• Molecules and Cells
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• 제37권12호
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• pp.873-880
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• 2014

In our previous study, miRNA-183, a miRNA in the miR-96-182-183 cluster, was significantly over-expressed in esophageal squamous cell carcinoma (ESCC). In the present study, we explored the oncogenic roles of miR-183 in ESCC by gain and loss of function analysis in an esophageal cancer cell line (EC9706). Genome-wide mRNA micro-array was applied to determine the genes that were regulated directly or indirectly by miR-183. 3'UTR luciferase reporter assay, RT-PCR, and Western blot were conducted to verify the target gene of miR-183. Cell culture results showed that miR-183 inhibited apoptosis (p < 0.05), enhanced cell proliferation (p < 0.05), and accelerated G1/S transition (p < 0.05). Moreover, the inhibitory effect of miR-183 on apoptosis was rescued when miR-183 was suppressed via miR-183 inhibitor (p < 0.05). Western blot analysis showed that the expression of programmed cell death 4 (PDCD4), which was predicted as the target gene of miR-183 by microarray profiling and bioinformatics predictions, decreased when miR-183 was over-expressed. The 3'UTR luciferase reporter assay confirmed that miR-183 directly regulated PDCD4 by binding to sequences in the 3'UTR of PDCD4. Pearson correlation analysis further confirmed the significant negative correlation between miR-183 and PDCD4 in both cell lines and in ESCC patients. Our data suggest that miR-183 might play an oncogenic role in ESCC by regulating PDCD4 expression.

• 식물병연구
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• 제22권1호
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• pp.25-31
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• 2016

2014년도 충남 당진의 고추포장 바이러스 발생 조사 중, 포장 주변에서 바이러스 병징을 보이는 속속이풀을 수집하였다. 수집한 시료에 대해 여러 고추감염바이러스의 감염여부를 조사한 결과, PMMoV와 CMV에 복합감염되어 있음을 확인하였다. 이는 PMMoV의 잡초 기주로서 속속이풀의 최초 동정이며, 속속이풀의 CMV 감염의 국내 첫 보고이다. 따라서 이들 신규 분리주들의 계통발생학적 위치를 파악하고자, 이들의 전체 게놈 염기서열을 분석하였고 이미 보고된 PMMoV 및 CMV 분리주의 유전정보와 비교 분석하였다. 유전적 측면에서 이미 보고된 고추감염바이러스와의 관계를 알아보고자 속속이풀에서 분리된 PMMoV와 CMV의 전체 염기서열을 분석하였고, 이들의 계통발생학적 특성을 구명하였다. 그 결과, 속속이풀에서 분리한 PMMoV 및 CMV의 분리주가 고추에서 분리한 분리주들과 매우 높은 유사성을 보임을 확인하였고, 이는 속속이풀이 PMMoV 및 CMV의 중간 기주로 작용할 수 있음을 시사한다.

• Asian Pacific Journal of Cancer Prevention
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• 제13권12호
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• pp.5917-5935
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• 2012

Background: Hepatitis C virus (HCV) causes acute and chronic human hepatitis infection and as such is an important global health problem. The virus was discovered in the USA in 1989 and it is now known that three to four million people are infected every year, WHO estimating that 3 percent of the 7 billion people worldwide being chronically infected. Humans are the natural hosts of HCV and this virus can eventually lead to permanent liver damage and carcinoma. HCV is a member of the Flaviviridae family and Hepacivirus genus. The diameter of the virus is about 50-60 nm and the virion contains a single-stranded positive RNA approximately 10,000 nucleotides in length and consisting of one ORF which is encapsulated by an external lipid envelope and icosahedral capsid. HCV is a heterogeneous virus, classified into 6 genotypes and more than 50 subtypes. Because of the genome variability, nucleotide sequences of genotypes differ by approximately 31-34%, and by 20-23% among subtypes. Quasi-species of mixed virus populations provide a survival advantage for the virus to create multiple variant genomes and a high rate of generation of variants to allow rapid selection of mutants for new environmental conditions. Direct contact with infected blood and blood products, sexual relationships and availability of injectable drugs have had remarkable effects on HCV epidemiology. Hundreds of thousands of people die each year from hepatitis and liver cancer caused by HCV virus infection. Approximately 80% of patients with acute hepatitis C progress into a chronic disease state leading to serious hepatic disorders, 10-20% of which develop chronic liver cirrhosis and hepatocellular carcinoma. The incubation period of HCV is 6-8 weeks and the infection is often asymptomatic so it is very hard to detect at early stages, making early treatment very difficult. Therefore, hepatitis C is called a "silent disease". Neutralizing antibodies are produced against several HCV proteins during infection but the virus mutates to escape from antibodies. Some patients with chronic hepatitis C may have some symptoms such as fatigue, muscle aches, nausea and pain. Autoimmune and immunecomplex-mediated diseases have also been reported with chronic HCV infection.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.140-140
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• 2017

Nutritious and functional foods from crop have received great attention in recent years. Colored-grain wheat contains high phenolic compound and a large number of flavonoid. The anthocyanin and polyphenolic synthesis and accumulation is generally stimulated in response to biotic or abiotic stresses. Here, we analyzed genome wide transcripts in seedling of colored-grain wheat response to ABA and PEG treatment. About 900 and 1500 transcripts (p-value < 0.05) from ABA and PEG treatment were aligned to IWGSC1+popseq DB which is composed of over 110,000 transcripts including 100,934 coding genes. NR protein sequences of Poaceae from NCBI and protein sequence of transcription factors originated from 83 species in plant transcription factor database v3.0 were used for annotation of putative transcripts. Gene ontology analysis were conducted and KEGG mapping was performed to show expression pattern of biosynthesis genes related in flavonoid, isoflavonoid, flavons and anthocyanin biopathway. DroughtDB (http://pgsb.helmholtz-muenchen.de/droughtdb/) was used for detection of DEGs to explain that physiological and molecular drought avoidance by drought tolerance mechanisms. Drought response pathway, such as ABA signaling, water and ion channels, detoxification signaling, enzymes of osmolyte biosynthesis, phospholipid metabolism, signal transduction, and transcription factors related DEGs were selected to explain response mechanism under water deficit condition. Anthocyanin, phenol compound, and DPPH radical scavenging activity were measured and antioxidant activity enzyme assays were conducted to show biochemical adaptation under water deficit condition. Several MYB and bHLH transcription factors were up-regulated in both ABA and PEG treated condition, which means highly expressed MYB and bHLH transcription factors enhanced the expression of genes related in the biosynthesis pathways of flavonoids, such as anthocyanin and dihydroflavonols in colored wheat seedlings. Subsequently, the accumulation of total anthocyanin and phenol contents were observed in colored wheat seedlings, and antioxidant capacity was promoted by upregulation of genes involved in maintaining redox state and activation of antioxidant scavengers, such as CAT, APX, POD, and SOD in colored wheat seedlings under water deficit condition. This work may provide valuable and basic information for further investigation of the molecular responses of colored-grain wheat to water deficit stress and for further gene-based studies.

• 인터넷정보학회논문지
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• 제15권1호
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• pp.29-43
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• 2014

차세대 유전체 해독 기술과 자동화 기술이 발전하면서 DNA 서열 분석 환경이 개선되고 있지만, 아직까지 제한된 컴퓨팅 리소스는 분석시간 단축의 장애요인으로 작용하고 있다. 대부분의 과학 워크플로우 시스템은 수 많은 기능들이 특정 시스템 환경에 맞추어 구현되어 있기 때문에 복잡하고 유동적이지 못하며, 이로 인해 기존 시스템의 컴포넌트들을 클라우드 환경의 새로운 시스템에 적용하기 어려운 한계를 지니고 있다. 본 연구에서는 대량의 DNA 데이터를 동시적으로 분석할 수 있는 가상 인스턴스 제공이 가능하며 시스템간의 상호 운용성을 개선시키기 위하여 웹 서비스, DBMS, 클라우드 컴퓨팅 기능을 지원하는 DNA 서열 분석용 미들웨어를 개발하였다. 본 연구에서 개발된 지능형 미들웨어는 DBMS를 사용하여 파이프라인 정보를 관리하고, 클라우드 환경에서 경량의 가상 인스턴스를 제공하며, 상호운용성 개선을 위하여 단순 URI와 XML을 기반으로 한 RESTful 웹서비스 기능을 제공한다.

• Biotechnology and Bioprocess Engineering:BBE
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• 제11권2호
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• pp.127-133
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• 2006

Shewanella oneidensis MR-1 has the ability to inhale certain metals and chemical compounds and exhale these materials in an altered state; as a result, this microorganism has been widely applied in bioremediation protocols. However, the relevant characteristics of cell growth and biosynthesis of PuFAs have yet to be thoroughly investigated. Therefore, in this study, we have attempted to characterize the growth and fatty acid profiles of S. oneidensis MR-1 under a variety of temperature conditions. The fastest growth of S. oneidensis MR-1 was observed at $30^{\circ}C$, with a specific growth rate and doubling time of $0.6885h^{-1}\;and\;1.007 h$. The maximum cell mass of this microorganism was elicited at a temperature of $4^{\circ}C$. The eicosapentaenoic acid (EPA) synthesis of S. oneidensis MR-1 was evaluated under these different culture temperatures. S. oneidensis MR-1 was found not to synthesize EPA at temperatures in excess of $30^{\circ}C$, but was shown to synthesize EPA at temperatures below $30^{\circ}C$. The EPA content was found to increase with decreases in temperature. We then evaluated the EPA biosynthetic pathway, using a phylogenetic tree predicted on 16s rRNA sequences, and the homology of ORFs between S. oneidensis MR-1 and Shewanella putrefaciens SCRC-2738, which is known to harbor a polyketide synthase (PKS)-like module. The phylogenetic tree revealed that MR-1 was very closely related to both Moritella sp., which is known to synthesize DHA via a PKS-like pathway, and S. putrefaciens, which has been reported to synthesize EPA via an identical pathway. The homology between the PKS-like module of S. putrefaciens SCRC-2738 and the entire genome of S. oneidensis MR-1 was also analyzed, in order to mine the genes associated with the PKS-like pathway in S. oneidensis MR-1. A putative PKS-like module for EPA biosynthesis was verified by this analysis, and was also corroborated by the experimental finding that S. oneidensis MR-1 was able to synthesize EPA without the expression of $dihomo-{\gamma}-linoleic$ acid (DGLA) and arachidonic acid (AA) formed during EPA synthesis via the FAS pathway.

• Journal of Animal Science and Technology
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• 제47권2호
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• pp.177-186
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• 2005

Xenotransplantation may help to overcome the critical shortage of human tissues and organs for human transplantation, Swine represents an ideal source of such organs owing to their anatomical and physiological similarities to human besides their plentiful supply, However, the use of organs across the species barrier may be associated with the risk of transmission of pathogens, specially porcine endogenous retroviruses (PERVs).• Although most of these potential pathogens could be eliminated by pathogen-free breeding, PERVs are not eliminated by this treatment. PERVs are integrated into the genome of all pigs and produced by normal pig cells and infect human cells. They belong to gamma retroviruses and are of three classes viruses: A, B and C. In the present study, PCR based cloning was performed with chromosomal DNA extracted from pigs from domestic pigs in Korea. Amplified PCR fragments of about 1.5 Kb, covering the partial env gene, were cloned into pCR2.l-TOPO vectors and sequenced. A total of 91 env clones were obtained from domestic pigs, Berkshire, Duroc, Landrace and Yorkshire in Korea. Phylogenetic analysis of these genes revealed the presence of only PERV class A and B in the proportion of 58 % and 42 %, respectively. Among these, 28 clones had the correct open reading frame: 18 clones in class A and 10 clones in class B. Since both these PERV classes are polytropic and have the capacity to infect human cells, our data suggest that proviral PERVs have the potential to generate infectious viruses during or after xenotransplantation in human.

• 식물병연구
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• 제22권3호
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• pp.178-183
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• 2016

SYMMV는 콩에서 빈번하게 발생하는 바이러스이며, 이 바이러스의 발생률은 계속해서 증가하고 있다. 본 연구에서는 콩에 발생하는 SYMMV를 신속하게 검출하기 위해서 RT-LAMP를 적용하였다. RT-LAMP 방법은 등온에서 단시간에 유전자 증폭이 가능하고, 전기영동 없이도 형광물질을 이용해 바이러스를 검출할 수 있는 이점이 있다. 프라이머는 SYMMV coat protein gene의 염기서열을 기반으로 4개의 프라이머를 설계하였다. 실험결과 SYMMV RT-LAMP는 $65^{\circ}C$에서 50분간 증폭시켰을 때 최적의 효율을 보였다. 또한, RT-LAMP와 RT-PCR과의 민감도를 비교한 결과 RT-LAMP 방법이 10-100배 정도 더 우수한 민감도를 가지는 것으로 밝혀졌다. 본 실험 결과를 토대로 기존의 진단법과 비교하여 높은 민감도와 짧은 소요시간에 이점이 있는 RT-LAMP는 SYMMV의 현장 및 연구실에서의 진단에 적용될 수 있을 것이라 생각된다.

• Plant Biotechnology Reports
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• 제3권2호
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• pp.147-155
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• 2009

Oryza grandiglumis Chitinase IVa (OgChitIVa) cDNA encoding a class IV chitinase was cloned from wild rice (Oryza grandiglumis). OgChitIVa cDNA contains an open reading frame of 867 nucleotides encoding 288 amino acid residues with a predicted molecular weight of 30.4 kDa and isoelectric point of 8.48. Deduced amino acid sequences of OgChitIVa include the signal peptide and chitin-binding domain in the N-terminal domain and conserved catalytic domain. OgChitIVa showed significant similarity at the amino acid level with related monocotyledonous rice and maize chitinase, but low similarity with dicotyledoneous chitinase. Southern blot analysis showed that OgChitIVa genes are present as two copies in the wild rice genome. It was shown that RNA expression of OgChitIVa was induced by defense/stress signaling chemicals, such as jasmonic acid, salicylic acid, and ethephon or cantharidin and endothall or wounding, and yeast extract. It was demonstrated that overexpression of OgChitIVa in Arabidopsis resulted in mild resistance against the fungal pathogen, Botrytis cinerea, by lowering disease rate and necrosis size. RT-PCR analysis showed that PR-1 and PR-2 RNA expression was induced in the transgenic lines. Here, we suggest that a novel OgChitIVa gene may play a role in signal transduction process in defense response against B. cinerea in plants.

• Journal of Plant Biotechnology
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• 제37권1호
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• pp.77-83
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• 2010

국립원예특작과학원에서 분양받은 토마토 18계통을 공시하여 재분화가 잘되는 적정 품종을 탐색한 결과, 계통번호 2001-58에서의 재분화율이 93%로 양호하였다. 또한 식물체로의 재분화 과정에서 보여 지는 갈변현상과 phenolic compound에 의한 식물조직의 괴사현상을 막기 위하여 항산화제인 ascorbic acid와 cystein을 단용 또는 혼용으로 첨가한 후 토마토 재분화에 미치는 영향을 살펴 본 결과, ascorbic acid $200{\sim}300\;{\mu}M/L$ 처리구에서 줄기형성율 및 생체중이 증가되는 현상을 관찰할 수 있었다. 토마토 엽록체 형질전환체 선발을 위해 spectinomycin의 적정 농도를 살펴본 결과, 재분화배지에 spectinomycin 20~25 mg/L 농도가 첨가되어진 처리구에서 재분화가 거의 이루어지지 않았다. 토마토 엽록체 형질전환을 위해 토마토 엽록체 게놈 일부를 분리하여 염기서열을 분석하여 담배와 비교 분석한 결과, homology가 매우 높음을 알 수 있었다. Homologous recombination에 의한 엽록체 형질전환이 되기 위해서 분리한 토마토 엽록체 게놈 일부를 border sequence로 이용하였고, transient assay를 위해 GFP 유전자가 포함된 토마토 엽록체 형질전환용 운반체 pKRT22-AG를 제작하였다. Bombardment을 한 후 원형질체를 나출하여 공초점 현미경하에서 관찰한 결과 엽록체 내에서만 GFP가 발현됨을 알 수 있었으며, DNA 농도 $1\;{\mu}g$, $0.6\;{\mu}m$ gold particle 1 mg, target distance 9 cm 조건이 가장 좋았다.