• Bioinformatics and Biosystems
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• v.2 no.2
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• pp.37-45
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• 2007

생물정보학은 컴퓨터를 이용하여 방대한 양의 생물학적 데이터를 처리하고 그 결과를 분석하는 학문으로서 IT의 고속성장과 맞물려 점차 그 활용도를 넓혀가고 있다. 특히 의학, 생명과학 연구에 사용되는 데이터는 그 종류도 다양하고 크기가 매우 큰 것이 일반적인데, 이의 처리를 위해서는 고속 네트워크가 바탕이 된 그리드-컴퓨팅(Grid-Computing) 기술 접목이 필연적이다. 고속 네트워크 기술의 발전은 슈퍼컴퓨터를 대체해 컴퓨터 풀 내에 분산된 시스템들을 하나로 묶을 수 있는 그리드-컴퓨팅 분야를 선도하고 있다. 최근 생물정보학 분야에서도 이처럼 발전된 고성능 분산 컴퓨팅 기술을 이용하여 데이터의 신속한 처리와 관리의 효율성을 증대시키고 있는 추세이다. 그리드-컴퓨팅 기술은 크게 데이터 가공을 위한 응용 프로그램 개발과 데이터 관리를 위한 데이터베이스 구축으로 구분 지을 수 있다. 전자에 해당하는 생물정보 연구용 프로그램들은 mpiBLAST, ClustalW-MPI와 같은 MSA서열정렬 프로그램들을 꼽을 수 있으며, BioSimGrid, Taverna와 같은 프로젝트는 그리드-데이터베이스 (Grid-Database)기술을 바탕으로 개발되었다. 본 고에서는 미지의 생명현상을 탐구하고 연구하기 위하여 현재까지 개발된 그리드-컴퓨팅 환경과 의생명과학 연구를 위한 응용 프로그램들, 그리고 그리드-데이터베이스 기술 등을 소개한다.

• Journal of Dairy Science and Biotechnology
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• v.40 no.2
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• pp.57-65
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• 2022

This study was conducted to evaluate the potential use of milk mineral (MM) as the calcium source for the production of calcium-fortified yogurt. MM was composed of 83% minerals, 7.5% lactose, 3.3% protein, and < 1% fat. Calcium (Ca) content in MM was about 46%; calcium: phosphorous ratio was 1.28:1. The aqueous solubility of Ca increased with the decrease in pH; the solubility at pH 4 and 5 was 98% and 53%, respectively. Ca-fortified yogurt with up to 200 mg Ca/100 mL did not show significant differences in acid production and number of viable cells; however, the viscosity increased significantly (p<0.05) with the increase in Ca levels. Microstructure analysis of Ca-fortified yogurt using confocal scanning laser microscopy indicated that the protein network became denser with increasing fortification with MM. There was no significant difference in the sensory quality between the control and Ca-fortified yogurts. Therefore, MM could be used for the production of Ca-fortified yoghurt without compromising the quality characteristics of yogurt.

• The Journal of the Korea institute of electronic communication sciences
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• v.8 no.12
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• pp.1875-1882
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• 2013

Micro-array technology contributes numerous achievements such as ordering of gene network and integration of genomic. This technology is well established as means for investigating patterns of gene expression. DNA micro-arrays utilize Affymetric chips where a large quantity of DNA sequences may be synthesized. There are two general type of conventional DNA array spotter: contact and piezoelectric. The contact technology used spotting pin technology to make contact with the glass slide surface. This may caused damage or scratches to the surface matrix where protein will be contaminated and may not bind specifically. Piezoelectric technology available at this present time on the other hand requires the analyzer to print the result that can only be done within the laboratory despite of mass production. Therefore, in this paper, high-throughput technology is developed for providing greater consistency in feature spot without touching the glass slide surface.

• Journal of Life Science
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• v.20 no.9
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• pp.1420-1425
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• 2010

Innate immunity is the first line of host defense consisting of various molecules against infectious challenges. Mannose-binding lectin (MBL) belongs to the collectin protein family which takes part of innate immunity and is able to recognize specific carbohydrates on the surface of a variety of infectious agents acting as a pattern recognition molecule. In this way, MBL differentiates self from non-self and interacts with other molecules of the immune system. MBL genotype shows various MBL2 polymorphisms which are responsible for MBL deficiency in a substantial portion of the entire human population and for susceptibility to infectious disease. Therefore, it has been highlighted in the relationship between genetic variants and clinical significance. Here we focus on presenting anoverview of our understanding of MBL structure and functions.

• Journal of Digital Contents Society
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• v.11 no.1
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• pp.99-104
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• 2010

Numerous bio-digital contents have been produced by new technology using biochip and others for analyzing early chemical-induced genes. These contents have little meaning by themselves, and so they should be modified and extracted after consideration of biological meaning. These include genomics, transcriptomics, protenomics, metabolomics, which combined into omics. Omics tools could be applied into toxicology, forming a new field of toxicogenomics. It is possible that approach of toxicogenomics can estimate toxicity more quickly and accurately by analyzing gene/protein/metabolite profiles. These approaches should help not only to discover highly sensitive and predictive biomarkers but also to understand molecular mechanism(s) of toxicity, based on the development of analysing technology. Furthermore, it is important that bio-digital contents should be obtained from specific cells having biological events more than from whole cells. Taken together, many bio-digital contents should be analyzed by careful calculating algorism under well-designed experimental protocols, network analysis using computational algorism and related profound databases.

• Journal of Life Science
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• v.30 no.1
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• pp.45-57
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• 2020

The prenatal period in livestock animals is crucial for meat production because net increase in the number of muscle fibers is finished before birth. However, there is no study on the growth and development mechanism of muscles in Hanwoo during this period. Therefore, to find candidate genes involved in muscle growth and development during this period in Hanwoo, mRNA expression data of longissimus in Hanwoo at 6 and 9 months post-conceptional age (MPA) were analyzed. We independently identified differentially expressed genes (DEGs) using DESeq2 and edgeR which are R software packages, and considered the overlaps of the results as final-DEGs to use in downstream analysis. The DEGs were classified into several modules using WGCNA then the modules' functions were analyzed to identify modules which involved in myogenesis and adipogenesis. Finally, the hub genes which had the highest WGCNA module membership among the top 10% genes of the STRING network maximal clique centrality were identified. 913(6 MPA specific DEGs) and 233(9 MPA specific DEGs) DEGs were figured out, and these were classified into five and two modules, respectively. Two of the identified modules'(one was in 6, and another was in 9 MPA specific modules) functions was found to be related to myogenesis and adipogenesis. One of the hub genes belonging to the 6 MPA specific module was axin1 (AXIN1) which is known as an inhibitor of Wnt signaling pathway, another was succinate-CoA ligase ADP-forming beta subunit (SUCLA2) which is known as a crucial component of citrate cycle.

• Journal of Life Science
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• v.30 no.11
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• pp.947-955
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• 2020

The foot-and-mouth disease virus (FMDV), a member of the Aphthovirus genus in the Picornaviridae family, affects wild and domesticated ruminants and pigs. During replication of the FMDV RNA (ribonucleic acid) genome, FMDV-encoding RNA polymerase 3D acts in a highly location-specific manner. This suggests that specific RNA structures recognized by 3D polymerase within non-coding regions of the FMDV genome assist with binding during replication. One such region is the cis-acting replication element (CRE), which functions as a template for RNA replication. The FMDV CRE adopts a stem-loop conformation with an extended duplex stem, supporting a novel 15-17 nucleotide loop that derives stability from base-stacking interactions, with the exact RNA nucleotide sequence of the CRE producing different RNA secondary structures. Here, we show that CRE sequences of FMDVs isolated in Korea from 2010 to 2017 exhibit A and O genotypes. Interestingly, variations in the RNA secondary structure of the Korean FMDVs are consistent with the phylogenetic relationships between these viruses and reveal the specificity of FMDV infections for particular host species. Therefore, we conclude that each genetic clade of Korean FMDV is characterized by a unique functional CRE and that the evolutionary success of new genetic lineages may be associated with the invention of a novel CRE motif. Therefore, we propose that the specific RNA structure of a CRE is an additional criterion for FMDV classification dependent on the host species. These findings will help correctly analyze CRE sequences and indicate the specificity of host species for future FMDV epidemics.

• Journal of Plant Biotechnology
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• v.43 no.3
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• pp.347-358
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• 2016

Brassinosteroid (BR), a plant steroid hormone, plays key roles in numerous growth and developmental processes as well as tolerance to both abiotic and biotic stress. To understand the biological networks involved in BR-mediated signaling pathways and stress tolerance, we performed comparative genome-wide transcriptome analysis of a constitutively activated BR bes1-D mutant with an Agilent Arabidopsis $4{\times}44K$ oligo chip. As a result, we newly identified 1,091 (562 up-regulated and 529 down-regulated) significant differentially expressed genes (DEGs). The combination of GO enrichment and protein network analysis revealed that stress-related processes, such as metabolism, development, abiotic/biotic stress, immunity, and defense, were critically linked to BR signaling pathways. Among the identified gene sets, we confirmed more than a 6-fold up-regulation of NB-ARC and FLS2 in bes1-D plants. However, some genes, including TIR1, TSA1 and OCP3, were down-regulated. Consistently, BR-activated plants showed higher tolerance to drought stress and pathogen infection compared to wild-type controls. In this study, we newly developed a useful, comprehensive method for large-scale identification of critical network and gene sets with global transcriptome analysis using a microarray. This study also showed that gain of function in the bes1-D gene can regulate the adaptive response of plants to various stressful conditions.

• Journal of Life Science
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• v.28 no.3
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• pp.376-387
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• 2018

Among a variety of environmental stresses heat, cold, chilling, high salt, drought, and so on exposed to plants, drought stress has been reported as a crucial factor to adversely affect the growth and productivity of plants. Therefore, to understand the mechanism for the drought stress signal transduction pathway in plants is more helpful to develop useful crops that display the enhanced tolerance against drought stress, and to expand crop growing areas. The signal transduction pathway for the drought stress in plants is largely categorized into two types; ABA-dependent pathway and ABA-independent pathway. It has been reported that two transcription factors, AREB/ABF and DREB2, play predominant roles in ABA-dependent and ABA-independent pathways, respectively. In addition to transcriptional regulation mediated by AREB/ABF and DREB2 transcription factors, post-translational modification (such as phosphorylation and ubiquitination) and epigenetic control are importantly involved in the signal transduction for drought stress. In this paper, we review current understanding of signal transduction pathway on drought stress in plants, especially focusing on the biological roles of a variety of signaling components related to drought stress response. Further understanding the mechanism of drought resistance in plants through this review will be useful to establish theoretical basis for developing drought tolerant crops in the future.

• Journal of Life Science
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• v.26 no.3
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• pp.364-375
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• 2016

Post-translational modification is an efficient process to rapidly transduce external stimulus into cellular response. Ubiquitination is a typical post-translational modification which is a highly conserved process in eukaryotes. UPS (Ubiquitin/Proteasome System) mediated by the ubiquitination is to target diverse cellular proteins for degradation. Among E3 ubiquitin ligases that function as the key determinant for substrate recognition, CRL (cullin–RING E3 ubiquitin ligase) is the largest family and forms the complex composed of cullin, RBX1, adaptor and substrate receptor. Although CRL1, also known as SCF complex, has been widely researched for its biological role, the functional studies of CRL4 have been relatively elusive. In Arabidopsis, there are 119 substrate receptors named DCAF (DDB1 CUL4 Associated Factor) proteins for CRL4 and a fraction of DCAF proteins have been identified for their potential functions so far. In this paper, current understanding on structure and biological roles of plant CRL4 complexes in a diverse of cellular events is reviewed, especially focusing on CRL4 substrate receptors. Moreover, the regulatory mechanism of CRL4’s activity is also introduced. These studies will be helpful to further understand the signal transduction pathways in which such CRL4 complexes are involved and give a clue to establish the action network of entire CRL4 complexes in plants.