• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.202-205
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• 2005

Cell phenotypes are determined by the concerted activity of thousands of genes and their products. This activity is coordinated by a complex network that regulates the expression of genes. Understanding this organization is crucial to elucidate cellular activities, and many researches have tried to construct gene regulatory networks from mRNA expression data which are nowadays the most available and have a lot of information for cellular processes. Several computational tools, such as Boolean network, Qualitative network, Bayesian network, and so on, have been applied to infer these networks. Among them, Bayesian networks that we chose as the inference tool have been often used in this field recently due to their well-established theoretical foundation and statistical robustness. However, the relative insufficiency of experiments with respect to the number of genes leads to many false positive inferences. To alleviate this problem, we had developed the algorithm of MONET(MOdularized NETwork learning), which is a new method for inferring modularized gene networks by utilizing two complementary sources of information: biological annotations and gene expression. Afterward, we have packaged and improved MONET by combining dispersed functional blocks, extending species which can be inputted in this system, reducing the time complexities by improving algorithms, and simplifying input/output formats and parameters so that it can be utilized in actual fields. In this paper, we present the architecture of MONET system that we have improved.

• 한국연초학회지
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• 제20권1호
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• pp.50-56
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• 1998

The complementary DNA (cDNA) of potato virus Y- vein necrosis strain (PVY-VN) replicase gene (Nlb) was transformed into tobacco (Nicotiana tabacum cv. Burley 21) plants. Out of 25 putative transformants regenerated, 3 were resistant to PVY-VN, one highly resistant plant with no symptom until seed harvest time and the other two with mild chlorotic spot symptoms at late stages after infection. No symptom was observed in the highly resistant plant, while mild vein necrotic symptoms were developed on suckers of the moderately resistant plants after seed harvest time, In the first generation (T1) via self fertilization, resistance to susceptibility frequency in transgenic plants from the highly resistant transformant was about 3 : 1, while it was lowered much (about 1:2 and 1:19) in T1 of the moderately resistant transformants. In the second generation (T2) of the highly resistant plant, resistance frequencies were similar to T1, but resistance levels varied greatly and appeared to be decreased. Key words : potato virus Y, viral replicate gene, transgenic tobacco plants, resistance.

• Asian-Australasian Journal of Animal Sciences
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• 제19권6호
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• pp.763-768
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• 2006

Genetic and pharmacological studies in mice have demonstrated a complementary role for the melanocortin 4 receptor (MC4R) in the control of food intake, energy balance and body weight. This study was designed to investigate the associations of a MC4R gene polymorphism on chicken growth and body composition traits in broiler lines divergently selected for abdominal fat. A SNP (G54C) was found in CDS region of chicken MC4R gene. The analysis of the least squares and variance revealed a significant association between the G54C SNP and BW, CW and SL at 7 wk of age, and there were significant differences in different genotypes (p<0.05). The results from protein secondary structure prediction and tertiary structure prediction showed that it appeared a helix in $13^{th}$ amino acid and two strands at $14^{th}$ and $15^{th}$ amino acid in mutant protein, respectively. It maybe induce the change of the activity or function of MC4R gene in poultry.

• 한국국제농업개발학회지
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• 제23권5호
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• pp.503-506
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• 2011

우리나라 재래종벼 6품종의 벼 흰잎마름병 저항성 유전자를 동정하고자 저항성 유전자 Xa1를 갖는 IR-BB 101과의 교배 조합을 양성하고 일본균주 IA(T7174)를 접종한 결과 청군벼의 벼 흰잎마름병 저항성 유전자는 Xa1 이었고, 육성재래, 아국도, 흑피 및 이천7일찰은 Xa1 및 다른 우성유전자 1개를 보유하였으며, 긴까락샤레는 Xa1 및 다른 우성유전자 2개를 갖고 있었고 이 중 2개는 저항성 발현에 보족적으로 작용하는 것으로 추정되었다.

• Genomics & Informatics
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• 제15권3호
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• pp.98-107
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• 2017

MicroRNAs (miRNAs) act as regulators of gene expression by binding to the 3' untranslated region (UTR) of target genes. They perform important biological functions in the various species. Among many miRNAs, miR-21-3p is known to serve vital functions in development and apoptosis in olive flounder. Using genomic and bioinformatic tools, evolutionary conservation of miR-21-3p was examined in various species, and expression pattern was analyzed in olive flounder. Conserved sequences (5'-CAGUCG-3') in numerous species were detected through the stem-loop structure of miR-21-3p. Thus, we analyzed target genes of miR-21-3p. Among them, 3' UTR region of PPIL2 gene indicated the highest binding affinity with miR-21-3p based on the minimum free energy value. The PPIL2 gene showed high expression levels in testis tissue of the olive flounder, whereas miR-21-3p showed rather ubiquitous expression patterns except in testis tissue, indicating that miR-21-3p seems to control the PPIL2 gene expression in a complementary repression manner in various tissues of olive flounder. Taken together, this current study contributes to infer the target gene candidates for the miR-21-3p using bioinformatics tools. Furthermore, our data offers important information on the relationship between miR-21-3p and target gene for further functional study.

• 한국작물학회지
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• 제29권3호
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• pp.203-208
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• 1984

수도의 도열병 저항성 육종을 위하여 국제도열병 검정시험에서 여러 균계에 대해 고도의 안정된 저항성을 나타낸 Tadukan, Tetep 두 장간 저항성 품종을 6개 단간 리병성 계통들과 교배하여 도열병 저항성과 장간형질간의 연관관계를 분석하였는데 그 결과를 요약하면 다음과 같다. 1. Tadukan과 Tetep은 모든 단간계통들과의 조합에서 간장은 장간대 단간이 3 : 1로 분리되었으므로 이들은 각각 단순우성 장간 유전자를 지닌 것으로 나타났다. 2. Tadukan 품종은 T-2$^{+2}$ , C-8$^{+t}$ 균계에 대하여 도열병 저항성과 간장과는 연관이 없는 것으로 나타났다. 3. Tetep 품종도 역시 T-2$^{+1}$, C-8$^{+t}$ 균계에 대하여 도열병 저항성은 간장과는 연관이 없는 것으로 나타났다. 4. C-8$^{+t}$ 균계에 대한 Tadukan과 Tetep 품종의 저항성은 단순우성 유전자에 지배되고 있다. 5. T-2$^{+t}$ 균계에 대한 Tadukan과 Tetep 품종의 저항성은 각각 2개의 우성유전자에 의해 지배되고 이들은 서로 보족적인 관계에 있다.

• Bulletin of the Korean Chemical Society
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• 제31권7호
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• pp.2077-2080
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• 2010

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.357-360
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• 2005

In this paper we consider the well-known semiparametric proportional hazards (PH) models for survival analysis. These models are usually used with few covariates and many observations (subjects). But, for a typical setting of gene expression data from DNA microarray, we need to consider the case where the number of covariates p exceeds the number of samples n. For a given vector of response values which are times to event (death or censored times) and p gene expressions (covariates), we address the issue of how to reduce the dimension by selecting the significant genes. This approach enable us to estimate the survival curve when n < < p. In our approach, rather than fixing the number of selected genes, we will assign a prior distribution to this number. The approach creates additional flexibility by allowing the imposition of constraints, such as bounding the dimension via a prior, which in effect works as a penalty. To implement our methodology, we use a Markov Chain Monte Carlo (MCMC) method. We demonstrate the use of the methodology to diffuse large B-cell lymphoma (DLBCL) complementary DNA(cDNA) data.

• BMB Reports
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• 제38권2호
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• pp.161-166
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• 2005

Functional protein of MB78 bacteriophage having apparent molecular weight of 22 kDa is expressed from 1.7 kb HindIII G fragment. The nucleotide sequence of this fragment showed two open reading frames of 222 and 196 codons in tail-to-tail orientation separated by a 62-nucleotide intercistronic region. The ORF of 22 kDa protein is present in opposite orientation, i.e. in the complementary strand, preceded by a strong ribosomal binding site and a promoter sequence. Another ORF started from the beginning of the fragment whose promoter region and translational start site lies in the 0.45 kb HincII U fragment which is located next to the HindIII G fragment, that has the sequence for DNA bending. 3' end of the fragment has high sequence homology to the EaA and EaI proteins of bacteriophage P22, a close relative of MB78 phage.

• BMB Reports
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• 제37권1호
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• pp.28-34
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• 2004

The discovery of biochemical and cellular functions of unannotated gene products begins with a database search of proteins with structure/sequence homologues based on known genes. Very recently, a number of frontier groups in structural biology proposed a new paradigm to predict biological functions of an unknown protein on the basis of its three-dimensional structure on a genomic scale. Structural proteomics (genomics), a research area for structure-based functional discovery, aims to complete the protein-folding universe of all gene products in a cell. It would lead us to a complete understanding of a living organism from protein structure. Two major complementary experimental techniques, X-ray crystallography and NMR spectroscopy, combined with recently developed high throughput methods have played a central role in structural proteomics research; however, an integration of these methodologies together with comparative modeling and electron microscopy would speed up the goal for completing a full dictionary of protein folding space in the near future.