• Biotechnology and Bioprocess Engineering:BBE
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• 제10권5호
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• pp.385-399
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• 2005

The phenotypic response of a cell results from a well orchestrated web of complex interactions which propagate from the genetic architecture through the metabolic flux network. To rationally design cell factories which carry out specific functional objectives by controlling this hierarchical system is a challenge. Transcriptome analysis, the most mature high-throughput measurement technology, has been readily applied In strain improvement programs in an attempt to Identify genes involved in expressing a given phenotype. Unfortunately, while differentially expressed genes may provide targets for metabolic engineering, phenotypic responses are often not directly linked to transcriptional patterns, This limits the application of genome-wide transcriptional analysis for the design of cell factories. However, improved tools for integrating transcriptional data with other high-throughput measurements and known biological interactions are emerging. These tools hold significant promise for providing the framework to comprehensively dissect the regulatory mechanisms that identify the cellular control mechanisms and lead to more effective strategies to rewire the cellular control elements for metabolic engineering.

• BMB Reports
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• 제28권4호
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• pp.359-362
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• 1995

The highly polymorphic variable number of tandem repeat (VNTR) loci in the human genome are informative markers for the genetic characterization of individuals in the paternity test and forensic science as well as for the study of human disease. In this study, VNTR loci D1S80 and D2S123 have been amplified by PCR and the amplified length polymorphic alleles were detected with a discontinuous vertical PAGE system and silver staining. For explicit DNA typing, PCR optimization, in which amplification efficiencies are similar over a wide range of allele sizes, non-specific amplifications are minimal, and new longer alleles have high amplification efficiency, has been performed by changing the PCR reaction buffer composition and thermal cycling conditions. It turned out that adding an appropriate amount of Tween 20 and NP40 to the PCR reaction buffer and raising the annealing temperature to $68^{\circ}C$ in thermal cycling made it possible for optimal VNTR loci amplification. A modified PAGE system for VNTR separation was established. Under these conditions, new longer alleles in the 01580 locus were discovered and 025123 pattern changes in colorectal tumors were observed. These technical tips are valuable for detecting various amplified fragment length polymorphisms.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2000년도 국제심포지움
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• pp.5-6
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• 2000

Nitric oxide (NO) is a simple combined molecule of oxygen and nitrogen, and has a wide variety of action on the physiological and pathophysiological function of the body. It is a key transducer of the vasodilator message from the endothelium to vascular cells. However, its different roles have been elucidated by numerous researches, which was undertaken in the 80's and 90's. Three types of NO synthase were involved in synthesizing NO and they are identified in different tissues and cells including macrophage, endothelial cells and even tumor cells. In the late 90's, we undertook a number of researches for elucidating the effect of NO on embryo development, since developmentally arrested bovine embryos contained large amount of NO metabolites in their cytoplasm. Subsequently, we found that the addition of a spontaneous NO donor to culture medium markedly inhibited embryo development and that its inhibitory role was independent of embryonic genome activation. Research was focused to find a way to prevent the inhibitory action of NO on embryo development and demonstrated that the addition of hemoglobin, a NO scavenger, to embryo culture medium greatly stimulated in vitro-development of bovine and mouse embryos. Based on these research outcomes, we developed a NO action-free culture system for embryos and other tissues. The efficacy of such system has subsequently been confirmed by achieving the high rates of preimplantation development and blastocyst formation in the NO action-free culture of mouse and bovine embryo. In this article, we briefly introduced the nature of NO and our research outcomes on the role of NO in embryo development.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2002년도 제1차워크샵
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• pp.5-23
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• 2002

Motivation: Protein-protein interaction plays a critical role in the biological processes. The identification of interacting proteins by bioinformatical methods can provide new lead In the functional studies of uncharacterized proteins without performing extensive experiments. Results: Protein-protein interactions are predicted by a computational algorithm based on the weighted scoring system for domain interactions between interacting protein pairs. Here we propose potential interaction domain (PID) pairs can be extracted from a data set of experimentally identified interacting protein pairs. where one protein contains a domain and its interacting protein contains the other. Every combinations of PID are summarized in a matrix table termed the PID matrix, and this matrix has proposed to be used for prediction of interactions. The database of interacting proteins (DIP) has used as a source of interacting protein pairs and InterPro, an integrated database of protein families, domains and functional sites, has used for defining domains in interacting pairs. A statistical scoring system. named "PID matrix score" has designed and applied as a measure of interaction probability between domains. Cross-validation has been performed with subsets of DIP data to evaluate the prediction accuracy of PID matrix. The prediction system gives about 50% of sensitivity and 98% of specificity, Based on the PID matrix, we develop a system providing several interaction information-finding services in the Internet. The system, named PreDIN (Prediction-oriented Database of Interaction Network) provides interacting domain finding services and interacting protein finding services. It is demonstrated that mapping of the genome-wide interaction network can be achieved by using the PreDIN system. This system can be also used as a new tool for functional prediction of unknown proteins.

• Molecular & Cellular Toxicology
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• 제4권3호
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• pp.205-210
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• 2008

Recent studies suggest that activated microglial cells play an essential role in the inflammatory responses and neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease. This study was conducted to evaluate the protective mechanisms of Asiasarum sieboldi (AS) on LPS-induced activation of BV-2 microglial cells. The effects of AS on gene expression profiles in activated BV-2 microglial cells were evaluated using microarray analysis. BV-2 microglial cells were cultured in a 100 mm dish ($1{\times}10^7$/mL) for 24 h and then pretreated with 1 ${\mu}g$/mL AS or left untreated for 30 min. Next, 1 ${\mu}g$/mL LPS was added to the samples and the cells were reincubated at $37^{\circ}C$ for 30 min and 1 hr. The gene expression profiles of the BV-2 microglial cells varied depending on the AS. The microarray analysis revealed that MAPK signaling pathway-related genes were downregulated in AS-treated BV-2 microglial cells. AS can affect the neuroinflammatory-related pathway such as MAPK signaling pathway in activated BV-2 microglial cells.

• Communications for Statistical Applications and Methods
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• 제17권5호
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• pp.667-678
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• 2010

인간의 유전자 상호작용을 분석하기 위해 제시된 다중인자 차원축소방법은 연속형자료에는 적용할 수 없다. 그래서 이를 보완한 CART 알고리즘을 활용한 확장된 다중인자 차원축소방법이 제안되었다. 하지만 CART 알고리즘을 활용한 확장된 다중인자 차원축소방법의 검정력이 밝혀지지 않았다. 따라서 본 연구에서는 모의실험을 통하여 CART 알고리즘을 활용한 확장된 다중인자 차원축소방법의 우수한 검정력을 평가하고, 확인된 검정력을 바탕으로 실제 한우 데이터에 적용하여 한우의 경제형질에 영향을 주는 우수 유전자조합을 규명하였다.

• Asian-Australasian Journal of Animal Sciences
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• 제28권9호
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• pp.1235-1243
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• 2015

The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.

• Journal of Microbiology and Biotechnology
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• 제28권5호
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• pp.816-820
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• 2018

The stringent response (SR), which is activated by accumulation of (p)ppGpp under conditions of growth-inhibiting stresses, plays an important role on growth and virulence in Vibrio cholerae. Herein, we carried out a genome-wide screen using transposon random mutagenesis to identify genes controlled by SR in a (p)ppGpp-overproducing mutant strain. One of the identified SR target genes was flaC encoding flagellin. Genetic studies using flaC and SR mutants demonstrated that FlaC was involved in bacterial growth, toxin production, and normal flagellum function under conditions of high (p)ppGpp levels, suggesting FlaC plays an important role in SR-induced pathogenicity in V. cholerae.

• Reproductive and Developmental Biology
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• 제37권1호
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• pp.17-22
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• 2013

Although assisted reproductive technology is very useful to develop novel and therapeutic biomaterials for reproduction, research on molecular mechanism of folliculogenesis in pig is not clear. Therefore, the alteration of gene expression during follicular development in pigs was examined in this study. The expression of folliculogenesis-related genes was quantified in preantral ($250{\sim}300{\mu}m$) and antral (> $300{\mu}m$ in diameter) follicles, and overall gene expression was evaluated by a genome-wide microarray. The microarray results showed that 219 genes were differentially expressed, and of those, 10 and 22 known genes showed higher and less expression at the preantral stage than at antral stages, respectively. Among them, the expression of NR0B1, PPARG, GATA4, and ANXA2 genes related to folliculogenesis was validated by quantitative real-time PCR analysis. The expression of PPARG and GATA4 genes were increased at antral stages, but a significantly stage-specific increase (p<0.05) was only detected in annexin A2 (ANXA2) in antral-stage follicles. The expression of NR0B1 genes was increased at preantral stage and these patterns of gene expression were comparable to the results obtained by microarray analysis. We propose that the systematical regulation of genes supporting specific follicle stage should be employed for improved in-vitro folliculognesis.

• Asian-Australasian Journal of Animal Sciences
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• 제16권6호
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• pp.910-927
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• 2003

Transgenesis is a very powerful tool not only to help understanding the basics of life science but also to improve the efficiency of animal production. Since the first transgenic mouse was born in 1980, rapid development and wide application of this technique have been made in laboratory animals as well as in domestic animals. Although pronuclear injection is the most widely used method and nuclear transfer using somatic cells broadens the choice of making transgenic domestic animals, the demand for precise manipulation of the genome leads to the utilization of gene targeting. To make this technique possible, a pluripotent embryonic cell line such as embryonic stem (ES) cell is required to carry genetic mutation to further generations. However, ES cell, well established in mice, is not available in domestic animals even though many attempt to establish the cell line. An alternate source of pluripotent cells is embryonic germ (EG) cells derived from primordial germ cells (PGCs). To make gene targeting feasible in this cell line, a better culture system would help to minimize the unnecessary loss of cells in vitro. In this review, general methods to produce transgenic domestic animals will be mentioned. Also, it will focus on germ cell engineering and methods to improve the establishment of pluripotent embryonic cell lines in domestic animals.