• 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.

• 생약학회지
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• 제50권3호
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• pp.232-238
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• 2019

Phytochemical study of Ganoderma lucidum (Polyporaceae) let to the isolation of five lanostane triterpenoid (1-5), along with two nitrogen derived phenolic compounds, N-phenylethylformamide (6) and N-acetylphenethylamine (7). The structures of the compounds were determined by 1D and 2D NMR, and MS experiments, as well as by comparison of their data with published values. Compounds 6 and 7 were isolated for the first time from the genus Ganoderma and this species. All the compounds were evaluated for cancer chemopreventive potential based on their ability to inhibit nitric oxide (NO) production induced by lipopolysaccharide (LPS) in mouse macrophage RAW 264.7 cells in vitro. Among the isolates, compounds 2 and 3 showed moderate inhibitory activity against NO production.

• Genomics & Informatics
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• 제4권1호
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• pp.1-10
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• 2006

Epigenetic alterations are common features of human solid tumors, though global DNA methylation has been difficult to assess. Restriction Landmark Genomic Scanning (RLGS) is one of technology to examine epigenetic alterations at several thousand Notl sites of promoter regions in tumor genome. To assess sequence information for Notl sequences in RLGS gel, we cloned 1,161 unique Notl-linked clones, compromising about 60% of the spots in the soluble region of RLGS profile, and performed BLAT searches on the UCSC genome server, May 2004 Freeze. 1,023 (88%) unique sequences were matched to the CpG islands of human genome showing a large bias of RLGS toward identifying potential genes or CpG islands. The cloned Notl-loci had a high frequency (71%) of occurrence within CpG islands near the 5' ends of known genes rather than within CpG islands near the 3' ends or intragenic regions, making RLGS a potent tool for the identification of gene-associated methylation events. By mixing RLGS gels with all Notl-linked clones, we addressed 151 Notl sequences onto a standard RLGS gel and compared them with previous reports from several types of tumors. We hope our sequence information will be useful to identify novel epigenetic targets in any types of tumor genome.

• 한국해양바이오학회지
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• 제1권3호
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• pp.213-217
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• 2006

본 연구는 황백에 함유되어 있는 주요 화합물인 berberine, palmatine, limonin 및 rutaecarpine의 CYP2D6 및 p-glycoprotein 활성에 대한 저해정도를 탐색함으로써, 황백을 다른 양약과 병용시 약물상호작용을 유발할 수 있는 가능성을 평가하고자 하였다. 인체 간 마이크로좀 시료에 CYP2D6 동효소의 기질약물인 dextromethorphan과 NADPH 재생성계 및 저해제 ($200{\mu}M$)를 첨가한 후 반응시켜 생성된 대사물을 LC/MS/MS를 이용하여 정량하여 CYP2D6 동효소 활성의 변화를 평가하였다. 또한 약물수송단백인 p-glycoprotein의 활성은 L-MDR1 세포주를 이용한 calcein AM 축적 실험을 통하여 평가하였다. 그 결과 식물 알카로이드인 berberine에서 강력한 CYP2D6 활성 저해능을 관찰하였으며, 저해 효과는 농도 의존적으로 증가하였으며, mechanism-based 저해 기전을 나타내었다. 그러나 limonine과 rutaecarpine은 CYP2D6 저해 활성을 보이지 않았고, p-glycoprotein 기능에 대해서는 평가한 어떤 화합물도 저해 활성을 나타내지 않았다. 황백의 주요 성분인 berberine의 CYP2D6 활성 저해능을 고려할 때, 황백을 CYP2D6 기질약제와 병용시 약물상호작용을 유발할 가능성을 보여준다. 이러한 황백의 CYP2D6를 매개로한 임상적인 약물상호작용 가능성은 임상시험을 통하여 추가적인 검정이 필요할 것으로 사료된다.

• BMB Reports
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• 제53권6호
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• pp.299-310
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• 2020

Chronic liver disease progresses through several stages, fatty liver, steatohepatitis, cirrhosis, and eventually, it leads to hepatocellular carcinoma (HCC) over a long period of time. Since a large proportion of patients with HCC are accompanied by cirrhosis, it is considered to be an important factor in the diagnosis of liver cancer. This is because cirrhosis leads to an irreversible harmful effect, but the early stages of chronic liver disease could be reversed to a healthy state. Therefore, the discovery of biomarkers that could identify the early stages of chronic liver disease is important to prevent serious liver damage. Biomarker discovery at liver cancer and cirrhosis has enhanced the development of sequencing technology. Next generation sequencing (NGS) is one of the representative technical innovations in the biological field in the recent decades and it is the most important thing to design for research on what type of sequencing methods are suitable and how to handle the analysis steps for data integration. In this review, we comprehensively summarized NGS techniques for identifying genome, transcriptome, DNA methylome and 3D/4D chromatin structure, and introduced framework of processing data set and integrating multi-omics data for uncovering biomarkers.

• Parasites, Hosts and Diseases
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• 제52권1호
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• pp.99-103
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• 2014

Mitochondrial genome sequence of malaria parasites has served as a potential marker for inferring evolutionary history of the Plasmodium genus. In Plasmodium falciparum, the mitochondrial genome sequences from around the globe have provided important evolutionary understanding, but no Indian sequence has yet been utilized. We have sequenced the whole mitochondrial genome of a single P. falciparum field isolate from India using novel primers and compared with the 3D7 reference sequence and 1 previously reported Indian sequence. While the 2 Indian sequences were highly divergent from each other, the presently sequenced isolate was highly similar to the reference 3D7 strain.

• Journal of Plant Biotechnology
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• 제30권3호
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• pp.251-255
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• 2003

An efficient system for in vitro bulblet formation of Lilium oriental hybrids(cvs). Casa Blanca and Siberia is described. Transverse thin cell layer(tTCL)(1mm thick) explants of 'Casa Blanca' formed bulblets at a frequency of 97.7％ when cultured on Murashige and Skoog (MS) medium supplemented with 1mg/L 2,4 dichlorophenoxyacetic acid(2,4-D) (On average 15.6 bulblets were formed per explant). The frequency of bulblet formation was drastically reduced when the explant ghickness was thinner than 1 mm. Explants from the outermost layer of bulb scale produced greater frequency of bulblet formation than middle or innermost layer. Among auxins supplemented to culture medium at 1 mg/L, 2,4-D led to greater frequency of bulblet formation on explants than dicamba, picamba, or phenylacetic acid(PAA). tTCL explants from the middle region of the outermost layer bulb scale yielded greater frequency of bulblet formation than the upper or lower region. tTCL stem explants of 'Siberia' formed bulblets at a frequency of 95.3% when cultured on MS medium with 1 mg/L 2,4-D(On average 9.1 bulblets were formed per explant). The system estabilished in this study will be useful for in vitro rapid propagation and genetic transformation of Lilium Oriental hybrids.

• Reproductive and Developmental Biology
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• 제37권4호
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• pp.225-232
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• 2013

Satellite cells were derived from muscular tissue in postnatal pig. Satellite cell is an important to growth and development in animal tissues or organs. However, the progress underlying induced differentiation is not clear. The aim of this study was to evaluate the morphologic and the transcriptome changes in porcine satellite cell (PSC) treated with insulin, rosiglitazone, or dexamethasone respectively. PSC was obtained from postnatal muscle tissue. In study 1, for study the effect of insulin and FBS on the differentiated satellite cells, cells were cultured at absence or presence of insulin treated with FBS. Total RNA was extracted for determining the expression levels of myogenic PAX3, PAX7, Myf5, MyoD, and myogenin genes by real-time PCR. Myogenic genes decreased expression levels of mRNA in treated with insulin. In study 2, in order to clarify the relationship between rosiglitazone and lipid in differentiated satellite cells, we further examined the effect of FBS on lipid accumulation in the presence or absence of the rosiglitazone and lipid. Significant differences were observed between rosiglitazone and lipid by FBS. The mRNA of FABP4 and $PPAR{\gamma}$ increased in rosiglitazone treatment. In study 3, we examined the effect of dexamethasone on osteogenic differentiation in PSC. The mRNA was increased osteoblasotgenic ALP and ON genes treated with dexamethasone in 2% FBS. Dexamethasone induces osteoblastogenesis in differentiated PSC. Taken together, in differentiated PSCs, FABP4 and $PPAR{\gamma}$ increased to rosiglitazone. Whereas, no differences to FBS and lipid. These results were not comparable with previous reports. Our results suggest that adipogenic, myogenic, and osteoblastogenic could be isolated from porcine skeletal muscle, and identify culture conditions which optimize proliferation and differentiation formation of PSC.

• Journal of Microbiology and Biotechnology
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• 제17권3호
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• pp.543-545
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• 2007

4-Hydroxy-3-(3'-methyl-2'-butenyl)-benzoic acid (HMBA) was previously isolated from Curvularia sp. KF119 as a cell-cycle inhibitor. However, the present study used a novel and practical synthetic method to prepare a large quantity of HMBA. The synthetic HMBA was found to inhibit the cell-cycle progression of HeLa cells with a comparable potency to the natural fungal metabolite. The inhibition of the cell-cycle progression by the synthetic HMBA involved both the activation of $p21^{WAF1}$ and the inhibition of cyclin D1 expression in the cells. Consequently, this new synthetic procedure provides an easy and convenient way to produce or manipulate the original fungal metabolite.

• Plant Biotechnology Reports
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• 제3권4호
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• pp.309-315
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• 2009

Molecular markers developed from the flanking sequences of two cytoplasmic male sterility (CMS)-associated genes, orf456 and ${\Psi}atp6-2$, have been used for marker-assisted selection of CMS in pepper. However, in practice, the presence of orf456 and ${\Psi}atp6-2$ at substoichiometric levels even in maintainer lines hampers reliable selection of plants containing the CMS gene. In this study, we developed a novel CMS-specific molecular marker, accD-U, for reliable determination of CMS lines in pepper, and used the newly and previously developed markers to determine the cytoplasm types of pepper breeding lines and germplasms. This marker was developed from a deletion in a chloroplast-derived sequence in the mitochondrial genome of a CMS pepper line. CMS pepper lines could be unambiguously determined by presence or absence of the accD-U marker band. Application of orf456, ${\Psi}atp6-2$and accD-U to various pepper breeding lines and germplasms revealed that accD-U is the most reliable CMS selection marker. A wide distribution of orf456, but not ${\Psi}atp6-2$, in germplasms suggests that the pepper cytoplasm containing both orf456 and ${\Psi}atp6-2$ has been selected as CMS cytoplasm from cytoplasm containing only orf456. Furthermore, factors other than orf456 may be required for the regulation of male sterility in pepper.