• Molecular & Cellular Toxicology
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• 제1권1호
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• pp.52-61
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• 2005

Transcript profiling is a particularly valuable tool in the field of steroid receptor biology, as these receptors are ligand-activated transcription factors and therefore exert their initial effects through altering gene expression in responsive cells. Also, an awareness of endocrine disrupting chemicals (EDCs) and their potential screening methods to identify endocrine activity have been increased. Here we developed an in-house cDNA microarray, named KISTCHIP-400 ver. 1.0, with 416 clones, based on public database and research papers. These clones contained estrogen, androgen, thyroid hormone & receptors, sex hormone signal transduction & regulation, c-fos, c-myc, ps2 gene, metabolism related genes etc. Also, to validate the KISTCHIP-400 ver. 1.0, we investigated gene expression profiles with reference hormones, $10^{8}\;M\;17{\beta}-estradiol,\;10^{-7}\;M\;testosterone\;and\;10^{-7}\;M$ progesterone in MCF-7 cell line. As the results, gene expression profiles of three reference hormones were distinguished from each other with significant and identified 33 $17{\beta}-estradiol$ responsive genes. This study is in first step of validation for KISTCHIP-400 ver. 1.0, as following step transcriptional profile analysis on not only low concentrations of EDCs but suspected EDCs using KISTCHIP-400 ver. 1.0 is processing. Our results indicate that the developed microarray may be a useful laboratory tool for screening EDCs and elucidating endocrine disrupting mechanism.

• BMB Reports
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• 제51권2호
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• pp.55-56
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• 2018

Long terminal repeat retrotransposons (LTR-Rs) are major elements creating new genome structure for expansion of plant genomes. However, in addition to the genome expansion, the role of LTR-Rs has been unexplored. In this study, we constructed new reference genome sequences of two pepper species (Capsicum baccatum and C. chinense), and updated the reference genome of C. annuum. We focused on the study for speciation of Capsicum spp. and its driving forces. We found that chromosomal translocation, unequal amplification of LTR-Rs, and recent gene duplications in the pepper genomes as major evolutionary forces for diversification of Capsicum spp. Specifically, our analyses revealed that the nucleotide-binding and leucine-rich-repeat proteins (NLRs) were massively created by LTR-R-driven retroduplication. These retoduplicated NLRs were abundant in higher plants, and most of them were lineage-specific. The retroduplication was a main process for creation of functional disease-resistance genes in Solanaceae plants. In addition, 4-10% of whole genes including highly amplified families such as MADS-box and cytochrome P450 emerged by the retroduplication in the plants. Our study provides new insight into creation of disease-resistance genes and high-copy number gene families by retroduplication in plants.

• Journal of Microbiology and Biotechnology
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• 제17권2호
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• pp.335-341
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• 2007

For the development of qualitative and quantitative PCR methods of genetically modified (GM) pepper developed in Korea, a capsanthin-capsorubin synthase (CCS) gene was used as the endogenous reference gene. The primer pair ccs-F/R amplifying the pepper endogenous gene gave rise to an amplicon of 102 bp. No amplified product was observed when DNA samples from 16 different plants were used as templates. The construct-specific primer pairs amplifying the junction region of the bar gene and Ti7 introduced in GM pepper gave rise to an amplicon of 182 bp. Quantitative PCR assay was performed using a TaqMan probe and a standard plasmid as a reference molecule, which contained both an endogenous and event-specific sequence. For the validation of this method, the test samples containing 0.1, 1, 3, 5, and 10% GM pepper were quantified.

• Asian Pacific Journal of Cancer Prevention
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• 제17권12호
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• pp.5229-5235
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• 2016

Prostate cancer (PCa) remains one of the most widespread and perplexing of all human malignancies. Assessment of gene expression is thought to have an important impact on cancer diagnosis, prognosis and therapeutic decisions. In this context, we explored combined expression of PCa related target genes AMACR and PCA3 in 126 formalin fixed paraffin embedded prostate tissues (FFPE) from Moroccan patients, using quantitative real time reverse transcription-PCR (RT-qPCR). This quantification required data normalization accomplished using stably expressed reference genes (RGs). A panel of twelve RG was assessed, data being analyzed using GenEx V6 based on geNorm, NormFinder and statistical methods. Accordingly, the hnRNP A1 gene was identified and selected as the most stably expressed RG for reliable and accurate gene expression quantification in prostate tissues. The ratios of both PCA3 and AMACR gene expression relative to that of the hnRNP A1 gene were calculated and the performance of each target gene for PCa diagnosis was evaluated using receiver-operating characteristics. PCA3 and AMACR mRNA quantification based on RT-qPCR may prove useful in PCa diagnosis. Of particular interesting, combining PCA3 and AMACR quantification improved PCa prediction by increasing sensitivity with retention of good specificity.

• 한국동물생명공학회지
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• 제34권4호
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• pp.280-291
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• 2019

Potential utility of 14 candidate housekeeping genes as normalization reference for RT-qPCR analysis with developmental samples (fertilized eggs to late veliger larvae) in Pacific abalone Haliotis discus hannai was evaluated using four different statistical algorithms (geNorm, NormFinder, BestKeeper and comparative ΔCT method). Different algorithms identified different genes as the best candidates, and geometric mean-based final ranking from the most to the least stable expression was as follow: RPL5, RPL4, RPS18, RPL8, RPL7, UBE2, RPL7A, GAPDH, RPL36, PPIB, EF1A, ACTB and B-TU. The findings were further validated via relative quantification of metallothionein (MT) transcripts using the stable and unstable reference genes, and expression levels of MT were greatly influenced according to the choice of reference genes. In overall, our data suggest that RPL5 and RPS18, either singly or in combination, are appropriate for normalizing gene expression in developmental samples of this abalone species, whereas ACTB, B-TU and EF1A are less stable and not recommended. In addition, our findings propose that standard deviations in geometric ranking as well as geometric mean itself should also be taken into account for the final selection of reference gene(s). This study could be a useful basis to facilitate the generation of accurate and reliable RT-qPCR data with developmental samples in this abalone species.

• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.337-353
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• 2018

We used Illumina/HiSeq sequencing for analysis of gene expression profiling among four maize seed types (dent, CM3 and CM6; waxy, CM5 and CM19) at 10 DAP (days after pollination). A total of 88,993,000 (CM3), 103,817,340 (CM6), 103,139,640 (CM5), and 66,978,958 (CM19) sequence reads were generated with read lengths of about 0.9, 1.0, 1.0, and 0.7 billion bp, respectively. We obtained 69.1 (CM3), 71.0 (CM6), 71.2 (CM5), and 71.8% (CM19) high quality reads from the raw data and compared them with reference RNA sequences in a public DB (NCBI). It was revealed that mapped reads were 58%, 63%, 62%, and 62% of the EST reference in CM3, CM6, CM5 and CM19, respectively; and more than 51,000 genes were expressed based on RPKM criteria (over 0.25 value) in each CM3, CM6, CM5, and CM19 inbred line. In differentially expressed gene (DEG) analysis, we found that 3,527 genes were differentially expressed by at least two-fold with 1,709 upregulated in the two waxy inbred lines and 1,818 upregulated in the two dent inbred lines. We also detected genes for the sucrose and starch biosynthesis pathways based on BINs, and different expression patterns between waxy and dent inbred lines were shown for the gene set for starch synthesis, such as sh2, bt2, du1, wx1, and ae1. Although some genes were more expressed in dent lines, most genes for starch synthesis were much expressed in waxy lines. Especially, there was greater expression of the sus2 gene in both waxy lines compared with the dent lines.

• Journal of Microbiology and Biotechnology
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• 제16권2호
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• pp.205-211
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• 2006

A quantitative analytical method to detect new lines of genetically modified (GM) maize, NK603 and TC1507, has been developed by using a real-time polymerase chain reaction (PCR). To detect these GM lines, two specific primer pairs and probes were designed. A plasmid as a reference molecule was constructed from an endogenous DNA sequence of maize, a universal sequence of a cauliflower mosaic virus (CaMV) 35S promoter used in most GMOs, and each DNA sequence specific to the NK603 and TC1507 lines. For the validation of this method, the test samples of 0, 0.1, 0.5, 1.0, 3.0, 5.0, and 10.0% each of the NK603 and TC1507 GM maize were quantitated. At the 3.0% level, the biases (mean vs. true value) for the NK603 and TC1507 lines were 3.3% and 15.7%, respectively, and their relative standard deviations were 7.2% and 5.5%, respectively. These results indicate that the PCR method developed in this study can be used to quantitatively detect the NK603 and TC1507 lines of GM maize.

• Parasites, Hosts and Diseases
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• 제54권1호
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• pp.39-46
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• 2016

Theileria annulata is a tick-borne intracellular protozoan parasite that causes tropical theileriosis, a fatal bovine lymphoproliferative disease. The parasite predominantly invades bovine B lymphocytes and macrophages and induces host cell transformation by a mechanism that is not fully comprehended. Analysis of signaling pathways by quantitative real-time PCR (qPCR) could be a highly efficient means to understand this transformation mechanism. However, accurate analysis of qPCR data relies on selection of appropriate reference genes for normalization, yet few papers on T. annulata contain evidence of reference gene validation. We therefore used the geNorm and NormFinder programs to evaluate the stability of 5 candidate reference genes; 18S rRNA, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ACTB (${\beta}-actin$), PRKG1 (protein kinase cGMP-dependent, type I) and TATA box binding protein (TBP). The results showed that 18S rRNA was the reference gene most stably expressed in bovine PBMCs transformed and non-transformed with T. annulata, followed by GAPDH and TBP. While 18S rRNA and GAPDH were the best combination, these 2 genes were chosen as references to study signaling pathways involved in the transformation mechanism of T. annulata.

• 한국가금학회지
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• 제38권2호
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• pp.89-96
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• 2011

몽골 산란계 농장에서 발생한 뉴캣슬병 사례로부터 뉴캣슬병 바이러스를 분리하고 그 특성을 조사하였다. 그 결과, 발생 농장 산란계 폐사계의 뇌 및 폐 조직으로부터 뉴캣슬병 바이러스 MN1/10 주가 분리되었다. 이 바이러스는 F 단백질 분절 부위가 특징적인 병원성 motif(RRQKRF)를 가지고 있었으며 종란 평균 치사 지수(MDT)가 54.7시간으로 강독형 NDV이었다. 또한 발생 농장 내 생존하고 있는 산란계에서 고역가의 NDV 특이항체가 검출되었다. 유적학적 계통 분석을 실시한 결과, 몽골 분리주는 Class II에 속하는 genotype VIId 바이러스로 확인되었다. 유전학적 계통 분석 결과, 몽골 분리주는 몽골과 인접한 중국에서 유행하는 바이러스 그룹(CN2)에 속하는 것으로 분류되었다. 우리의 연구 결과는 몽골에서의 뉴캣슬병 최초 발생은 동북아시아 지역에서 유행하는 강독형 NDV의 유입에 의해서 이루어졌음을 말해 준다.

• Mycobiology
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• 제50권4호
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• pp.254-257
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• 2022

Wolfiporia cocos is a wood-decay brown rot fungus belonging to the family Polyporaceae. While the fungus grows, the sclerotium body of the strain, dubbed Bokryeong in Korean, is formed around the roots of conifer trees. The dried sclerotium has been widely used as a key component of many medicinal recipes in East Asia. Wolfiporia cocos strain KMCC03342 is the reference strain registered and maintained by the Korea Seed and Variety Service for commercial uses. Here, we present the first draft genome sequence of W. cocos KMCC03342 using a hybrid assembly technique combining both short- and long-read sequences. The genome has a total length of 55.5 Mb comprised of 343 contigs with N50 of 332 kb and 95.8% BUSCO completeness. The GC ratio was 52.2%. We predicted 14,296 protein-coding gene models based on ab initio gene prediction and evidence-based annotation procedure using RNAseq data. The annotated genome was predicted to have 19 terpene biosynthesis gene clusters, which was the same number as the previously sequenced W. cocos strain MD-104 genome but higher than Chinese W. cocos strains. The genome sequence and the predicted gene clusters allow us to study biosynthetic pathways for the active ingredients of W. cocos.