• Journal of The Korean Society of Grassland and Forage Science
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• v.36 no.3
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• pp.243-247
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• 2016

Arsenic (As) is a toxic element that easily taken up by plants root. Several toxic forms of As disrupt plant metabolism by a series of cellular alterations. In this study, we applied annealing control primer (ACP)-based reverse transcriptase PCR (polymerase chain reaction) technique to identify differentially expressed genes (DEGs) in alfalfa roots in response to As stress. Two-week-old alfalfa seedlings were exposed to As treatment for 6 hours. DEGs were screened from As treated samples using the ACP-based technique. A total of six DEGs including heat shock protein, HSP 23, plastocyanin-like domain protein162, thioredoxin H-type 1 protein, protein MKS1, and NAD(P)H dehydrogenase B2 were identified in alfalfa roots under As stress. These genes have putative functions in abiotic stress homeostasis, antioxidant activity, and plant defense. These identified genes would be useful to increase As tolerance in alfalfa plants.

• Journal of the Korean Institute of Illuminating and Electrical Installation Engineers
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• v.27 no.11
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• pp.57-68
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• 2013

The market for distributed power generation based on renewable energy is increasing, particularly for standalone mini-grid applications in developing countries with limited energy resources. Stand-alone power systems (SAPS) are of special interest combined with renewable energy design in areas not connected to the electric grid. Traditionally, such systems have been powered by diesel engine generator sets (DEGS), but also hybrid systems with photovoltaic and/or wind energy conversion systems (WECS) are becoming quite common nowadays. Hybrid energy systems can now be used to generate energy consumed in remote areas and stand-alone microgrids. This paper describes the design, simulation and feasibility study of a hybrid energy system for a stand-alone power system. A simulated model is developed to investigate the design and performance of stand-alone hydrogen renewable energy systems. The analysis presented here is based on transient system simulation program (TRNSYS) with realistic ventilation load of a large store. Design of a hybrid energy system is site specific and depends on the resources available and the load demand.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.124-130
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• 2004

Microarray expression datasets are incessantly cumulated with the aid of recent technological advances. One of the first steps for analyzing these data under various experimental conditions is determining differentially expressed genes (DEGs) in each condition. Reasonable choices of thresholds for determining differentially expressed genes are used for the next -step-analysis with suitable statistical significances. We present a model for identifying DEGs using pathway information based on the global connectivity structure. Pathway information can be regarded as a collection of biological knowledge, thus we are tying to determine the optimal threshold so that the consequential connectivity structure can be the most compatible with the existing pathway information. The significant feature of our model is that it uses established knowledge as a reference to determine the direction of analyzing microarray dataset. In the most of previous work, only intrinsic information in the miroarray is used for the identifying DEGs. We hope that our proposed method could contribute to construct biologically meaningful network structure from microarray datasets.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.5
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• pp.2273-2278
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• 2014

Purpose: The purpose of our study was to explore the molecular mechanisms in the process of oral squamous cells carcinoma (OSCC) development. Method: We downloaded the affymetrix microarray data GSE31853 and identified differentially expressed genes (DEGs) between OSCC and normal tissues. Then Gene Ontology (GO) and Protein-Protein interaction (PPI) networks analysis was conducted to investigate the DEGs at the function level. Results: A total 372 DEGs with logFCI >1 and P value < 0.05 were obtained, including NNMT, BAX, MMP9 and VEGF. The enriched GO terms mainly were associated with the nucleoplasm, response to DNA damage stimuli and DNA repair. PPI network analysis indicated that GMNN and TSPO were significant hub proteins and steroid biosynthesis and synthesis and degradation of ketone bodies were significantly dysregulated pathways. Conclusion: It is concluded that the genes and pathways identified in our work may play critical roles in OSCC development. Our data provides a comprehensive perspective to understand mechanisms underlying OSCC and the significant genes (proteins) and pathways may be targets for therapy in the future.

• Journal of The Korean Society of Grassland and Forage Science
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• v.37 no.3
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• pp.237-241
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• 2017

Drought is one of the detrimental factors that impair plant growth and productivity. In this study, we applied annealing control primer (ACP)-based reverse transcriptase PCR (polymerase chain reaction) technique to identify differentially expressed genes (DEGs) in maize leaves in response to drought stress. Two-week-old maize seedlings were exposed to drought (DT) by suspending water supply. DEGs were screened after 3 days of DT-treated samples using the ACP-based technique. Several DEGs encoding 16.9 protein, antimicrobial protein, hypothetical protein NCLIV_068840, thioredoxin M-type were identified in maize leaves under drought stress. These genes have putative functions in plant defense response, growth and development. These identified genes would be useful for predictive markers of plant defense, and growth responses under drought stress in plants.

• Genomics & Informatics
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• v.19 no.2
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• pp.16.1-16.14
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• 2021

Even in the current age of advanced medicine, the prognosis of malignant peritoneal mesothelioma (MPM) remains abysmal. Molecular mechanisms responsible for the initiation and progression of MPM are still largely not understood. Adopting an integrated bioinformatics approach, this study aims to identify the key genes and pathways responsible for MPM. Genes that are differentially expressed in MPM in comparison with the peritoneum of healthy controls have been identified by analyzing a microarray gene expression dataset. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of these differentially expressed genes (DEG) were conducted to gain a better insight. A protein-protein interaction (PPI) network of the proteins encoded by the DEGs was constructed using STRING and hub genes were detected analyzing this network. Next, the transcription factors and miRNAs that have possible regulatory roles on the hub genes were detected. Finally, survival analyses based on the hub genes were conducted using the GEPIA2 web server. Six hundred six genes were found to be differentially expressed in MPM; 133 are upregulated and 473 are downregulated. Analyzing the STRING generated PPI network, six dense modules and 12 hub genes were identified. Fifteen transcription factors and 10 miRNAs were identified to have the most extensive regulatory functions on the DEGs. Through bioinformatics analyses, this work provides an insight into the potential genes and pathways involved in MPM.

• Journal of Veterinary Clinics
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• v.40 no.2
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• pp.164-174
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• 2023

Canine splenic tumors (STs) are commonly diagnosed during imaging examinations, such as in X-ray and ultrasonography examinations, suggesting their higher prevalence, especially in older dogs. Despite this high prevalence, there are no effective treatment options for STs because of the difficulties in determining therapeutic targets. However, recently, the importance of microRNAs (miRNAs) has evolved owing to their ambivalent characteristics. Biomarkers and novel therapies using miRNAs have been well-studied in human cancer research compared to canine research, except for mammary gland tumors. Therefore, this study aimed to comparatively analyze miRNA expression profiles according to malignancy and biopsy sites to identify novel therapeutic and diagnostic targets. Tissue samples were collected directly from splenic tumor masses and immersed in RNAlater solution for further analysis. To investigate differentially expressed genes (DEGs) between tumor and normal tissues, we used RNA-seq and miRNA microarray analysis. Then, functional analysis based on DEGs was conducted to sort tumor-related DEGs. We found that cfa-miR-150 was upregulated in benign tumors, whereas cfa-miR-134 was upregulated in malignant tumors. Despite limited information on canine miRNAs, we identified two potential biomarkers for the differential diagnosis of STs.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.188-188
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• 2022

Our previous study identified a resistance locus to Phytophthora sojae (isolate 2457) in an interval of 3.8-4.7 Mbp on chromosome 3 via genetic mapping using a 'Daepung'×'Daewon' recombinant inbred population. Since differential gene expression between Daepung (susceptible) and Daewon (resistant) after inoculation of P. sojae is unknown, RNA sequencing was carried out to compare transcriptomic changes between the two genotypes following inoculation with P. sojae isolate 2457. The two varieties were inoculated using hypocotyl inoculation at the VC stage and stem tissue of 1 cm above and below of the inoculated site were sampled at 0, 6, 12 hours after inoculation (hai), respectively. Differentially expressed genes (DEGs) under same cultivar in different time point and Daepung vs. Daewon in same time point were investigated. In comparison of Daepung vs. Daewon at 12 hai, a total of 3,513 DEGs were identified, including two nucleotide-binding site-leucine rich repeat (NBS-LRR) genes (Glyma.03g034800 and Glyma.03g034900) that are located in the previously reported resistance locus on chromosome 3. In addition, 14,966 DEGs were detected between 0 vs. 6 hai, containing one of candidate genes (Glyma.03g035300). This gene was upregulated by up to 4-fold in Daewon and Daepung. Additional results will be further discussed in the presentation. This study will provide valuable information for soybean crop improvement.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.9
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• pp.1334-1341
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• 2007

This study identified hepatic differentially expressed genes (DEGs) affecting the marbling of muscle. Most dietary nutrients bypass the liver and produce plasma lipoproteins. These plasma lipoproteins transport free fatty acids to the target tissue, adipose tissue and muscle. We examined hepatic genes differentially expressed in a differential-display reverse transcription-polymerase chain reaction (ddRT-PCR) analysis comparing high- and low-marbled Hanwoo steers. Using 60 arbitrary primers, we found 13 candidate genes that were upregulated and five candidate genes that were downregulated in the livers of high-marbled Hanwoo steers compared to low-marbled individuals. A BLAST search for the 18 DEGs revealed that 14 were well characterized, while four were not annotated. We examined four DEGs: ATP synthase F0, complement component CD, insulin-like growth factor binding protein-3 (IGFBP3) and phosphatidylethanolamine binding protein (PEBP). Of these, only two genes (complement component CD and IGFBP3) were differentially expressed at p<0.05 between the livers of high- and low-marbled individuals. The mean mRNA levels of the PEBP and ATP synthase F0 genes did not differ significantly between the livers of high- and low-marbled individuals. Moreover, these DEGs showed very high inter-individual variation in expression. These informative DEGs were assigned to the bovine chromosome in a BLAST search of MS marker subsets and the bovine genome sequence. Genes related to energy metabolism (ATP synthase F0, ketohexokinase, electron-transfer flavoprotein-ubiquinone oxidoreductase and NADH hydrogenase) were assigned to BTA 1, 11, 17, and 22, respectively. Syntaxin, IGFBP3, decorin, the bax inhibitor gene and the PEBP gene were assigned to BTA 3, 4, 5, 5, and 17, respectively. In this study, the in silico physical maps provided information on the specific location of candidate genes associated with economic traits in cattle.

• Journal of Plant Biotechnology
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• v.43 no.2
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• pp.204-212
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• 2016

To understand the responses of grapevines in response to cold stress causing the limited growth and development, differentially expressed genes (DEGs) were screened through transcriptome analysis of shoots from 2 grapevine cultivars ('Campbell Early' and 'Muscat Baily A') kept at -$2^{\circ}C$ for 4 days. In gene ontology analysis of DEGs from 'Campbell Early', there were 17,424 clones related with biological process, 28,954 with cellular component, and 6,972 with molecular function genes in response to freezing temperature. The major induced genes included dehydrin xero 1, K-box region and MADS-box transcription factor family protein, and MYB domain protein 36, and inhibited genes included light-harvesting chlorophyll B-binding protein 3, FASCICLIN-like arabinoogalactan 9, and pectin methylesterase 61 in 'Campbell Early' grapevines. In gene ontology analysis of DEGs from 'Muscat Baily A', there were 1,157 clones related with biological process, 1,350 with cellular component, and 431 with molecular function gene. The major induced genes of 'Muscat Baily A' included NB-ARC domain-containing disease resistance protein, fatty acid hydrozylase superfamily, and isopentenyltransferase 3, and inhibited genes included binding, IAP-like protein 1, and pentatricopeptide repeat superfamily protein. All major DEGs were shown to be expressed differentially by freezing temperature in real time-PCR analysis. Protein domain analysis using InterPro Scan revealed that ubiquitin-protein ligase was redundant in both tested grapevines. Transcriptome profile of shoots exposed to cold can provide new insights into the molecular basis of tolerance to low-temperature in grapevines, and can be used as resources for development new grapevines tolerant to coldness.