus cell for the clinical application of the prenatal and preimplantational genetic diagnosis. We analysed 7 gene loci simultaneously which are 46, 47 exons related to dystrophin gene, two VNTR (variable number tandem repeat) markers using 5'dysIII, 3'CA related to dystrophin gene and DYZ1, DYZ3, DYS14 regions on chromosome Y. In all the tests, 97.5% of PEP-PCR amplifications with single cells were successful. We obtained 38/40 (95%) accuracy in gender determination through chromosome analysis comparison. Therefore, these results have significant implications for a sperm or oocyte analysis and prenatal or preimplantational genetic diagnosis.

• Genomics & Informatics
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• 제8권4호
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• pp.201-205
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• 2010

The H1 histone family, member N, testis-specific (H1FNT) is exclusively expressed in the testis, and had its possible role for sperm chromatin formation. The purpose of this study is to investigate any genetic association of H1FNT gene with male infertility, especially at the promoter region. We examined the promoter single nucleotide polymorphisms (SNP) of H1FNT gene which is located within transcription factor binding site for its association with male infertility. The statistical analysis showed that the -1129A>T polymorphism was present at a statistically significance in male infertility (p=0.0059 and 0.0349 for hetero and risk type, respectively). The dual-luciferase promoter assay was performed to examine the polymorphic effect of this promoter SNP by the cloning of promoter region (1700bp fragment) into pGL3-basic vector. In our plasmid based reporter system, there is no big difference between wild and risk type. In conclusion, H1FNT -1129A>T promoter SNP is statistically significant with male infertility, especially with subfertile (non-azoospermia) group. Further analysis of its functional polymorphic effect in vivo may provide the biological significance of testis-specific histone with spermatogenesis.

• BMB Reports
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• 제38권3호
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• pp.354-359
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• 2005

Open reading frame 29 (ha29) is a gene specific for Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HearSNPV). Sequence analyses showed that the transcription factor Tfb2 motif, bromodomain and Half-A-TPR (HAT) repeat were present at aa 66-82, 4-76, 55-90 of the Ha29 protein respectively. The product of Ha29 was detected in HearSNPV-infected HzAM1 cells at 3 h post-infection. Western blot analysis using a polyclonal antibody produced by immunizing a rabbit with purified GST-Ha29 fusion protein indicates that Ha29 is an early gene. The size of Ha29 product in infected HzAM1 cells was about 25 kDa, which was larger than the presumed size of 20.4 kDa. Tunicamycin treatment of HearSNPV-infected HzAM1 cells suggested that the Ha29 protein is N-glycosylated. Fluorescent confocal laser scanning microscope examination, and Western blot analysis of purified budded virus (BVs), occlusion-derived virus (ODVs), cell nuclear and cytoplasmic fraction, showed that the Ha29 protein was localized in the nucleus. Our results suggested that ha29 of HearSNPV encodes a non-structurally functional protein that may be associated with virus gene transcription in Helicoverpa hosts.

• Journal of Crop Science and Biotechnology
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• 제11권2호
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• pp.101-106
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• 2008

To identify inheritance of clubroot disease resistance genes in Chinese cabbage, seedling tests of $BC_1P_1,\;BC_1P_2$, and $F_2$ populations derived from $F_1$ hybrid(var. CR Saerona) using single spore isolate(race 4 identified with William's differential host) from Plasmodiophora brassciae were conducted. Resistance(R) and susceptible(S) plants segregated to 1:0 in backcross to the resistant parent. The $F_2$ population segregated in a 3(R):1(S) ratio. This result implied that the resistance of clubroot disease is controlled by a single dominant gene to the race 4 of P. brassicae in CR Saerona. To develop DNA markers linked to clubroot resistance genes, 185 plants of CR Saerona among $F_2$ populations were used. A total of 300 arbitrary decamer was applied to $F_2$ population using BSARAPD(Bulked segregant analysis-Randomly amplified polymorphic DNA). One RAPD marker linked to clubroot resistance gene in CR Saerona($OPJ_{1100}$) was identified. This marker was 3.1 cM in distance from resistance gene in $F_2$ population. This marker may be useful for a marker-assisted selection(MAS) and gene pyramiding of the clubroot disease resistant gene in Chinese cabbage breeding programs.

• Molecular & Cellular Toxicology
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• 제2권1호
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• pp.7-10
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• 2006

We performed comprehensive SNP validation and linkage disequilibrium (LD) analysis of the c-fos induced growth factor (Figf) gene in Korean population. Out of 32 SNPs, only 9 SNPs were polymorphic in Korean population. Validated SNPs formed a single extended haplotype block with strong LD through the entire length of the gene. Tagging SNP analysis picked only 2 SNPs to represent most of the genetic variation information of the Figf gene. Our results demonstrate the utility of LD block and tagging SNP analysis for an efficient way of performing a candidate gene based association study.

• Journal of Plant Biotechnology
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• 제8권1호
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• pp.9-14
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• 2006

As an alternative method to produce low cost reagents for immunodiagnosis and protect the plants from viral disease, a gene encoding a single chain variable fragment(scFv) recombinant antibody targeted to the coat protein of cucumber mosaic virus (CMV) was expressed in Nacotiana tabacum. The source of the scFv recombinant antibody gene was from spleen tissue of an immunized mouse. The gene was initially cloned into the pCANTAB5E phagemid and expressed in E. coli. In the following study, the antibody gene was subcloned into the plant expression vector, pCAMBIA-1301 and introduced into tobacco leaf tissue via Agrobacterium tumefacients mediated transformation. After transformation, 56 out of 58 plants were shown to carry the desired anti-CMV scFv gene by PCR analysis. Overall, only 12.5% of the 56 putative transgenic plants were found to express the antibody to a detectable level.