• Molecules and Cells
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• 제39권5호
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• pp.367-374
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• 2016

Since the RNA world hypothesis was proposed, a large number of regulatory noncoding RNAs (ncRNAs) have been identified in many species, ranging from microorganisms to mammals. During the characterization of these newly discovered RNAs, RNAs having both coding and noncoding functions were discovered, and these were considered bifunctional RNAs. The recent use of computational and high-throughput experimental approaches has revealed increasing evidence of various sources of bifunctional RNAs, such as protein-coding mRNAs with a noncoding isoform and long ncRNAs bearing a small open reading frame. Therefore, the genomic diversity of Janusfaced RNA molecules that have dual characteristics of coding and noncoding indicates that the functional roles of RNAs have to be revisited in cells on a genome-wide scale. Such studies would allow us to further understand the complex gene-regulatory network in cells. In this review, we discuss three major genomic sources of bifunctional RNAs and present a handful of examples of bifunctional RNA along with their functional roles.

• Journal of Animal Science and Technology
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• 제55권4호
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• pp.231-235
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• 2013

Carcass weight (CW) is one of the most important economic traits in pigs, directly affecting the income of farmers. In this study, a genome wide association study was performed to detect significant single nucleotide polymorphisms (SNPs) affecting CW in pigs derived from a $F_2$ intercross between Landrace and Korean native pig (KNP). Using high-density porcine SNP chips, highly significant SNPs were identified on SSC12. Two candidate genes, LOC100523510 and LOC100621652, were subsequently selected within this region and further investigated. Within these candidate genes, five SNPs were identified and genotyped using the VeraCode GoldenGate assay. The results revealed that one SNP in the LOC100621652 gene and four SNPs in the LOC100523510 gene are highly associated with CW. These SNP markers can thus have significant applications for improving CW in KNP. However, the functions of these candidate genes are not fully understood and require further study.

• 혜화의학회지
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• 제21권2호
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• pp.73-84
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• 2013

단삼(丹蔘) (Salvia miltiorrhiza Bunge)은 꿀풀과 배암차즈기속에 속하며 중국(中國)이 원산지(原産地)인 여러해살이풀로, 동의보감(東醫寶鑑)에는 "성질(性質)은 약간 차고 맛이 쓰며 독(毒)이 없다. 다리가 약하면서 저리고 아픈것과 팔다리를 쓰지 못하는 것을 치료한다. 또는 고름을 빨아내고 아픈 것을 멎게 하며 살찌게 하고 오래된 어혈(瘀血)을 헤치며${\ldots}$" 등으로 기술되어 있으며 이전부터 부인과(婦人科)에 많이 응용하는 약재 중 하나로 그 효능이 어혈(瘀血)을 없애는데 있기 때문이다. 임상(臨床)에서는 부인과(婦人科) 질환(疾患)뿐만 아니라 심혈관(心血管) 질환(疾患)에도 사용되고 있다. 본 연구에서는 이러한 효능의 객관적 근거를 마련하고 약재의 작용 기전 중 일부를 확인하기 위해 고지혈증이 유발된 생쥐에 단삼(丹蔘) 추출물을 투여하여 혈중 콜레스테롤 및 트리글리세라이드 수치를 낮추는 작용을 확인했으며 동시에 간조직 내 지방의 축적도 억제하는 것으로 나타났다. 이러한 변화가 간조직 내 유전자의 변화와 어떠한 관련이 있는지 확인하기 위해 RNA를 분리하여 Microarray 분석을 수행한 결과 고지혈증으로 인해 변화된 유전자들이 단삼(丹蔘) 추출물의 투여로 인해 정상에 가까운 정도로 조절됨을 확인하였으며 향후 본 연구를 통해 확인된 핵심 유전자를 고지혈증 치료의 지표 등으로 활용할 수 있을 것으로 기대된다.

• Journal of Microbiology and Biotechnology
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• 제27권4호
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• pp.709-717
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• 2017

Mucosal tissues are the initial site through which most pathogens invade. As such, vaccines and adjuvants that modulate mucosal immune functions have emerged as important agents for disease prevention. Herein, we investigated the immunomodulatory mechanisms of the B subunit of Escherichia coli heat-labile enterotoxin type IIa ($LT-IIa-B_5$), a potent non-toxic mucosal adjuvant. Alternations in gene expression in response to $LT-IIa-B_5$ were identified using a genome-wide transcriptional microarray that focused on dendritic cells (DC), a type of cell that broadly orchestrates adaptive and innate immune responses. We found that $LT-IIa-B_5$ enhanced the homing capacity of DC into the lymph nodes and selectively regulated transcription of pro-inflammatory cytokines, chemokines, and cytokine receptors. These data are consistent with a model in which directional activation and differentiation of immune cells by $LT-IIa-B_5$ serve as a critical mechanism whereby this potent adjuvant amplifies mucosal immunity to co-administered antigens.

• 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.