• Proceedings of the Korea Information Processing Society Conference
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• 2012.11a
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• pp.1326-1329
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• 2012

전사체(transcript)는 유전자로부터 전사된 DNA 시퀀스 코드를 말한다. 전사체(transcript)의 발현된 형태에 따라 생성되는 단백질의 형태 역시 달라지므로 전사체 모델의 형태는 중요한 의미를 가지며 특정 위치의 전사체가 정상과 다르게 모델이 변할 경우 심각한 경우에는 유전자 질병에 노출될 수 있다. 현재 실험체에 대한 전사체 모형은 SpliceGrapher, Cufflinks와 같은 상용화된 도구들을 사용하여 얻을 수 있다. 하지만 이런 도구 간의 결과 값 및 어노테이션 정보와 결과 값 간의 유사도 비교를 위한 방법론은 현재 알려진 바 없다. 대신 전사체 비교를 위해 모형 간의 차이를 눈으로 하나씩 비교하거나 전사체 위치를 이용한 산수 값을 이용한다. 본 논문에서는 전사체 모형 간의 유사도를 비교하기 위한 방법론을 제시하고 Homo sapiens grch37 어노테이션 파일과 SRR387514 실험 데이터 간의 유사도를 제시한 방법론을 이용하여 측정한 결과 값을 분석하였다.

• Proceedings of the Korea Information Processing Society Conference
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• 2012.11a
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• pp.1340-1343
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• 2012

정보의 시각화는 추상적 정보를 직관적으로 이해하기 쉽도록 시각적으로 명확하게 표현하는 방법을 말한다. 대용량의 바이오 데이터를 다루는 생물정보학(bioinformatics) 분야에서는 컴퓨터의 높은 성능을 활용하여 수많은 유전학적 데이터들을 분석하고 있다. 다양한 생물정보학 실험에서 전사체는 특정한 조건에서 발현된 RNA의 총합을 말한다. 분석된 전사체 정보는 텍스트형태로 제공이 되는데 이를 사용자가 수작업으로 비교하는 데에는 한계가 있다. 따라서 분석된 전사체 정보를 효과적으로 인지할 수 있도록 시각화하는 연구들이 진행되고 있다. 본 논문에서는 그래프 라이브러리인 yFile을 활용하여 추정된 전사체를 실시간으로 시각화하여 제공하는 방법을 제안한다. GTF파일을 입력받아서 데이터베이스에 저장하고 이 정보를 이용하여 그래프를 생성한다. 실험 결과는 전사체를 시각화 하는 방법을 통하여 다양한 전사체 정보를 알아 낼 수 있고, 최종적으로는 novel gene을 찾는 것이 가능할 것으로 기대한다.

• Proceedings of the Korean Information Science Society Conference
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• 2012.06c
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• pp.113-115
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• 2012

전사체(transcriptome) 분석이란 주어진 조건 하에서 현재 세포 내에 발현된 모든 트랜스크립트의 종류와 양을 밝히는 것을 의미하며, 분석 결과는 질병 관련성/유전적 요인 규명 등의 연구에 직접 활용한다. 우리는 선행 연구에서 RNA-Seq 데이터를 이용하여 선택 스플라이싱 과정에 의하여 생성되는 모든 트랜스크립트의 유형을 분류/추출하는 새로운 방법론을 제안한 바 있다. 그 후속 연구로서 본 연구에서는 시간/공간 효율적인 알고리즘 구현을 위한 최적화 방법론을 제안하고, 실용화를 위한 전사체 분석 도구 개발에 대하여 논한다. 개발된 전사체 분석 도구에서는 기존의 분석 도구와 달리 RNA-Seq 데이터의 단계적 분석 결과를 시각적 뷰어를 통하여 검색 가능하며, 이들 기능은 복잡한 전사체 분석 결과의 이해와 타당성 검증에 활용한다.

• Journal of Life Science
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• v.21 no.3
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• pp.459-463
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• 2011

The genome of the rhesus monkey has diverged as an average sequence identity of ~93%. The rhesus monkey has been widely used as a non-human primate in the field of biomedical and evolutional research. Insertion of transposable elements (TEs) induced several events such as transcriptional diversity and different expression in host genes. In this study, 112 transcripts were identified from a full-length cDNA library of brain tissues of the rhesus monkey. One transcript (R54) showed a different expression pattern between human and rhesus monkey tissues. This phenomenon can be an explanation that R54 transcript was acquired by splicing a donor site derived from exonization of the L2A element. Therefore, integration of TEs during primate radiation could contribute to transcriptional diversity and gene regulation.

• Proceedings of the Korean Institute of Surface Engineering Conference
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• 2014.11a
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• pp.153-154
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• 2014

전사 방식은 금속 패턴을 다른 기판에 전사시키는 방법으로, 대면적 디스플레이에 응용하기 위해 나노 사이즈 패턴을 반복적으로 전사하는 새로운 공정을 개발하였다. 나노선 임베드 구조체와 전해 도금 방식을 이용하여 나노선 네트워크 구조체를 반복적으로 이종 기판에 전사시키는데 성공하였으며, 기존의 전사 방식인 건식 방식에 비해 공정 속도를 높이고 전사되는 패턴의 사이즈를 효과적으로 낮추는 것을 확인하였다.

• Journal of Plant Biotechnology
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• v.46 no.3
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• pp.189-204
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• 2019

In this study, we analyzed the changes in glucosinolate content and gene expression in TO1000DH3 and Early big seedling upon methyl jasmonate (MeJA) treatment. Analysis of glucosinolate contents after MeJA treatment at $200{\mu}M$ concentration showed that the total glucosinolate content increased by 1.3-1.5 fold in TO1000DH3 and 1.3-3.8 fold in Early big compared to those before treatment. Aliphatic glucosinolates, progoitrin and gluconapin, were detected only in TO1000DH3, and the changes in the content of neoglucobrassicin were the greatest at 48 hours after MeJA treatment in TO1000DH3 and Early big. The transcriptomic analysis showed that transcripts involved in stress or defense reactions, or those related to growth were specifically expressed in TO1000DH3, while transcripts related to nucleosides or ATP biosynthesis were specifically expressed in Early big. GO analysis on transcripts with more than two-fold change in expression upon MeJA treatment, corresponding to 12,020 transcripts in TO1000DH3 and 13,510 transcripts in Early big, showed that the expression of transcripts that react to stimulus and chemical increased in TO1000DH3 and Early big, while those related to single-organism and ribosome synthesis decreased. In particular, the expression increased for all transcripts related to indole glucosinolate biosynthesis, which is associated with increase in glucobrassicin and neoglucobrassicin contents. Upon MeJA treatment, the expression of AOP3 (Bo9g006220, Bo9g006240), TGG1 (Bo14804s010) increased only in TO1000DH3, while the expression of Dof1.1 (Bo5g008360), UGT74C1 (Bo4g177540), and GSL-OH (Bo4g173560, Bo4g173550, Bo4g173530) increased specifically in Early big.

• Development and Reproduction
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• v.5 no.2
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• pp.131-136
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• 2001

The developmental profiles of rpr, grim, dcp-1, diapl, diap2 transcripts, which were involved in programmed cell death, were analyzed using competitive RT-PCR in whole animals during Drosophila development. The fluctuation patterns of transcript levels of the apoptotic initiators(rpr and grim) were similar to those of the ecdysone titer in Drosophila life cycle. The transcript of dcp-1, which is considered as effector caspase, was expressed strong1y at early embryo and female adult stages. However, the transcript levels of anti-apoptotic factors diap1 and diap2, showed the reverse pattern comparing with those of apoptotic factors(rpr and grim). Also, the transcript levels of rpr, diap2 and dcp-1 were quantified in the salivary glands and wing discs dissected from the wandering late third instar larva. The transcript levels of rpr and diap2 were changed reversely each other in both tissues from wandering stage to puparium formation. These results suggest that the expressions of cell death related genes are regulated by the ecdysone signals during normal development.

• Journal of Life Science
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• v.15 no.6 s.73
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• pp.928-934
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• 2005

ATF2 is a cellular transcription factor which belongs to the CREB/ATF class and it is leucine zipper protein which generally binds to DNA as dimers. This paper presents the procedure for subcloning the ATF2 gene and the results of experiment used the expressed ATF2. The pET expression vector was used since it produced 6xHis fusion protein for easy purification using affinity column. The Nickel chelating chromatography was used for Purifying the expressed ATE2 from E- codi BL2l. Subsequen시y In vitro binding pull-down assay showed the binding specificity of ATF2 with AP-1 family factors such as BATF, c-Fos, c-Jun and ATF2 itselgf. ATF2 forms homodimer as well as strong heterodimer with BATF. It also forms stable dimer with c-Jun but barely binds with c-Fos.

• Journal of Plant Biotechnology
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• v.42 no.4
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• pp.342-349
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• 2015

Kiwifruit is a new fruit crop that was commercialized in the late 1970s. Recently, its cultivation and consumption have increased rapidly worldwide. Kiwifruit is a dioecious, deciduous, and climbing plant having fruit with hairs and various flesh colors and a variation in ploidy level; however, the industry consists of very simple cultivars or genotypes. The need for efficient cultivar improvement together with the evolutional and biological perspectives based on unique plant characteristics, have recently encouraged genome analysis and bioinformatics application. The draft genome sequence and chloroplast genome sequence of kiwifruit were released in 2013 and 2015, respectively; and gene annotation has been in progress. Recently, transcriptome analysis has shifted from previous ESTs analysis to the RNA-seq platform for intensive exploration of controlled genetic expression and gene discovery involved in fruit ascorbic acid biosynthesis, flesh coloration, maturation, and vine bacterial canker tolerance. For improving conventional breeding efficiency, molecular marker development and genetic linkage map construction have advanced from basic approaches using RFLP, RAPD, and AFLP to the development of NGS-based SSR and SNP markers linked to agronomically important traits and the construction of highly saturated linkage maps. However, genome and transcriptome studies have been limited in Korea. In the near future, kiwifruit genome and transcriptome studies are expected to translate to the practical application of molecular breeding.

• Korean Journal of Microbiology
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• v.44 no.4
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• pp.271-276
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• 2008

Ribosome stalling by nascent sticky peptide has been reported in several organisms across the kingdom. To test whether small subunit (SSU) rRNA is involved in this phenomenon, we developed a genetic system that utilized the specialized ribosome system to isolate SSU rRNA mutants that enable ribosomes to bypass the SecM-derived sticky peptide in protein synthesis. In this system, CAT-SecM mRNA, which encodes CAT protein containing the sticky peptide derived from SecM, is only translated by specialized ribosomes. These ribosomes were shown to transiently stall on CAT-SecM mRNA followed by the synthesis of the sticky peptide. Expression of specialized ribosomes resulted in the decreased steady-state level of CAT-SecM mRNA, which is consistent with a notion that ribosome stalling induces mRNA degradation. Isolation and characterization of SSU rRNA mutations using this genetic system that are sufficient to circumvent ribosome stalling induced by the SecM-derived sticky peptide will provide evidence of SSU rRNA function in mRNA cleavage.