• Reproductive and Developmental Biology
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• 제31권1호
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• pp.21-28
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• 2007

During early embryo development, Oct-4 is an important transcription factor for the early differentiation the present study was first examined methylation status in distal enhancer and promoter region of Oct-4 during mouse pre-implantation embryo development. In oocyte and sperm, high methylation was observed in both distal and proximal of promoter in Oct-4. Following fertilization relatively high methylation level remained until 8-cell stage embryos, but decreased at the morula and blastocyst stage. Specific gene knock down of Oct-4 by siRNA injection into zygote induced higher methylation rates of both distal and proximal region of promoter of Oct-4. These results suggest a functional link between the DNA methylation status of distal and promoter resign in the Oct-4 gene and the gene sequence-specific transcriptional silencing by exogenous siRNA injection during mouse preimplantation embryos.

• Journal of Genetic Medicine
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• 제2권1호
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• pp.31-34
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• 1998

The N-methylpurine-DNA glycosylase (MPG), a ubiquitous DNA repair enzyme, removes N-methylpurine and other damaged purines induced in DNA. Tissue-specific mRNA levels of the N-methylpurine-DNA glycosylase (MPG) were investigated in Balb/c mice of four different growing stages; newborn, 1, 4 and 8-weeks postpartum. MPG expressions in the newborn and the 8-week-old mice were the highest in thymus and testis, respectively. The tested tissues of the newborn mice had consistently higher MPG mRNA level than 8-week-old adults except in testis and thymus. The MPG mRNA level in testis was the lowest in the newborn mice, but it attained the highest in the 8-week-old mice. The levels of MPG mRNA among the different tissues in the newborn and the 8-week-old mice were more than 9.0 and 19.0-fold respectively. These results suggest that the of MPG expression was dependent on the growing stage and had tissue-specificity.

• BMB Reports
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• 제45권10호
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• pp.545-553
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• 2012

Determination of the type and origin of the body fluids found at a crime scene can give important insights into crime scene reconstruction by supporting a link between sample donors and actual criminal acts. For more than a century, numerous types of body fluid identification methods have been developed, such as chemical tests, immunological tests, protein catalytic activity tests, spectroscopic methods and microscopy. However, these conventional body fluid identification methods are mostly presumptive, and are carried out for only one body fluid at a time. Therefore, the use of a molecular genetics-based approach using RNA profiling or DNA methylation detection has been recently proposed to supplant conventional body fluid identification methods. Several RNA markers and tDMRs (tissue-specific differentially methylated regions) which are specific to forensically relevant body fluids have been identified, and their specificities and sensitivities have been tested using various samples. In this review, we provide an overview of the present knowledge and the most recent developments in forensic body fluid identification and discuss its possible practical application to forensic casework.

• 식물병연구
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• 제10권1호
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• pp.30-33
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• 2004

현재까지 벼 줄무의잎마름병(Rice stripe virus, RSV)은 남부지방에 국한되어 발생되어 왔다. 그러나 최근에는 RSV의 발생이 충청도, 경기도를 포함한 중부지방까지 확산되는 경향을 나타내고 있다. 이병의 병징은 육안으로는 생리적인 장해 현상과 구분하기가 힘들다 본 실험에서는 이병주 및 애멸구(Laodelphax striatellus)로 부터 viral RNA를 추출한 후 RNA복제효소 및 외피단백질유전자에 특이적인 primer를 제작하여 RT-PCR법에 의해 RSV를 검정하였다. 그결과 이병식물체 및 보독 애멸구로부터 RNA복제효소 유전자에 특이적인 band(1,023 bp) 및 외피단백질유전자에 특이적인 band(969 bp)가 관찰되었다.

• Animal cells and systems
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• 제5권3호
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• pp.263-266
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• 2001

Metallothionein (MT) is induced in the regenerating rat liver. We have investigated expression of MT gene by RT PCR as well as specific localization of MT by immunocytochemistry in regenerating rat liver after partial hepatectomy (PH). MT mRNA level started to increase from 1 h and reached the peak at 8 h after PH. The level decreased gradually by 24 h, and became similar to that of control group. In the immunocytochemical study, in all groups treated with primary antibody, immunogold particles indicating the presence of MT were evenly distributed throughout both cytoplasm and nucleus of the rat hepatocytes. Within the nucleus, the gold particles appeared to be intensely localized in the areas of euchromatin and nucleolus. Within the cytoplasm, gold particles did not seem to adhere to mitochondria or Iysosomes, but were freely distributed. However, rough endoplasmic reticulum was the obvious compartment on which the gold particles were localized. Time course of MT immunoreactivity revealed that distribution of gold particles in hepatocytes increased gradually by 24 h, and decreased at 48 h after PH. Briefly, PH resulted in the sharpest increase in the expression of MT mRNA at 8 h and in the immunoreactivity of MT at 24 h, respectively. It is suggested that the increase of MT mRNA expression, the intensity of immunoreactivity and the specific localization of MT may be associated with the compensatory cell proliferation followed by PH.

• BMB Reports
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• 제37권4호
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• pp.487-492
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• 2004

The extent of codon usage in the protein coding genes of the mycobacteriophage, Bxz1, and its plating bacteria, M. smegmatis, were determined, and it was observed that the codons ending with either G and / or C were predominant in both the organisms. Multivariate statistical analysis showed that in both organisms, the genes were separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons. The second major explanatory axis differentiates the genes according to their genome type. A comparison of the relative synonymous codon usage between 20 highly- and 20 lowly expressed genes from Bxz1 identified 21 codons, which are statistically over represented in the former group of genes. Further analysis found that the Bxz1- specific tRNA species could recognize 13 out of the 21 over represented synonymous codons, which incorporated 13 amino acid residues preferentially into the highly expressed proteins of Bxz1. In contrast, seven amino acid residues were preferentially incorporated into the lowly expressed proteins by 10 other tRNA species of Bxz1. This analysis predicts for the first time that the Bxz1-specific tRNA species modulates the optimal expression of its proteins during development.

• BMB Reports
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• 제55권3호
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• pp.113-124
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• 2022

Single-cell RNA sequencing (scRNA-seq) has greatly advanced our understanding of cellular heterogeneity by profiling individual cell transcriptomes. However, cell dissociation from the tissue structure causes a loss of spatial information, which hinders the identification of intercellular communication networks and global transcriptional patterns present in the tissue architecture. To overcome this limitation, novel transcriptomic platforms that preserve spatial information have been actively developed. Significant achievements in imaging technologies have enabled in situ targeted transcriptomic profiling in single cells at single-molecule resolution. In addition, technologies based on mRNA capture followed by sequencing have made possible profiling of the genome-wide transcriptome at the 55-100 ㎛ resolution. Unfortunately, neither imaging-based technology nor capture-based method elucidates a complete picture of the spatial transcriptome in a tissue. Therefore, addressing specific biological questions requires balancing experimental throughput and spatial resolution, mandating the efforts to develop computational algorithms that are pivotal to circumvent technology-specific limitations. In this review, we focus on the current state-of-the-art spatially resolved transcriptomic technologies, describe their applications in a variety of biological domains, and explore recent discoveries demonstrating their enormous potential in biomedical research. We further highlight novel integrative computational methodologies with other data modalities that provide a framework to derive biological insight into heterogeneous and complex tissue organization.

• 대한임상검사과학회지
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• 제43권3호
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• pp.89-97
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• 2011

The Human Papilloma Virus (HPV) infection has been strongly associated with pathogenesis of uterine cervix carcinoma. HPV type 16, a causative agent of uterine cervix carcinoma, encodes the E6 and E7 oncogenes, expression of which is pivotal for malignant transformation and maintenance of malignant phenotypes. To develop a gene therapy for HPV-related carcinoma, We investigated the effect of E6 short-interfering RNA (E6 siRNA) on the expression of this oncogene and on the growth of HPV 16-related uterine cervix carcinoma cells. SiHa cells, a uterine cervix carcinoma cell line, which contain a single copy of HPV 16 integrated in the chromosome and express the E6 and E7 oncogenes. Before 24 hr of transfection, cells were seeded and transfected with control plasmid or E6 siRNA-expressing plasmid. The mRNA was analysed by reverse transcriptase polymerase chain reaction (RT-PCR). The cell growth rate was investigated by MTT method. The E6 mRNA level in SiHa cells was decreased in HPV 16 E6 siRNA-expression vector transfected cells and a decrease in the growth of these cells was also observed. From these results. it is evident that E6 siRNA played a role in suppression of growth of SiHa cells and has a fair chance as a candidate for gene specific therapy for HPV related uterine cervix carcinoma.

• Genomics & Informatics
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• 제9권1호
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• pp.39-43
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• 2011

MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.

• Archives of Pharmacal Research
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• 제19권6호
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• pp.486-489
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• 1996

A simple, rapid, specific and sensitive method for the detection of serum hepatitis C virus (HCV) RNA using the reverse transcription-polymerase chain reaction (RT-PCR) technique without conventional RNA extraction was developed. HCV template RNA from serum was obtained by boiling the serum at $95^{\circ}C$ for 2 min, cooling rapidly in ice and removing the proteins by cetrifugation. RT-PCR amplifications including the reverse transcription and first PCR amplification were performed in one vessel containing both of reverse transcriptase and Taq DNA polymerase. The detection of HCV RNA from $10^{-3}{\mu}l$. serum was possible with this method. The suitability of this method for clinical analysis was evaluated by assaying HCV RNA in 225 patient samples including anti-HCV antibody negatives (13 samples) and positives (212 samples) by enzyme-linked immunosorbent assay test (ELISA). Detections of HCV RNA with this method were in 4 of 13 anti-HCV antibody negative samples (30.8%) and 95 of 212 positive samples (44.8%). The present method can be completed in 1 hr and has a wide range of application for the clinical utilities to determine the viral RNAS.