• Parasites, Hosts and Diseases
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• 제49권4호
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• pp.341-347
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• 2011

Acanthamoeba infection is difficult to treat because of the resistance property of Acanthamoeba cyst against the host immune system, diverse antibiotics, and therapeutic agents. To identify encystation mediating factors of Acanthamoeba, we compared the transcription profile between cysts and trophozoites using microarray analysis. The DNA chip was composed of 12,544 genes based on expressed sequence tag (EST) from an Acanthamoeba ESTs database (DB) constructed in our laboratory, genetic information of Acanthamoeba from TBest DB, and all of Acanthamoeba related genes registered in the NCBI. Microarray analysis indicated that 701 genes showed higher expression than 2 folds in cysts than in trophozoites, and 859 genes were less expressed in cysts than in trophozoites. The results of real-time PCR analysis of randomly selected 9 genes of which expression was increased during cyst formation were coincided well with the microarray results. Eukaryotic orthologous groups (KOG) analysis showed an increment in T article (signal transduction mechanisms) and O article (posttranslational modification, protein turnover, and chaperones) whereas significant decrement of C article (energy production and conversion) during cyst formation. Especially, cystein proteinases showed high expression changes (282 folds) with significant increases in real-time PCR, suggesting a pivotal role of this proteinase in the cyst formation of Acanthamoeba. The present study provides important clues for the identification and characterization of encystation mediating factors of Acanthamoeba.

• 한국광학회지
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• 제14권1호
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• pp.97-102
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• 2003

이차원 표면 플라즈몬의 공명 흡수와 포토 마스크를 이용하여 11-MUA(11-Mercaptoundecanoic acid)와 11-MUOH(11-Mercaptoundecanol) 둥으로 이루어진 자기조립 단분자막(Self-Assembled Monolayer; SAM)의 다채널 영상을 얻었다. 통상의 Photoresist를 이용한 리토그래피 대신에 Thiol bonding의 광산화를 이용하여 패터닝 과정을 줄이고, 백색광 및 대역통과 필터(λ$_{0}$=633nm)를 이용하여 입사광으로써 레이저를 사용할 때 나타나는 간섭무늬를 줄였다. 이로부터 나타나는 이차원 영상의 명암을 정량적으로 보정하면 수 나노미터(nm) 두께의 변화를 측정할 수 있다. 또한 표면 플라즈몬 공명법은 국소화된 근접장 (소산장)을 이용하는 방법으로서, 통상 많이 이용되는 형광법 등에서 나타나는 광탈색(Photobleaching)이나 소광(Quenching) 현상이 없이 시료의 처리가 간단하고, 영상 신호의 시간에 따른 변화가 극히 적으며, 실시간으로 신호의 변화를 측정할 수 있다는 장점이 있다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.13-16
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• 2000

Microorganisms have been widely employed for the production of useful bioproducts including primary metabolites such as ethanol, succinic acid, acetone and butanol, secondary metabolites represented by antibiotics, proteins, polysaccharides, lipids and many others. Since these products can be obtained in small quantities under natural condition, mutation and selection processes have been employed for the improvement of strains. Recently, metabolic engineering strategies have been employed for more efficient production of these bioproducts. Metabolic engineering can be defined as purposeful modification of cellular metabolic pathways by introducing new pathways, deleting or modifying the existing pathways for the enhanced production of a desired product or modified/new product, degradation of xenobiotics, and utilization of inexpensive raw materials. Metabolic flux analysis and metabolic control analysis along with recombinant DNA techniques are three important components in designing optimized metabolic pathways, This powerful technology is being further improved by the genomics, proteomics, metabolomics and bioinformatics. Complete genome sequences are providing us with the possibility of addressing complex biological questions including metabolic control, regulation and flux. In silico analysis of microbial metabolic pathways is possible from the completed genome sequences. Transcriptome analysis by employing ONA chip allows us to examine the global pattern of gene expression at mRNA level. Two dimensional gel electrophoresis of cellular proteins can be used to examine the global proteome content, which provides us with the information on gene expression at protein level. Bioinformatics can help us to understand the results obtained with these new techniques, and further provides us with a wide range of information contained in the genome sequences. The strategies taken in our lab for the production of pharmaceutical proteins, polyhydroxyalkanoate (a family of completely biodegradable polymer), succinic acid and me chemicals by employing metabolic engineering powered by genomics, proteomics, metabolomics and bioinformatics will be presented.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.53-55
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• 2000

Xenie is the JAVA application software that integrates and represents 'gene to function'information of human gene. Xenie extracts data from several heterogeneous molecular biology databases and provides integrated information in human readable and machine usable way. We defined 7 semantic frame classes (Gene, Transcript, Polypeptide, Protein_complex, Isotype, Functional_object, and Cell) as a common schema for storing and integrating gene to function information and relationship. Each of 7 semantic frame classes has data fields that are supposed to store biological data like gene symbol, disease information, cofactors, and inhibitors, etc. By using these semantic classes, Xenie can show how many transcripts and polypeptide has been known and what the function of gene products is in General. In detail, Xenie provides functional information of given human gene in the fields of semantic objects that are storing integrated data from several databases (Brenda, GDB, Genecards, HGMD, HUGO, LocusLink, OMIM, PIR, and SWISS-PROT). Although Xenie provide fully readable form of XML document for human researchers, the main goal of Xenie system is providing integrated data for other bioinformatic application softwares. Technically, Xenie provides two kinds of output format. One is JAVA persistent object, the other is XML document, both of them have been known as the most favorite solution for data exchange. Additionally, UML designs of Xenie and DTD for 7 semantic frame classes are available for easy data binding to other bioinformatic application systems. Hopefully, Xenie's output can provide more detailed and integrated information in several bioinformatic systems like Gene chip, 2D gel, biopathway related systems. Furthermore, through data integration, Xenie can also make a way for other bioiformatic systems to ask 'function based query'that was originally impossible to be answered because of separatly stored data in heterogeneous databases.

• BMB Reports
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• 제49권9호
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• pp.514-519
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• 2016

Korean cattle (Hanwoo) are categorized into three breeds based on color: brown, brindle, and black. Among these breeds, brown Hanwoo has been subjected to intensive selection to improve meat traits. To identify genetic traces driven by recent selection in brown Hanwoo, we scanned the genomes of brown and brindle Hanwoo using a bovine SNP chip. We identified 17 candidate selection signatures in brown Hanwoo and sequenced four candidate regions from 10 individuals each of brown and brindle Hanwoo. In particular, non-synonymous SNPs in the ADSL gene (K88M, L189H, and R302Q) might have had mutational effects on protein structure as a result of altering the purine pathway during nucleotide breakdown. The ADSL gene was previously reported to affect meat quality and yield in livestock. Meat quality and yield are main breeding goals for brown Hanwoo, and our results support a potential causal influence of non-synonymous SNPs in the ADSL gene.

• Korean Chemical Engineering Research
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• 제51권6호
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• pp.760-765
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• 2013

액적기반 미세유체 시스템을 이용해 난백단백질인 라이소자임의 결정화실험을 하였다. Flow-focusing 칩을 이용해 water-in-oil 형태의 액적을 만들고 페트리 디쉬와 십자몰드에 넣은 후, 액적 내부에서 라이소자임 수용액과 침전제 (NaCl) 사이의 액-액 반응을 관찰하였다. 그리고 수용액의 pH가 4.8일 때와 7.2일 때의 결정형태를 비교하였다. 그 결과, pH 4.8에서는 다면체 또는 판상형의 결정이 형성되었고, pH 7.2에서는 침상형 결정이 생성되었다. pH 4.8, 7.2 두 경우 액적이 홀로 있을 때에는 액적부피가 유지되거나 감소하면서 결정이 형성되었다. 하지만 액적이 서로 인접해 있을 때는 액적사이의 상호작용이 관찰되었고, 두 pH에서 다른 경향성을 보였다. pH 4.8에서는 인접한 액적의 부피에 영향을 주어 한 액적의 부피가 커졌고, 부피가 커진 액적에서 결정이 형성되었다. pH 7.2에서는 부피에 영향을 서로 주지 않고 각각의 액적에서 결정이 형성되었다.

• Genomics & Informatics
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• 제8권3호
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• pp.131-137
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• 2010

Genome-wide association studies (GWASs) have greatly contributed to the identification of common variants responsible for numerous complex traits. There are, however, unavoidable limitations in detecting causal and/or rare variants for traits in this approach, which depends on an LD-based tagging SNP microarray chip. In an effort to detect potential casual and/or rare variants for complex traits, such as type 2 diabetes (T2D) and triglycerides (TGs), we conducted a targeted resequencing of loci identified by the Korea Association REsource (KARE) GWAS. The target regions for resequencing comprised whole exons, exon-intron boundaries, and regulatory regions of genes that appeared within 1 Mb of the GWA signal boundary. From 124 individuals selected in population-based cohorts, a total of 0.7 Mb target regions were captured by the NimbleGen sequence capture 385K array. Subsequent sequencing, carried out by the Roche 454 Genome Sequencer FLX, generated about 110,000 sequence reads per individual. Mapping of sequence reads to the human reference genome was performed using the SSAHA2 program. An average of 62.2% of total reads was mapped to targets with an average 22X-fold coverage. A total of 5,983 SNPs (average 846 SNPs per individual) were called and annotated by GATK software, with 96.5% accuracy that was estimated by comparison with Affymetrix 5.0 genotyped data in identical individuals. About 51% of total SNPs were singletons that can be considered possible rare variants in the population. Among SNPs that appeared in exons, which occupies about 20% of total SNPs, 304 nonsynonymous singletons were tested with Polyphen to predict the protein damage caused by mutation. In total, we were able to detect 9 and 6 potentially functional rare SNPs for T2D and triglycerides, respectively, evoking a further step of replication genotyping in independent populations to prove their bona fide relevance to traits.

• The Korean Journal of Physiology and Pharmacology
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• 제10권5호
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• pp.263-271
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• 2006

Since astrocytes were shown to play a central role in maintaining neuronal viability both under normal conditions and during stress such as ischemia, studies of the astrocytic response to stress are essential to understand many types of brain pathology. The micro array system permitted screening of large numbers of genes in biological or pathological processes. Therefore, the gene expression patterns in the in vitro model of astrocytes following exposure to oxygen-glucose deprivation (OGD) were evaluated by using the micro array analysis. Primary astrocytic cultures were prepared from postnatal Swiss Webster mice. The cells were exposed to OGD for 4 hrs at $37^{\circ}C$ prior to cell harvesting. From the cultured cells, we isolated mRNA, synthesized cDNA, converted to biotinylated cRNA and then reacted with GeneChips. The data were normalized and analyzed using dChip and GenMAPP tools. After 4 hrs exposure to OGD, 4 genes were increased more than 2 folds and 51 genes were decreased more than 2 folds compared with the control condition. The data suggest that the OGD has general suppressive effect on the gene expression with the exception of some genes which are related with ischemic cell death directly or indirectly. These genes are mainly involved in apoptotic and protein translation pathways and gap junction component. These results suggest that microarray analysis of gene expression may be useful for screening novel molecular mediators of astrocyte response to ischemic injury and making profound understanding of the cellular mechanisms as a whole. Such a screening technique should provide insights into the molecular basis of brain disorders and help to identify potential targets for therapy.

• Asian-Australasian Journal of Animal Sciences
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• 제31권12호
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• pp.1852-1862
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• 2018

Objective: The purpose of this study was to investigate a single step genome-wide association study (ssGWAS) for identifying genomic regions affecting reproductive traits in Landrace and Large White pigs. Methods: The traits included the number of pigs weaned per sow per year (PWSY), the number of litters per sow per year (LSY), pigs weaned per litters (PWL), born alive per litters (BAL), non-productive day (NPD) and wean to conception interval per litters (W2CL). A total of 321 animals (140 Landrace and 181 Large White pigs) were genotyped with the Illumina Porcine SNP 60k BeadChip, containing 61,177 single nucleotide polymorphisms (SNPs), while multiple traits single-step genomic BLUP method was used to calculate variances of 5 SNP windows for 11,048 Landrace and 13,985 Large White data records. Results: The outcome of ssGWAS on the reproductive traits identified twenty-five and twenty-two SNPs associated with reproductive traits in Landrace and Large White, respectively. Three known genes were identified to be candidate genes in Landrace pigs including retinol binding protein 7, and ubiquitination factor E4B genes for PWL, BAL, W2CL, and PWSY and one gene, solute carrier organic anion transporter family member 6A1, for LSY and NPD. Meanwhile, five genes were identified to be candidate genes in Large White, two of which, aldehyde dehydrogenase 1 family member A3 and leucine rich repeat kinase 1, associated with all of six reproduction traits and three genes; retrotransposon Gag like 4, transient receptor potential cation channel subfamily C member 5, and LHFPL tetraspan subfamily member 1 for five traits except W2CL. Conclusion: The genomic regions identified in this study provided a start-up point for marker assisted selection and estimating genomic breeding values for improving reproductive traits in commercial pig populations.

• Journal of Ginseng Research
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• 제45권1호
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• pp.176-182
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• 2021

Background: Atopic dermatitis (AD) is associated with chronic skin inflammatory reactions. p-coumaric acid (pCA) is an active ingredient of Panax ginseng Meyer (Araliaceae). Methods: Here, we estimated an anti-AD effect of pCA on activated mast cells, activated splenocytes, and a mouse model of AD. Cytokines levels were measured by ELISA and protein activation was analyzed by Western blotting. 2,4-dinitrofluorobenzene (DNFB) was used to induce AD-like skin lesions. Results: The treatment with pCA suppressed the productions and mRNA expressions of thymic stromal lymphopoietin (TSLP), TNF-α, IL-6, and IL-1β in HMC-1 cells. pCA downregulated the expressions of RIP2 and caspase-1, phosphorylated-(p)p38/pJNK/pERK, and pIKKβ/pIkBα/NF-κB in HMC-1 cells. pCA also decreased the productions of TSLP, TNF-α, IL-6, IL-4, and IFN-γ in the supernatant of stimulated splenic cells. Comparing to DNFB-sensitized control group, pCA-treated group alleviated pathological changes of AD-like lesions. pCA decreased the proteins and mRNA expressions levels of TSLP, IL-6, and IL-4 in the skin lesions. Caspase-1 activation was also downregulated by pCA treatment in the AD-like lesions. The serum levels of histamine, IgE, TSLP, TNF-α, IL-6, and IL-4 were suppressed following treatment with pCA. Conclusion: This study suggests that pCA has the potential to improve AD by suppressing TSLP as well as inflammatory cytokines via blocking of caspase-1/NF-κB signal cascade.