• Genomics & Informatics
• /
• 제19권3호
• /
• pp.27.1-27.4
• /
• 2021

Due to the rapid evolution of high-throughput technologies, a tremendous amount of data is being produced in the biological domain, which poses a challenging task for information extraction and natural language understanding. Biological named entity recognition (NER) and named entity normalisation (NEN) are two common tasks aiming at identifying and linking biologically important entities such as genes or gene products mentioned in the literature to biological databases. In this paper, we present an updated version of OryzaGP, a gene and protein dataset for rice species created to help natural language processing (NLP) tools in processing NER and NEN tasks. To create the dataset, we selected more than 15,000 abstracts associated with articles previously curated for rice genes. We developed four dictionaries of gene and protein names associated with database identifiers. We used these dictionaries to annotate the dataset. We also annotated the dataset using pretrained NLP models. Finally, we analysed the annotation results and discussed how to improve OryzaGP.

• 한국생물공학회:학술대회논문집
• /
• 한국생물공학회 2005년도 생물공학의 동향(XVI)
• /
• pp.515-515
• /
• 2005

• 한국가금학회지
• /
• 제32권4호
• /
• pp.239-244
• /
• 2005

Uncoupling protein(UCP)은 갈색 지방세포에서 특이적으로 발현하고 있으며 복잡한 세포의 열 생산 작용에 관여한다고 알려져 있다. 본 연구는 한국 재래 닭 집단의 UCP 유전자 내에 존재하는 SNP를 검출하였다. 한국 재래 닭 집단의 UCP유전자 exon 3지역의 염기서열 분석 결과 1316 bp에서 T염기가 C염기로 치환되어짐을 확인하였다. T+11316C 지역의 PCR-RFLP 분석을 위해 제한효소 Afl III를 사용하였다. 한국 재래닭 집단내 유전자형 빈도는 TT가 0.7875, TC가 0.1875 그리고 CC가 0.025로 검출되었으며 대립유전자의 빈도는 T가 0.881 그리고 C가 0.119로 나타났다. 또한 검출된 SNP가 경제형질에 미치는 영향을 분석한 결과 한국 재래 닭 집단의 T/T 유전자형과 C/C유전자형에서 일당 산란율에서 통계적으로 유의한 차이가 있음을 확인하였다. 본 연구의 결과는 향후 더 많은 UCP 유전자와 관련된 연구와 한국 재래 닭의 육종 전략에 도움이 될 것으로 사료된다.

• Asian Pacific Journal of Cancer Prevention
• /
• 제16권13호
• /
• pp.5311-5317
• /
• 2015

Cigarette smoke derivatives like NNK (4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone) and NNAL (4-(methylnitrosamino)-1-(3-pyridyl)-1-butan-1-ol) are well-known carcinogens. We analyzed the interaction of enzymes involved in the NER (nucleotide excision repair) pathway with ligands (NNK and NNAL). Binding was characterized for the enzymes sharing equivalent or better interaction as compared to +Ve control. The highest obtained docking energy between NNK and enzymes RAD23A, CCNH, CDK7, and CETN2 were -7.13 kcal/mol, -7.27 kcal/mol, -8.05 kcal/mol and -7.58 kcal/mol respectively. Similarly the highest obtained docking energy between NNAL and enzymes RAD23A, CCNH, CDK7, and CETN2 were -7.46 kcal/mol, -7.94 kcal/mol, -7.83 kcal/mol and -7.67 kcal/mol respectively. In order to find out the effect of NNK and NNAL on enzymes involved in the NER pathway applying protein-protein interaction and protein-complex (i.e. enzymes docked with NNK/NNAL) interaction analysis. It was found that carcinogens are well capable to reduce the normal functioning of genes like RAD23A (HR23A), CCNH, CDK7 and CETN2. In silico analysis indicated loss of functions of these genes and their corresponding enzymes, which possibly might be a cause for alteration of DNA repair pathways leading to damage buildup and finally contributing to cancer formation.

• Asian-Australasian Journal of Animal Sciences
• /
• 제19권8호
• /
• pp.1065-1070
• /
• 2006

The avian uncoupling protein (avUCP) is a member of the mitochondrial transporter superfamily that uncouples proton entry in the mitochondrial matrix from ATP synthesis. The sequencing analysis method was used to identify nucleotide polymorphisms within the avUCP gene in Korean native chicken (KNC). This study identified ten single nucleotide polymorphisms (SNPs) in the avUCP gene. We analyzed the SNPs of the avUCP gene to investigate whether polymorphism in the gene might be responsible for quantitative variations in economic traits in KNC. Three significant polymorphic sites for economic traits were avUCP C+282T (mean body weight, p<0.05), avUCP C+433T (daily percent lay, p<0.05), and avUCP T+1316C (daily percent lay, p<0.05). The frequency of each SNP was 0.125 (C+282T in avUCP gene exon 1 region), 0.150 (C+433T in avUCP gene intron 1 region), and 0.15 (T+1316C in avUCP gene exon 3 region), respectively. Among the identified SNPs, one pair of SNPs (genotype CC, C+282T and TT, avUCP C+433T) showed the highest daily percent lay (p<0.05) and mean body weight (p<0.05) and the frequency was 0.067. This study of the avUCP gene could be useful for genetic studies of this gene and selection on economic traits for KNC.

• 한국자기공명학회논문지
• /
• 제10권2호
• /
• pp.155-162
• /
• 2006

Angiogenin is unique among angiogenic molecules in that it is a member of the pancreatic ribonuclease superfamily and, in fact, is a ribonucleolytic enzyme. Its enzymatic activity is extremely weak compared to that of the digestive RNases but is critical for its capacity to induce neovascularization. In this study, we completed the backbone resonance assignment of bovine angiogenin using triple resonance NMR experiments of $^{15}N\;and/or\;^{13}C$ isotope labeled protein and investigated the chemical shift variation upon binding with inhibitor phosphate ion and determine the phosphate binding site.

• BMB Reports
• /
• 제46권12호
• /
• pp.594-599
• /
• 2013

The anti-inflammatory activity of eriodictyol and its mode of action were investigated. Eriodictyol suppressed tumor necrosis factor (mTNF)-${\alpha}$, inducible nitric oxide synthase (miNOS), interleukin (mIL)-6, macrophage inflammatory protein (mMIP)-1, and mMIP-2 cytokine release in LPS-stimulated macrophages. We found that the anti-inflammatory cascade of eriodictyol is mediated through the Toll-like Receptor (TLR)4/CD14, p38 mitogen-activated protein kinases (MAPK), extracellular-signal-regulated kinase (ERK), Jun-N terminal kinase (JNK), and cyclooxygenase (COX)-2 pathway. Fluorescence quenching and saturation-transfer difference (STD) NMR experiments showed that eriodictyol exhibits good binding affinity to JNK, $8.79{\times}10^5M^{-1}$. Based on a docking study, we propose a model of eriodictyol and JNK binding, in which eriodictyol forms 3 hydrogen bonds with the side chains of Lys55, Met111, and Asp169 in JNK, and in which the hydroxyl groups of the B ring play key roles in binding interactions with JNK. Therefore, eriodictyol may be a potent anti-inflammatory inhibitor of JNK.

• Bulletin of the Korean Chemical Society
• /
• 제29권8호
• /
• pp.1479-1484
• /
• 2008

Protein tyrosine phosphatase (PTP) 1B is the superfamily of PTPs and a negative regulator of multiple receptor tyrosine kinases (RTKs). Inhibition of protein tyrosine phosphatase 1B (PTP1B) has been proposed as a strategy for the treatment of type 2 diabetes and obesity. Recently, it has been reported that amentoflavone, a biflavonoid extracted from Selaginella tamariscina, inhibited PTP1B. In the present study, docking model between amentoflavone and PTP1B was determined using automated docking study. Based on this docking model and the interactions between the known inhibitors and PTP1B, we determined multiple pharmacophore maps which consisted of five features, two hydrogen bonding acceptors, two hydrogen bonding donors, and one lipophilic. Using receptor-oriented pharmacophore-based in silico screening, we searched the biflavonoid database including 40 naturally occurring biflavonoids. From these results, it can be proposed that two biflavonoids, sumaflavone and tetrahydroamentoflavone can be potent allosteric inhibitors, and the linkage at 5',8''-position of two flavones and a hydroxyl group at 4'-position are the critical factors for their allosteric inhibition. This study will be helpful to understand the mechanism of allosteric inhibition of PTP1B by biflavonoids and give insights to develop potent inhibitors of PTP1B.

• Bulletin of the Korean Chemical Society
• /
• 제32권5호
• /
• pp.1645-1649
• /
• 2011

[ ${\beta}$ ]Ketoacyl acyl carrier protein synthase I (KAS I) is involved in the elongation of unsaturated fatty acids in bacterial fatty acid synthesis and a therapeutic target of designing novel antibiotics. In this study, we performed receptor-oriented pharmacophore-based in silico screening of E. coli KAS I (ecKAS I) with the aim of identifying novel inhibitors. We determined one pharmacophore map and selected 8 compounds as candidates ecKAS I inhibitors. We discovered one antimicrobial compound, YKAe1008, N-(3-pyridinyl) hexanamide, displaying minimal inhibitory concentration (MIC) values in the range of 128-256 ${\mu}g/mL$ against MRSA and VREF. YKAe1008 was subsequently assessed for binding to ecKAS I using saturation-transfer difference NMR spectroscopy. Further optimization of this compound will be carried out to improve its antimicrobial activity and membrane permeability against bacterial cell membrane.

• Journal of Microbiology and Biotechnology
• /
• 제19권12호
• /
• pp.1612-1616
• /
• 2009

Isoflavonoids are a class of phytoestrogens. Isoflavonone synthase (IFS) is responsible for the conversion of naringenin to genistein. IFS is a cytochrome P450 (CYP), and requires cytochrome P450 reductase (CPR) for its activity. Additionally, the majority of cytochrome P450s harbor a membrane binding domain, making them difficult to express in Escherichia coli. In order to resolve these issues, we constructed an inframe fusion of the IFS from red clover (RCIFS) and CPR from rice (RCPR) after removing the membrane binding domain from RCIFS and RCPR. The resultant fusion gene, RCIFS-RCPR, was expressed in E. coli. The conversion of naringenin into genistein was confirmed using this E. coli transformant. Following the optimization of the medium and cell density for biotransformation, $60\;{\mu}M$ of genistein could be generated from $80\;{\mu}M$ of naringenin. This fusion protein approach may be applicable to the expression of other P450s in E. coli.