• Nuclear Medicine and Molecular Imaging
• /
• 제41권4호
• /
• pp.299-308
• /
• 2007

Purpose: The aim of this study was to develop a bioinformatics software and to test it in serum samples of papillary thyroid cancer using mass spectrometry (SELDI-TOF-MS). Materials and Methods: Development of 'Protein analysis' software performing decision tree analysis was done by customizing C4.5. Sixty-one serum samples from 27 papillary thyroid cancer, 17 autoimmune thyroiditis, 17 controls were applied to 2 types of protein chips, CM10 (weak cation exchange) and IMAC3 (metal binding - Cu). Mass spectrometry was performed to reveal the protein expression profiles. Decision trees were generated using 'Protein analysis' software, and automatically detected biomarker candidates. Validation analysis was performed for CM10 chip by random sampling. Results: Decision tree software, which can perform training and validation from profiling data, was developed. For CM10 and IMAC3 chips, 23 of 113 and 8 of 41 protein peaks were significantly different among 3 groups (p<0.05), respectively. Decision tree correctly classified 3 groups with an error rate of 3.3% for CM10 and 2.0% for IMAC3, and 4 and 7 biomarker candidates were detected respectively. In 2 group comparisons, all cancer samples were correctly discriminated from non-cancer samples (error rate = 0%) for CM10 by single node and for IMAC3 by multiple nodes. Validation results from 5 test sets revealed SELDI-TOF-MS and decision tree correctly differentiated cancers from non-cancers (54/55, 98%), while predictability was moderate in 3 group classification (36/55, 65%). Conclusion: Our in-house software was able to successfully build decision trees and detect biomarker candidates, therefore it could be useful for biomarker discovery and clinical follow up of papillary thyroid cancer.

• Archives of Pharmacal Research
• /
• 제21권6호
• /
• pp.712-717
• /
• 1998

The complete nucleotide sequence of the cDNA clone encoding rat skeletal muscle myosin- binding protein H (MyBP-H) was determined and amino acid sequence was deduced from the nucleotide sequence (GenBank accession number AF077338). The full-length cDNA of 1782 base pairs(bp) contains a single open reading frame of 1454 bp encoding a rat MyBP-H protein of the predicted molecular mass 52.7kDa and includes the common consensus 1CA__TG' protein binding motif. The cDNA sequence of rat MyBP-H show 92%, 84% and 41% homology with those of mouse, human and chicken, respectively. The protein contains tandem internal motifs array (-FN III-Ig C2-FN III- Ig C2-) in the C-terminal region which resembles to the immunoglobulin superfamily C2 and fibronectin type III motifs. The amino acid sequence of the C-terminal Ig C2 was highly conserved among MyBPs family and other thick filament binding proteins, suggesting that the C-terminal Ig C2 might play an important role in its function. All proteins belonging to MyBP-H member contains `RKPS` sequence which is assumed to be cAMP- and cGMP-dependent protein kinase A phosphorylation site. Computer analysis of the primary sequence of rat MyBP-H predicted 11 protein kinase C (PKC)phosphorylation site, 7 casein kinase II (CK2) phosphorylation site and 4N-myristoylation site.

• Journal of Microbiology
• /
• 제42권4호
• /
• pp.292-298
• /
• 2004

This study reports, for the first time, the ivestigation of the distribution of Korean saxicolous lichens in the coastal rocks of U-do islet, which is known as an unpolluted zone in Jeju. More than thirty lichens were obtained and investigated from the coastal rocks frequently contacted by seawater. A molecular analysis using PCR amplification of the rRNA ITS regions revealed the coastal rock lichens could be placed into 8 families and 14 genera, Ramalinaceae (Bacidia, Ramalina), Physciaceae (Buellia, Dirinaria, Phaeophyscia, Physcia, Pyxine), Lecanoraceae (Candelaria, Lecanora), Parmeliaceae (Xan­thopannelia), Graphidaceae (Graphis), Pertusariaceae (Pertusaria), Rhizocarpaceae (Rhizocarpon), and Teloschistaceae (Caloplaca), showing a diversity of lichens, with foliose (flat leaf-like), crustose (crust­like), and fruticose (miniature shrub-like) life forms might be distributed in the coastal rocks. These findings suggested the possibility that the lichens identified in the present work might be resistant to a salty environment.

• Journal of Photoscience
• /
• 제9권2호
• /
• pp.436-438
• /
• 2002

Since solar radiation contains wavelength essential for photosynthesis accompanying with near-UV light, UV-B effects on biological parameters and acclimation mechanisms are influenced by photosynthetically active radiation (PAR). Therefore, to elucidate near-UV shielding mechanism in higher plants, we cultivated cauliflower under usual solar radiation and increased UV-B from fluorescent lamps, two- or three-fold excess over continuously estimated UV-B dose in PAR during daytime, using computer regulated systems. Increased UV-B radiation had little effect on growth expressed as fresh weigh and leaf area. Water soluble low molecular weight compounds showing absorption in near UV region were enhanced according to the irradiated UV-B dose. One of compounds in cauliflower leaves was identified as chlorogenic acid. This was found to have no near-UV photosenSitizerable activity and is known to have an ability to scavenge a wide species of active oxygen. Another pro-oxidant compound that generates superoxide anion radical under near-UV irradiation was not induced by increased UV-B during cultivation, and identified as lumazine, a degradation product from folic acid.

• Korean Journal of Materials Research
• /
• 제26권6호
• /
• pp.298-305
• /
• 2016

In this work, recent progress on graphene/metal oxide composites as advanced materials for $HgCl_2$ and $CO_2$ capture was investigated. Density Functional Theory calculations were used to understand the effects of temperature on the adsorption ability of $HgCl_2$ and water vapor on $CO_2$ adsorption on CaO (001) with reinforced carbon-based nanostructures using B3LYP functional. Understanding the mechanism by which mercury and $CO_2$ adsorb on graphene/CaO (g-CaO) is crucial to the design and fabrication of effective capture technologies. The results obtained from the optimized geometries and frequencies of the proposed cluster site structures predicted that with respect to molecular binding the system possesses unusually large $HgCl_2$ ($0.1-0.4HgCl_2g/g$ sorbent) and $CO_2$ ($0.2-0.6CO_2g/g$ sorbent) uptake capacities. The $HgCl_2$ and $CO_2$ were found to be stable on the surface as a result of the topology and a strong interaction with the g-CaO system; these results strongly suggest the potential of CaO-doped carbon materials for $HgCl_2$ and $CO_2$ capture applications, the functional gives reliable answers compared to available experimental data.

• Bulletin of the Korean Chemical Society
• /
• 제33권10호
• /
• pp.3423-3426
• /
• 2012

Dielectric measurement on binary mixtures of Allyl chloride (ALC) with 2-Pentanone (2-PE) and 2-Hexanone (2-HE) has been carried out over the entire concentration range using Time Domain Reflectometry (TDR) technique at various temperatures in microwave frequency range of 10 MHz to 10 GHz. The static dielectric constant, excess static dielectric constant (${\varepsilon}^E_S$), effective Kirkwood correlation factor ($g^{eff}$) of binary mixtures over entire concentration range were determined to study the effect of increasing alkyl group of ketones on hetero molecular interaction. It was found that magnitude of excess static dielectric constant of mixtures increases with increase of alky group of ketones. The study reveals that the dipole moment of Allyl chloride in mixture have antiparallelism tendency where as 2-pentanone and 2-hexanone have parallelism tendency. Excess static dielectric constant is also fitted to Redlich-Kister equation to get information about rates of multimers formation.

• Journal of Magnetics
• /
• 제15권2호
• /
• pp.61-63
• /
• 2010

We used $^1H$ nuclear magnetic resonance (NMR) to study the phase transitions and molecular dynamics in a characteristic ferroelectric liquid crystal with a carbon number n = 7, S-2-methylbutyl 4-n-heptyloxybiphenyl-4'-carboxylate (C7). The results were compared with those of our recent work on S-2-methylbutyl 4-n-octanoyloxybiphenyl-4'-carboxylate (C8), with a carbon number n = 8. While the recrystallization and isotropic phase transitions exhibited a first-order nature in the $^1H$ NMR spin-lattice and spin-spin relaxation measurements, a second-order nature was shown at the Sm-A - Sm-$C^*$ liquid crystalline phase transition. A soft-mode anomaly arising from the tilt angle amplitude fluctuation of the director, of which only a hint had been noticed in the C8 system, was manifested in the C7 system at this transition.

• Genomics & Informatics
• /
• 제12권1호
• /
• pp.2-11
• /
• 2014

After the initial enthusiasm of the human genome project, it became clear that without additional data pertaining to the epigenome, i.e., how the genome is marked at specific developmental periods, in different tissues, as well as across individuals and species-the promise of the genome sequencing project in understanding biology cannot be fulfilled. This realization prompted several large-scale efforts to map the epigenome, most notably the Encyclopedia of DNA Elements (ENCODE) project. While there is essentially a single genome in an individual, there are hundreds of epigenomes, corresponding to various types of epigenomic marks at different developmental times and in multiple tissue types. Unprecedented advances in next-generation sequencing (NGS) technologies, by virtue of low cost and high speeds that continue to improve at a rate beyond what is anticipated by Moore's law for computer hardware technologies, have revolutionized molecular biology and genetics research, and have in turn prompted innovative ways to reduce the problem of measuring cellular events involving DNA or RNA into a sequencing problem. In this article, we provide a brief overview of the epigenome, the various types of epigenomic data afforded by NGS, and some of the novel discoveries yielded by the epigenomics projects. We also provide ample references for the reader to get in-depth information on these topics.

• Journal of Microbiology
• /
• 제38권3호
• /
• pp.145-149
• /
• 2000

GroEL is a typical molecular chaperone. GroEL synthesis patterns at various culture temperatures in Escherichia coli were investigated in this study. No significant differences in the amount of GroEL produced from the chromosome were found at 30 and 37$^{\circ}C$. However, GroEL production increased 3.4-fold at 42$^{\circ}C$. GroEL synthesis was not transient but continuous at 42$^{\circ}C$, although most heat shock gene expression is known to be transient. To understand the role of the groEL structural gene, a groE promoter-lacZ fusion was constructed. Interestingly , while transcriptional fusion is not thermally inducible, it is inducible by ethanol, suggesting that the secondary structure of the groEL transcript is involved in thermal regulation of the groEL gene. Secondary structures of groE mRNA at 37 and 42$^{\circ}C$ were compared using the computer program RNAdraw. Distinct structures at the two temperatures were found, and these structures may be related to a high level of GroEL expression at 42$^{\circ}C$.

• Proceedings of the Korean Society for Cognitive Science Conference
• /
• 한국인지과학회 2005년도 춘계학술대회
• /
• pp.130-134
• /
• 2005

본 연구는 애너그램(anagram) 문제해결 과제에서 발생하는 제약들(영어 철자연쇄 집합의 출현 확률과 단어 내 위치 확률)을 동시에 병렬적으로 만족시키는 확률 모델 학습과정을 보인다. 애너그램에 관한 많은 선행연구들은 이 문제해결 과정이 단순히 기호처리적인 층위뿐만 아니라 하위기호적(subsymbolic) 층위에서의 상향식 처리로 인해 일어남을 밝혀왔고, 주로 영어 철자의 연쇄체의 확률값을 이용해왔다. 본 연구는 확률 라이브러리 모델(Probabilistic Library Model)을 통해 애너그램 문제해결이 한 번씩 끝날 때마다 철자 연쇄체의 출현 및 위치 분포 확률이 어떻게 유연한 변화를 갖는지에 집중한다. 하나의 문제를 풀고 나면 본 모델은 그 전 문제를 풀었을 때의 상태 패턴으로부터 변화를 보인다. 이러한 분포 변화를 통해 하위기호적 활동의 영향이 문제해결에 있어서 학습구조의 유연한 변화에 중요한 영향을 끼친다는 점을 확인했다.