• Advances in nano research
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• 제2권1호
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• pp.57-67
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• 2014

This article shows the coarsening behavior of nanoparticle multilayers during heat treatments which produce larger metallic nanostructures with varying shapes and sizes on glass slides. Nanoparticle multilayer films are initially constructed via the layer-by-layer self-assembly of small and monodispersed gold and/or palladium nanoparticles with different compositions (gold only, palladium only, or both gold and palladium) and assembly orders (compounding layers of gold layers over palladium layers or vice versa). Upon heating the slides at $600^{\circ}C$, the surface nanoparticles undergo coalescence becoming larger nanostructured metallic films. UV-Vis results show a clear reliance of the layering sequence on the optical properties of these metal films, which demonstrates an importance of the outmost (top) layers in each nanoparticle multilayer films. Topographic surface features show that the heat treatments of nanoparticle multilayer films result in the nucleation of nanoparticles and the formation of metallic cluster structures. The results confirm that different composition and layering sequence of nanoparticle multilayer films clearly affect the coalescence behavior of nanoparticles during heat treatments.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.83-85
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• 2000

A lot of microbial genome sequencing projects is being done in many genome centers around the world, since the first genome, Haemophilus influenzae, was sequenced in 1995. The deluge of microbial genome sequence data demands new and highly automatic data flow system in order for genome researchers to manage and analyze their own bulky sequence data from low-level to high-level. In such an aspect, we developed the automatic data management system for microbial genome projects, which consists mainly of local database, analysis programs, and user-friendly interface. We designed and implemented the local database for large-scale sequencing projects, which makes systematic and consistent data management and retrieval possible and is tightly coupled with analysis programs and web-based user interface, That is, parsing and storage of the results of analysis programs in local database is possible and user can retrieve the data in any level of data process by means of web-based graphical user interface. Contig assembly, homology search, and ORF prediction, which are essential in genome projects, make analysis programs in our system. All but Contig assembly program are open as public domain. These programs are connected with each other by means of a lot of utility programs. As a result, this system will maximize the efficiency in cost and time in genome research.

• 미생물학회지
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• 제35권2호
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• pp.121-127
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• 1999

염기서열 해독작업에서 각 핵산 단편을 조립하는 contig 구성문제에 활용이 가능한 computer program을 개발하였다. 본 프로그램은 국내에서 광범위하게 사용되고 있는 MS-Windows 운영체제의 개인용 컴퓨터에서 작동이 가능하며, GenBank, FASTA, ASCII 등과 같은 다양한 형태의 염기서열 자료를 입력할 수 있다. 두 단편에서 최대 유사도를 나타내는 부분을 정렬하는 작업에는 염기서열의 국부적 상동성을 계산하고 dynamic programming 알고리즘을 적용하는 방법을 이용하였다. 또한 사용하기 편리한 그래픽 방식의 인터페이스를 제공하여 초보자라도 손쉽게 조작할 수 있다는 장점을 갖는다. 본 프로그램의 성능을 검증하기 위하여 세균과 곰팡이로부터 해독된 16S rRNA 와 18S rRNA 유전자의 단편 염기서열을 재구성하는 작업에 프로그램을 사용하였을 때에 효율적인 작업이 가능하였다.

• Animal Systematics, Evolution and Diversity
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• 제36권4호
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• pp.336-346
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• 2020

Mitochondrial genome is an important molecule for systematic and evolutionary studies in metazoans. The development of next-generation sequencing (NGS) technique has rapidly increased the number of mitogenome sequences. The process of generating mitochondrial genome based on NGS includes different steps, from DNA preparation, sequencing, assembly, and annotation. Despite the effort to improve sequencing, assembly, and annotation methods of mitogenome, the low quality and/or quantity sequence in the final map can still be generated through the work. Therefore, it is necessary to check and curate mitochondrial genome sequence after annotation for proofreading and feedback. In this study, we introduce the pipeline for sequencing and curation for mitogenome based on NGS. For this purpose, two mitogenome sequences of Dermatobranchus otome were sequenced by Illumina Miseq system with different amount of raw read data. Generated reads were targeted for assembly and annotation with commonly used programs. As abnormal repeat regions present in the mitogenomes after annotation, primers covering these regions were designed and conventional PCR followed by Sanger sequencing were performed to curate the mitogenome sequences. The obtained sequences were used to replace the abnormal region. Following the replacement, each mitochondrial genome was compared with the other as well as the sequences of close species available on the Genbank for confirmation. After curation, two mitogenomes of D. otome showed a typically circular molecule with 14,559 bp in size and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes. The phylogenetic tree revealed a close relationship between D. otome and Tritonia diomea. The finding of this study indicated the importance of caution and curation for the generation of mitogenome from NGS.

• The Plant Pathology Journal
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• 제37권2호
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• pp.162-172
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• 2021

Soybean mosaic virus (SMV) is the predominant viral pathogen that affects the yield and quality of soybean. The natural host range for SMV is very narrow, and generally limited to Leguminosae. However, we found that SMV can naturally infect Pinellia ternata and Atractylodes macrocephala. In order to clarify the molecular mechanisms underlying the cross-family infection of SMV, we used double-stranded RNA extraction, rapid amplification of cDNA ends polymerase chain reaction and Gibson assembly techniques to carry out SMV full-length genome amplification from susceptible soybeans and constructed an infectious cDNA clone for SMV. The genome of the SMV Shanxi isolate (SMV-SX) consists of 9,587 nt and encodes a polyprotein consisting of 3,067 aa. SMV-SX and SMV-XFQ008 had the highest nucleotide and amino acid sequence identities of 97.03% and 98.50%, respectively. A phylogenetic tree indicated that SMV-SX and SMV-XFQ018 were clustered together, sharing the closest relationship. We then constructed a pSMV-SX infectious cDNA clone by Gibson assembly technology and used this clone to inoculate soybean and Ailanthus altissima; the symptoms of these hosts were similar to those caused by the virus isolated from natural infected plant tissue. This method of construction not only makes up for the time-consuming and laborious defect of traditional methods used to construct infectious cDNA clones, but also avoids the toxicity of the Potyvirus special sequence to Escherichia coli, thus providing a useful cloning strategy for the construction of infectious cDNA clones for other viruses and laying down a foundation for the further investigation of SMV cross-family infection mechanisms.

• 한국경영과학회:학술대회논문집
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• 한국경영과학회 2000년도 추계학술대회 및 정기총회
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• pp.157-160
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• 2000

This study is concerned with how to optimize the Input sequence of product models with sequence -dependent setup time in Mixed-Model Assembly Line (MMAL) using conveyor system. Usually MMAL consists of a number of stations linked by conveyor belt and each station has a work zone limited by upstream and downstream boundaries. To avoid improper interference between operators in the adjacent stations and excess of machine moving range, operators are forced to complete their operations within their predetermined work zone. In this study, our goal is to determine sequence of models for minimizing the total work unfinished within their work zone. A generalized formulation of the product sequencing problem in MMAL is presented and we developed an optimal procedure using Branch & Bound. Also we developed a heuristic procedure using local search.

• 한국정밀공학회:학술대회논문집
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• 한국정밀공학회 2005년도 추계학술대회 논문집
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• pp.814-817
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• 2005

Today recycling has been one of the most important Issues In industry as it is required to save the limited amount of natural resources and to keep the environment green. In spite of many efforts to increase recycling rate in industry, however, the practical solutions are very limited. The difficulties are caused by the existence of many parts made of diverse materials and their inevitably complicated assembly structures to satisfy different needs. This paper represents a study on the disassembly sequence generator system for parts recycling. With disassembly costs and revenues, the optimum disassembly sequence can be found with a linear programming.

• 항공우주기술
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• 제7권2호
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• pp.144-150
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• 2008

보기는 특별한 지상이송장치로서 총조립 발사체를 단별조립동에서 발사 장까지 운반하는 수단뿐만 아니라 발사운용을 위한 주요한 도구로서 사용된다. 이런 보기의 다양한 역할로 인하여, 요구되어 지는 기술적 요건들은 복잡하다 특히 발사 운용 부분은 보기뿐만 아니라 여러 가지 지상 장비들이 함께 얽혀있고, 전체적인 발사운용에 대한 이해가 없이는 그 기술 요구조건을 정립하기도 힘들다. 이를 위해 이 문건은 보기에 의한 발사운용과정을 정리하고, 이를 바탕으로 보기의 기술적 요건을 정리하였다.

• Macromolecular Research
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• 제17권8호
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• pp.597-602
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• 2009

Although the existing design principle of full-sequence ionic complement is convenient for the development of peptides, it greatly constrains the exploration of peptides with other possible assembly mechanisms and different yet essential functions. Herein, a novel designed half-sequence ionic complementary peptide (referred to as P9), AC-Pro-Ser-Phe-Asn-Phe-Lys-Phe-Glu-Pro-$NH_2$, is reported. When transferred from pure water to sodium chloride solution, P9 underwent a dramatic morphological transformation from globular aggregations to nanofibers. Moreover, the rheological experiment showed that the P9 could form a hydrogel with a storage modulus of about 30 Pa even at very low peptide concentration (0.5% (wt/vol)). The P9 hydrogel formed in salt solution could recover in a period of about 1,800 sec, which is faster than that in the pure water. The data suggestcd that the half-sequence, ionic complementary peptide might be worthy of further research for its special properties.

• 생명과학회지
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• 제24권11호
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• pp.1187-1192
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• 2014

고추는 한국, 중국, 멕시코를 포함한 온대 및 아열대 지역을 중심으로 전세계적으로 전형적인 향신료로 식용되고 있으며 그 생산량 및 사용량은 해마다 증가하는 추세에 있다. 고추역병균인 Phytophthora capsici는 고추의 생산에 있어, 질적, 양적으로 많은 피해를 야기하는 식물병원균으로 알려져 있다. 난균강에 속하는 이 병원균은 기주식물의 뿌리, 줄기, 잎과 함께 과실에 이르기까지 식물체 전체를 가해한다. 고추역병의 발병을 분자수중에서 이해하기 위해서는, 발병과정에서 발현되는 유전자에 대한 연구분석이 필수적이며, 이를 위해 최근 개발되어 응용되고 있는 발현서열표지(expressed sequence tags, ESTs)의 분석을 시도하였다. 고추역병균을 접종한후 3일째 발병초기의 고추잎으로부터 추출한 total RNA를 이용하여 고추-고추역병균 발병초기 cDNA library를 구축하였다. 이 cDNA library에서 무작위로 선발된 5,760 clone에 대하여 말단 염기서열 분석을 수행하여 5,148개의 양질의 염기서열을 확보하고 contig assembly에 적용한 결과, 2,990개의 unigenes을 확보하였다. 이들 2,990개의 unigenes에 대한 BLASTX를 이용한 상동성 분석결과, 2,409개가 기존에 알려진 서열과 matching을 보였으며, 이중 606개가 기능적으로 구분되었다.