• 한국수정란이식학회지
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• 제25권2호
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• pp.127-131
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• 2010

The objective of this study was to determine the mRNA expression patterns of several putative imprinted genes in in vivo and in vitro fertilized, parthenogenetic, and cloned porcine preimplantation embryos. Both maternally (Dlk1, IGF2, Peg1/Mest and Ndn) and paternally (IGF2r, H19 and Xist) imprinted genes were selected. We have used reverse transcription polymerase chain reaction (RT-PCR) to investigate gene expression patterns in the porcine embryos. IGF2 transcripts were detected in the most of embryos. In nuclear transfer (NT), Peg1/MEST transcripts showed fluctuating pattern. Dlk1 was only expressed partially from the morula and blastocyst stage of NT embryos. Ndn gene expression was started somewhat early for in vivo embryos. However, the expressions of maternally imprinted genes were similar in all types of blastocysts (NT, in vivo and in vitro fertilized, and parthenogenetic embryos). The IGF2R gene expression level was somewhat irregular and varied among samples. However, for the majority samples of all types of embryos, IGF2R expression was diminished after one- to two-cell stages and reappeared at the morulae or blastocyst stage embryos. H19 gene was only expressed early in parthenogenetic and in vivo embryos. For NT embryos, H19 was only expressed in blastocysts. Xist expression was detected in all blastocysts with the earliest being in vivo 8-cell stage embryos and the last one being NT blastocysts. These putative imprinted genes appeared to have stage specific expression patterns with a fluctuating pattern for some genes (Peg/Mest, IGF2r, H19). These results suggest that stage specific presence of imprinted genes can affect the embryo implantation and fetal development.

• 한국정보과학회논문지:컴퓨팅의 실제 및 레터
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• 제11권2호
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• pp.133-148
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• 2005

단백질 구조에 대한 유사성과 특이성에 대한 이해는 단백질의 기능을 파악하는데 있어 중요한 역할을 하고 있기 때문에, 많은 단백질 구조를 비교하는 시스템이 개발되고 있다. 그러나 이러한 시스템들은 단백질 구조 비교를 위한 자신의 알고리즘에 맞게 PDB에서 제공하는 데이타를 가공해야 한다 더욱이 PDB 데이타베이스에 저장된 데이타가 증가함에 따라 대용량의 단백질 구조 데이타베이스를 대상으로 주어진 단백질과 유사한 부분구조를 찾는 시스템은 보다 많은 계산량이 필요하여진다. 본 논문에서는 XML 데이타베이스인 eXist를 이용하여 PSAML 문서를 제공하는 PSAML 데이타베이스에 기반을 둔 WS4E(A Web-Based Searching Substructures of Secondary Structure Elements) 단백질 구조 비교 시스템을 소개한다. PSAML(Protein Structure Abstraction Markup Language)은 XML기반의 단백질 구조 표현 기법으로서 단백질의 2차구조 구성요소와 그들 사이의 관계를 이용하여 단백질 구조를 정형화된 방법으로 기술한다. 구축된 PSAML 데이타베이스를 이용하여, WS4E는 PSAML로 표현된 단백질 구조에서 유사한 부분 구조를 찾는 웹서비스를 제공한다. 또한, PSAML 데이타베이스에서 비교 대상이 되는 단백질의 숫자를 감소시키기 위하여, 단백질 2차구조가 가지는 공간상의 정보를 이용하여 하나의 단백질 구조를 표현하는 기법인 topology string을 이용하였다.

• Genomics & Informatics
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• 제14권1호
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• pp.34-40
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• 2016

Due to advances in omics technologies, numerous genome-wide studies on human samples have been published, and most of the omics data with the associated clinical information are available in public repositories, such as Gene Expression Omnibus and ArrayExpress. While analyzing several public datasets, we observed that errors in gender information occur quite often in public datasets. When we analyzed the gender description and the methylation patterns of gender-specific probes (glucose-6-phosphate dehydrogenase [G6PD], ephrin-B1 [EFNB1], and testis specific protein, Y-linked 2 [TSPY2]) in 5,611 samples produced using Infinium 450K HumanMethylation arrays, we found that 19 samples from 7 datasets were erroneously described. We also analyzed 1,819 samples produced using the Affymetrix U133Plus2 array using several gender-specific genes (X (inactive)-specific transcript [XIST], eukaryotic translation initiation factor 1A, Y-linked [EIF1AY], and DEAD [Asp-Glu-Ala-Asp] box polypeptide 3, Y-linked [DDDX3Y]) and found that 40 samples from 3 datasets were erroneously described. We suggest that the users of public datasets should not expect that the data are error-free and, whenever possible, that they should check the consistency of the data.

• Reproductive and Developmental Biology
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• 제32권3호
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• pp.183-191
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• 2008

This study was conducted to investigate the development and gene expression in miniature pig nuclear transfer (mNT) embryos produced under different osmolarity culture conditions. Control group of mNT embryos was cultured in PZM-3 for 6 days. Treatment group of mNT embryos was cultured in modified PZM-3 with NaCl (mPZM-3, 320 mOsmol) for 2 days, and then cultured in PZM-3 (270 mOsmol) for 4 days. Blastocyst formation rate of the treatment group was significantly higher than the control and the apoptosis rate was significantly lower in treatment group. Bax-$\alpha$ and caspase-3 mRNA expression were significantly higher in the control than the treatment group. Also, the majority of imprinting genes were expressed aberrantly in in vitro produced mNT blastocysts compared to in vivo derived blastocyst H19 and Xist mRNA expression were significantly lower in the control than the treatment group or in vivo. IGF2 mRNA expression was significantly higher in the control than the treatment group or in vivo. IGF2r mRNA expression was significantly lower in the control. Methylation profiles of individual DNA strands in H19 upstream T-DMR sequences showed a similar methylation status between treatment group and in vivo. These results indicate that the modification of osmolarity in culture medium at early culture stage could provide more beneficial culture environments for mNT embryos.