• Mycobiology
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• 제46권4호
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• pp.429-439
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• 2018

To develop a convenient promoter analysis system for fungi, a null-pigment mutant (NPG) of Aspergillus nidulans was used with the 4'-phosphopantetheinyl transferase (PPTase) gene, npgA, which restores the normal pigmentation in A. nidulans, as a new reporter gene. The functional organization of serially deleted promoter regions of the A. nidulans trpC gene and the Cryphonectria parasitica crp gene in filamentous fungi was representatively investigated to establish a novel fungal promoter assay system that depends on color complementation of the NPG mutant with the PPTase npgA gene. Several promoter regions of the trpC and crp genes were fused to the npgA gene containing the 1,034-bp open reading frame and the 966-bp 3' downstream region from the TAA, and the constructed fusions were introduced into the NPG mutant in A. nidulans to evaluate color recovery due to the transcriptional activity of the sequence elements. Serial deletion of the trpC and crp promoter regions in this PPTase reporter assay system reaffirmed results in previous reports by using the fungal transformation step without a laborious verification process. This approach suggests a more rapid and convenient system than conventional analyses for fungal gene expression studies.

• Genomics & Informatics
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• 제21권2호
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• pp.24.1-24.7
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• 2023

Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation PCR, can be applied in various fields by overcoming the shortcomings of typical PCR and qRT-PCR assays. We selected Stilla Naica System (Stilla Technologies), Droplet Digital PCR Technology (Bio-Rad), and Lab on an Array Digital Real-Time PCR analyzer system (OPTOLANE) for comparative analysis among the various droplet digital PCR platforms currently in use commercially. Our previous study discovered a molecular marker that can distinguish Hanwoo species (Korean native cattle) using Hanwoo-specific genomic structural variation. Here, we report the pros and cons of the operation of each dPCR platform from various perspectives using this species identification marker. In conclusion, we hope that this study will help researchers to select suitable dPCR platforms according to their purpose and resources.

• 한국응용곤충학회:학술대회논문집
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• 한국응용곤충학회 2004년도 춘계 학술발표회
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• pp.143-143
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• 2004

• Genomics & Informatics
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• 제3권2호
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• pp.47-51
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• 2005

Molecular mechanisms of biological processes are typically represented as 'pathways' that have a graph­analogical network structure. However, due to the diversity of topics that pathways cover, their constituent biological entities are highly diverse and the semantics is embedded implicitly. The kinds of interactions that connect biological entities are likewise diverse. Consequently, how to model or process pathway data is not a trivial issue. In this review article, we give an overview of the challenges in pathway database development by taking the INOH project as an example.

• Genomics & Informatics
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• 제12권4호
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• pp.187-194
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• 2014

Metabolic syndrome (METS) is a disorder of energy utilization and storage and increases the risk of developing cardiovascular disease and diabetes. To identify the genetic risk factors of METS, we carried out a genome-wide association study (GWAS) for 2,657 cases and 5,917 controls in Korean populations. As a result, we could identify 2 single nucleotide polymorphisms (SNPs) with genome-wide significance level p-values (< $5{\times}10^{-8}$), 8 SNPs with genome-wide suggestive p-values ($5{\times}10^{-8}{\leq}$ p < $1{\times}10^{-5}$), and 2 SNPs of more functional variants with borderline p-values ($5{\times}10^{-5}{\leq}$ p < $1{\times}10^{-4}$). On the other hand, the multiple correction criteria of conventional GWASs exclude false-positive loci, but simultaneously, they discard many true-positive loci. To reconsider the discarded true-positive loci, we attempted to include the functional variants (nonsynonymous SNPs [nsSNPs] and expression quantitative trait loci [eQTL]) among the top 5,000 SNPs based on the proportion of phenotypic variance explained by genotypic variance. In total, 159 eQTLs and 18 nsSNPs were presented in the top 5,000 SNPs. Although they should be replicated in other independent populations, 6 eQTLs and 2 nsSNP loci were located in the molecular pathways of LPL, APOA5, and CHRM2, which were the significant or suggestive loci in the METS GWAS. Conclusively, our approach using the conventional GWAS, reconsidering functional variants and pathway-based interpretation, suggests a useful method to understand the GWAS results of complex traits and can be expanded in other genomewide association studies.

• 한국사회복지학
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• 제68권4호
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• pp.199-224
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• 2016

본 연구는 현 정신건강증진센터 사례관리가 탈원화와 사회복귀의 측면에서 한계를 보이는 현상을 제도적 맥락에서 이해해보고자 사례관리 실천의 제도적 조직화를 탐구한 연구이다. 이를 위해 제도적 문화기술지(Institutional Ethnography)의 연구방법을 적용하여, 11명의 연구 참여자와의 심층면접과 3개월간의 현장관찰을 통해 얻어진 일 지식과 텍스트 자료를 분석하였다. 분석 결과, 정신건강증진센터 사례관리 실천의 한계는 효율 담론(신공공관리론)과 생의학 담론이 담지된 표준화 정책, 치료율 향상 정책, 성과주의 예산 방식, 성과 평가 체계, 인프라 기능 분할 및 연속적 연계 정책, 복지 자원 연계에 대한 무계획으로부터 텍스트적 실천을 통해 조형되었다. 제도적 조직화의 결과로써 드러난 정신건강증진센터 사례관리는 욕구의 재단과 획일화, 의료적 욕구의 편향, 접촉의 표피화, 사회복귀의 비연속적 미포괄적 지원의 특성을 띠고 있었는데 이는 그간 정책적으로 표방되어 온 사례관리의 유용성과는 간극이 크다. 연구 결과에 따라, 생의학 담론 및 효율 담론의 영향력에 주목하고, 대안 담론을 토대로 한 새로운 정책과 전략의 고안, 성과 관리 체계의 변화, 현장 텍스트들의 재검토와 내용의 재구성, 정신질환자지원에 대한 사회적 관점의 고취, 새로운 사례관리 사업에 대한 논의의 활성화 등을 제언하였다.

• Genomics & Informatics
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• 제9권4호
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• pp.181-188
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• 2011

In planning a model-based phylogenic study for highly related ethnic data, the SNP marker number is an important factor to determine for relationship inferences. Genotype frequency data, utilizing a sub sampling method, from 63 Pan Asian ethnic groups was used for determining the minimum SNP number required to establish such relationships. Bootstrap random sub-samplings were done from 5.6K PASNPi SNP data. DA distance was calculated and neighbour-joining trees were drawn with every re-sampling data set. Consensus trees were made with the same 100 sub-samples and bootstrap proportions were calculated. The tree consistency to the one obtained from the whole marker set, improved with increasing marker numbers. The bootstrap proportions became reliable when more than 7,000 SNPs were used at a time. Within highly related ethnic groups, the minimum SNPs number for a robust neighbor-joining tree inference was about 7,000 for a 95% bootstrap support.

• Genomics & Informatics
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• 제6권3호
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• pp.142-146
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• 2008

In order to understand the protein functions that are related to disease, it is important to detect the correlation between amino acid mutations and disease. Many mutation studies about disease-related proteins have been carried out through molecular biology techniques, such as vector design, protein engineering, and protein crystallization. However, experimental protein mutation studies are time-consuming, be it in vivo or in vitro. We therefore performed a bioinformatic analysis of known disease-related mutations and their protein structure changes in order to analyze the correlation between mutation and disease. For this study, we selected 111 diseases that were related to 175 proteins from the PDB database and 710 mutations that were found in the protein structures. The mutations were acquired from the Human Gene Mutation Database (HGMD). We selected point mutations, excluding only insertions or deletions, for detecting structural changes. To detect a structural change by mutation, we analyzed not only the structural properties (distance of pocket and mutation, pocket size, surface size, and stability), but also the physico-chemical properties (weight, instability, isoelectric point (IEP), and GRAVY score) for the 710 mutations. We detected that the distance between the pocket and disease-related mutation lay within $20\;{\AA}$ (98.5%, 700 proteins). We found that there was no significant correlation between structural stability and disease-causing mutations or between hydrophobicity changes and critical mutations. For large-scale mutational analysis of disease-causing mutations, our bioinformatics approach, using 710 structural mutations, called "Structural Mutatomics," can help researchers to detect disease-specific mutations and to understand the biological functions of disease-related proteins.

• 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.

• Fisheries and Aquatic Sciences
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• 제20권12호
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• pp.31.1-31.11
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• 2017

Background: Liver-expressed antimicrobial peptide-2 (LEAP-2) is an important component of innate immune system in teleosts. In order to understand isoform-specific involvement and regulation of LEAP-2 genes in mud loach (Misgurnus mizolepis, Cypriniformes), a commercially important food fish, this study was aimed to characterize gene structure and expression characteristics of two paralog LEAP-2 isoforms. Results: Mud loach LEAP-2 isoforms (LEAP-2A and LEAP-2B) showed conserved features in the core structure of mature peptides characterized by four Cys residues to form two disulfide bonds. The two paralog isoforms represented a tripartite genomic organization, known as a common structure of vertebrate LEAP-2 genes. Bioinformatic analysis predicted various transcription factor binding motifs in the 5'-flanking regions of mud loach LEAP-2 genes with regard to development and immune response. Mud loach LEAP-2A and LEAP-2B isoforms exhibited different tissue expression patterns and were developmentally regulated. Both isoforms are rapidly modulated toward upregulation during bacterial challenge in an isoform and/or tissue-dependent fashion. Conclusion: Both LEAP-2 isoforms play protective roles not only in embryonic and larval development but also in early immune response to bacterial invasion in mud loach. The regulation pattern of the two isoform genes under basal and stimulated conditions would be isoform-specific, suggestive of a certain degree of functional divergence between isoforms in innate immune system in this species.