• The Plant Pathology Journal
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• 제20권4호
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• pp.313-315
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• 2004

The coat protein gene of Korean isolate of Ricer stripe virus (RSV-Kr) was cloned and its nucleotide sequence was determined. Total RNA was extracted from infected leaves and RSV viral RNA was detected by using RT-PCR with specific primer of coat protein gene. The result of RT-PCR showed a specific band. Purified RT-PCR products of coat protein gene were ligated into the pGEM-T Easy plasmid vector and cloned cDNA was obtained for nucleotide sequence determination. Coat protein gene of RSV-Kr consisted of 969 bp long encoding a protein of 322 amino acids. RSV-Kr showed 94%-99% sequence identities to that of Japanese- and Chinese isolates.

• BMB Reports
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• 제37권1호
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• pp.133-138
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• 2004

Proteomics is a leading technology for the high-throughput analysis of proteins on a genome-wide scale. With the completion of genome sequencing projects and the development of analytical methods for protein characterization, proteomics has become a major field of functional genomics. The initial objective of proteomics was the large-scale identification of all protein species in a cell or tissue. The applications are currently being extended to analyze various functional aspects of proteins such as post-translational modifications, protein-protein interactions, activities and structures. Whereas the proteomics research is quite advanced in animals and yeast as well as Escherichia coli, plant proteomics is only at the initial phase. Major studies of plant proteomics have been reported on subcellular proteomes and protein complexes (e.g. proteins in the plasma membranes, chloroplasts, mitochondria and nuclei). Here several plant proteomics studies will be presented, followed by a recent work using multidimensional protein identification technology (MudPIT).

• 자연과학논문집
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• 제10권1호
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• pp.27-32
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• 1998

HIV-1 gp41의 세포내 부분과 상호작용하는 단백질 유전자를 분리할 목적으로 yeast two hybrid system을 사용하여 검색하였다. 전체 $1.4 \times 10^6 colony를 검색하여 최종적으로 20개의 colony를 얻었다. 이들 colony로부터 분리된 유전자의 염기배열을 결정하여 본 결과, acidic ribosomal protein P0, beta tubulin, alpha catenin등의 세가지 종류임을 밝혔다. 이들은 yeast system 내에서 매우 특이적으로 gp41과 상호작용하고 있음을 알았다.

• Genomics & Informatics
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• 제11권4호
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• pp.200-210
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• 2013

Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.

• Parasites, Hosts and Diseases
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• 제54권6호
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• pp.751-758
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• 2016

This study aimed at constructing a draft genome of the adult female worm Toxocara canis using next-generation sequencing (NGS) and de novo assembly, as well as to find new genes after annotation using functional genomics tools. Using an NGS machine, we produced DNA read data of T. canis. The de novo assembly of the read data was performed using SOAPdenovo. RNA read data were assembled using Trinity. Structural annotation, homology search, functional annotation, classification of protein domains, and KEGG pathway analysis were carried out. Besides them, recently developed tools such as MAKER, PASA, Evidence Modeler, and Blast2GO were used. The scaffold DNA was obtained, the N50 was 108,950 bp, and the overall length was 341,776,187 bp. The N50 of the transcriptome was 940 bp, and its length was 53,046,952 bp. The GC content of the entire genome was 39.3%. The total number of genes was 20,178, and the total number of protein sequences was 22,358. Of the 22,358 protein sequences, 4,992 were newly observed in T. canis. Following proteins previously unknown were found: E3 ubiquitin-protein ligase cbl-b and antigen T-cell receptor, zeta chain for T-cell and B-cell regulation; endoprotease bli-4 for cuticle metabolism; mucin 12Ea and polymorphic mucin variant C6/1/40r2.1 for mucin production; tropomodulin-family protein and ryanodine receptor calcium release channels for muscle movement. We were able to find new hypothetical polypeptides sequences unique to T. canis, and the findings of this study are capable of serving as a basis for extending our biological understanding of T. canis.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2002년도 춘계학술발표대회 발표논문초록집
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• pp.90-90
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• 2002

In this study, we report the cloning of the porcine UPII genomic DNA, which contains a putative full-length open reading frame encoding the UPII protein. A comparison of the porcine UPII gene coding sequence with the previously published mouse UPII sequence demonstrates that only the exon sequences are partially conserved. Northern and immunohistochemical analyses show that the porcine UPII gene is expressed only in the urothelium and that the protein specifically localizes to urothelial superficial cells. (omitted)

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2001년도 학술 발표회 진행표 및 논문초록
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• pp.19-19
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• 2001

The genome sequencing has revealed a large number of proteins of unknown or little characterized functions that have been well conserved during evolution. It remains a great challenge to decipher the molecular and physiological functions of these proteins. One example of the evolutionarily conserved protein family with little understood function is the surE family.(omitted)

• 대한바이러스학회지
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• 제30권3호
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• pp.211-217
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• 2000

Nef is a lentiviral protein involved in pathogenesis of AIDS, but its molecular mechanism of action remains incompletely understood. Here we report the isolation of the interacting protein with the HIV-1 Nef, using the yeast two hybrid system for expression cloning. One of the positive colonies was selected as the final candidate for the interacting protein gene. The nucleotide sequencing revealed that this interacting protein is Human Ikaros/LyF-1. This protein interacted with the C-terminal region of Nef specifically in yeast system, not with the N-terminal region. This interaction was also confirmed by in vitro binding assay.

• 대한수의학회지
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• 제35권3호
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• pp.515-530
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• 1995

Coronaviridae에 속하는 transmissible gastroenteritis virus(TGEV)와 porcine epidemic diarrhea virus(PEDV)를 specific하게 detection할 수 있는 방법을 개발하고자 본 연구를 수행하였다. 두 바이러스 모두 RNA 바이러스이기 때문에 reverse transcription-polymerase chain reaction(RT-PCR)으로 nucleocapsid(N) protein gene의 cDNA를 증폭시켰다. SmaI으로 처리한 pTZ19R에 ligation시킨 후 염기서열을 밝히고자 sequencing하였다. 각각의 prototype virus와 비교하여 상동성을 밝혔다. 두 바이러스에 대한 cDNA probe를 제작하여 Southern blot hybridization을 실시하였다. TGEV의 경우 백신주인 P45와 병독주인 Miller strain을 사용하였다. cDNA를 증폭시키기 위해 N1/N1R과 N2/N2R 두 가지 primer를 이용한 결과, N1/N1R primer의 경우 586bp 크기의 PCR product를 얻을 수 있었고, N2/N2R primers로 582bp의 cDNA를 증폭시킬 수 있었다. PEDV 실험을 위하여 PED 임상 증상을 나타내는 분변을 이용하여 RT-PCR을 실시하였다. P2/P2R primer로 753bp의 PCR product를 얻을 수 있었다. TGEV의 두 가지 strain의 N protein gene을 sequencing하여 prototype인 Purdue strain과 염기서열 상동성을 조사한 결과, 97%이상의 높은 homology를 나타내었다. PED-V 역시 N protein gene을 sequencing하여 CV777과 염기서열 상동성을 조사한 결과 97%이상의 homology로 PEDV임을 알 수 있었다. TGEV와 PEDV의 염기서열을 비교한 결과 29%의 낮은 homology를 관찰할 수 있었다. 두 가지 바이러스의 N protein gene에 대한 cDNA probe를 제작하여 Southern blot hybridization을 한 결과, 각 바이러스에 매우 특이적 반응을 나타내었다.

• Animal cells and systems
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• 제1권1호
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• pp.135-142
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• 1997

Random sequencing of expressed sequence tags in roots of Chinese cabbage led to isolation of a partial cDNA clone, BR77, which encoded a putative protein kinase. Using the BR77 cDNA as a probe, we isolated a full-length cDNA encoding the Brassica campestris protein kinase 1 (Bcpk1). The Bcpt1 cDNA contained one open reading frame encoding a polypeptide of 439 amino acids. The putative polypeptide consisted of a short N-terminal region and a protein kinase catalytic domain. The catalytic domain of Bcpkl showed a high homology to cAMP- and calcium- phospholipid-dependent subfamilies of serine/threonine protein kineses. Eleven major catalytic domains in protein kineses were well conserved in Bcpk1. However, Bcpk1 contained a unique nonhomologous intervening sequence between subdomains VII and VIII, which was not found in protein kineses of animals and lower eukaryotes. Genomic DNA gel blot analysis showed that Bcpt1 genes might be present as three copies in the Chinese cabbage genome. These imply that Bcpk1 belongs to a plant-specific serine/threonine protein kinase subfamily.