• 한국균학회소식:학술대회논문집
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• 한국균학회 2014년도 추계학술대회 및 정기총회
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• pp.13-13
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• 2014

Species belonging to the genus Fusarium are widely distributed and cause diseases in many plants. Isolation of fungal strains from air or cereals is necessary for disease forecasting, disease diagnosis, and population genetics [1]. Previously we showed that Fusarium species are resistant to toxoflavin produced by the bacterial rice pathogen Burkholderia glumae while other fungal genera are sensitive to the toxin, resulting in the development of a selective medium for Fusarium species using toxoflavin [2]. In this study, we have tried to elucidate the resistant mechanism of F. graminearum against toxoflavin and interaction between the two pathogens in nature. To test whether B. glumae affects the development of F. graminearum, the wild-type F. graminearum strains were incubated with either the bacterial strain or supernatant of the bacterial culture. Both conditions increased the conidial production five times more than when the fungus was incubated alone. While co-incubation resulted in dramatic increase of conidial production, conidia germination delayed by either the bacterial strain or supernatant. These results suggest that certain factors produced by B. glumae induce conidial production and delay conidial germination in F. graminearum. To identify genes related to toxoflavin resistance in F. graminearum, we screened the transcriptional factor mutant library previously generated in F. graminearum [3] and identified one mutant that is sensitive to toxoflavin. We analyzed transcriptomes of the wild-type strain and the mutant strain under either absence or presence of toxoflavin through RNAseq. Expression level of total genes of 13,820 was measured by reads per kilobase per million mapped reads (RPKM). Under the criteria with more than two-fold changes, 1,440 genes were upregulated and 1,267 genes were down-regulated in wild-type strain than mutant strain in response to toxoflavin treatment. A comparison of gene expression profiling between the wild type and mutant through gene ontology analysis showed that genes related to metabolic process and oxidation-reduction process were highly enriched in the mutant strain. The data analyses will focus on elucidating the resistance mechanism of F. graminearum against toxoflavin and the interaction between the two pathogens in rice. Further evolutionary history will be traced through figuring out the gene function in populations and in other filamentous fungi.

• BMB Reports
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• 제52권7호
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• pp.463-468
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• 2019

Autosomal dominant polycystic kidney disease (ADPKD), one of the most common human monogenic diseases (frequency of 1/1000-1/400), is characterized by numerous fluid-filled renal cysts (RCs). Inactivation of the PKD1 or PKD2 gene by germline and somatic mutations is necessary for cyst formation in ADPKD. To mechanistically understand cyst formation and growth, we isolated RCs from Korean patients with ADPKD and immortalized them with human telomerase reverse transcriptase (hTERT). Three hTERT-immortalized RC cell lines were characterized as proximal epithelial cells with germline and somatic PKD1 mutations. Thus, we first established hTERT-immortalized proximal cyst cells with somatic PKD1 mutations. Through transcriptome sequencing and Gene Ontology (GO) analysis, we found that upregulated genes were related to cell division and that downregulated genes were related to cell differentiation. We wondered whether the upregulated gene for the chemokine CXCL12 is related to the mTOR signaling pathway in cyst growth in ADPKD. CXCL12 mRNA expression and secretion were increased in RC cell lines. We then examined CXCL12 levels in RC fluids from patients with ADPKD and found increased CXCL12 levels. The CXCL12 receptor CXC chemokine receptor 4 (CXCR4) was upregulated, and the mTOR signaling pathway, which is downstream of the CXCL12/CXCR4 axis, was activated in ADPKD kidney tissue. To confirm activation of the mTOR signaling pathway by CXCL12 via CXCR4, we treated the RC cell lines with recombinant CXCL12 and the CXCR4 antagonist AMD3100; CXCL12 induced the mTOR signaling pathway, but the CXCR4 antagonist AMD3100 blocked the mTOR signaling pathway. Taken together, these results suggest that enhanced CXCL12 in RC fluids activates the mTOR signaling pathway via CXCR4 in ADPKD cyst growth.

• The Korean Journal of Physiology and Pharmacology
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• 제23권2호
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• pp.151-159
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• 2019

Pruritus (itching) is classically defined as an unpleasant cutaneous sensation that leads to scratching behavior. Although the scientific criteria of classification for pruritic diseases are not clear, it can be divided as acute or chronic by duration of symptoms. In this study, we investigated whether skin injury caused by chemical (contact hypersensitivity, CHS) or physical (skin-scratching stimulation, SSS) stimuli causes initial pruritus and analyzed gene expression profiles systemically to determine how changes in skin gene expression in the affected area are related to itching. In both CHS and SSS, we ranked the Gene Ontology Biological Process terms that are generally associated with changes. The factors associated with upregulation were keratinization, inflammatory response and neutrophil chemotaxis. The Kyoto Encyclopedia of Genes and Genomes pathway shows the difference of immune system, cell growth and death, signaling molecules and interactions, and signal transduction pathways. Il1a, Il1b and Il22 were upregulated in the CHS, and Tnf, Tnfrsf1b, Il1b, Il1r1 and Il6 were upregulated in the SSS. Trpc1 channel genes were observed in representative itching-related candidate genes. By comparing and analyzing RNA-sequencing data obtained from the skin tissue of each animal model in these characteristic stages, it is possible to find useful diagnostic markers for the treatment of itching, to diagnose itching causes and to apply customized treatment.

• Mycobiology
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• 제49권4호
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• pp.406-420
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• 2021

Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined the GiC-126 genome with the published genome of G. incarnatum strain CCMJ2665 to construct a genetic linkage map (GiC-126 genome) that had 10 linkage groups (LGs), and the 15 assembly sequences of CCMJ2665 were integrated into 8 LGs. We identified 1912 simple sequence repeat (SSR) loci and detected 700 genes containing 768 SSRs in the genome; 65 and 100 of them were annotated with gene ontology (GO) terms and KEGG pathways, respectively. Carbohydrate-active enzymes (CAZymes) were identified in 20 fungal genomes and annotated; among them, 144 CAZymes were annotated in the GiC-126 genome. The A mating-type locus (MAT-A) of G. incarnatum was located on scaffold885 at 38.9 cM of LG1 and was flanked by two homeodomain (HD1) genes, mip and beta-fg. Fourteen segregation distortion markers were detected in the genetic linkage map, all of which were skewed toward the parent GiC-126. They formed three segregation distortion regions (SDR1-SDR3), and 22 predictive genes were found in scaffold1920 where three segregation distortion markers were located in SDR1. In this study, we corrected and updated the genomic information of G. incarnatum. Our results will provide a theoretical basis for fine gene mapping, functional gene cloning, and genetic breeding the follow-up of G. incarnatum.

• 현장농수산연구지
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• 제23권1호
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• pp.117-128
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• 2021

한우의 성장단계별 부위 근육발달을 이해하는 것은 도체율 개선에 따른 소득증대와 증체율 증가에 따른 생산효율 향상에 긍정적인 영향을 미친다. 본 연구에서는 한우의 등심과 사태 유래 근육위성세포를 분리 후 세포단위의 발달 및 분화를 비교하여 transcriptome 단위의 작용기전을 제시하였다. 한우의 부위별 근육 유래 근육위성세포의 근섬유의 양은 4일에 가장 높게 나타났고 이후 감소하였다. 한우의 근육위성세포의 발달 단계에 따라 발현되는 총 전사체 유전자의 종류는 사태근육 위성세포에서 높게 나타났다. 등심과 사태 근육 유래 위성세포의 발달단계에 따라 유의적인 차등 유전자 453개를 찾아냈고 이를 이용한 기능유 전체 분석이 필요하다. 등심과 사태유래 근육위성세포를 이용한 동일조건 분화 비교에서 사태유래 근육 위성세포의 분화 시 myosin complex, skeletal muscle contraction, troponin complex, skeletal muscle tissue development 와 같은 근섬유 형성관련 유전자의 발현이 높게 나타나는 것으로 보아 같은 개체의 근육조직에서도 부위별로 차등 발달이 되고 있다는 것을 알 수 있다. 기존 연구에서는 근육의 성장에 대한 이해를 위해 사양과 영양관련 시험이 많이 이루어졌다. 향후 세포단위의 연구들이 많이 이루어져 작용기작에 대한 생물정보 자료를 추가로 적용한다면 한우의 정밀사양을 적용할수 있는 바탕이 마련될 것이다. 또한 근육위성세포의 연구는 추후 동물실험 윤리제도 강화에 따른 비동물 전임상 screening 시험 활용과 대체단백질 산업의 주요 이슈인 배양육 소재 개발 연구와 같이 축산시험연구의 지속적인 확장성에 많은 영향을 미칠 것으로 생각된다.

• 생명과학회지
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• 제25권8호
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• pp.861-869
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• 2015

가축화된 동물종 중 하나인 개는, 다양한 목적을 위해 인간에 의하여 선택적으로 육종되었다. 개는 많은 품종을 갖고 있고, 특정한 행동과 형태를 갖도록 인공적으로 선택되어 왔다. 개들은 그들의 삶을 안내, 구조 혹은 탐지 등의 특수 목적에 대하여 인간에게 헌신하고 있다. 특수 목적견에게 요구되는 좋은 품성, 이를테면 온순함, 강건성, 그리고 인내심과 같은 특성은 그들의 특수 임무를 수행하는 데 필요하다. 많은 연구들이 우수한 특수 목적견의 선정을 위한 유전적 마커를 찾는 데 집중되었다. 본 연구에서는, 뇌에서 발현함으로써 기능하는 것으로 알려진 총 8개의 유전자(ABAT; 4-Aminobutyrate Aminotransferase, PLCB1; Phospholipase C, Beta 1, SLC10A4; Solute Carrier Family 10, Member 4, WNT1; Wingless-Type MMTV Integration Site Family, Member 1, BARX2; BarH-Like Homeobox 2, NEUROD6; Neuronal Differentiation 6, SEPT9; Septin 9 그리고 TBR1; T-Box, Brain, 1)들의 정량적인 발현 양상을 개의 네 품종의 뇌 조직에서 확인하였다. 특히, BARX2, SEPT9, SLC10A4, TBR1 그리고 WNT1 유전자들은 비글과 진돗개에서 많이 발현되는데 반하여, 삽살이와 세퍼드에서는 반대되는 발현 양상을 보여 주었다. 본 연구의 유전자들에 대한 Gene ontology (GO) 결정을 위하여 DAVID (Database for annotation, visualization and integrated discovery) 분석이 수행되었고, 이러한 유전자들이 뇌 발생과 개체의 지능에 중요한 기능을 제공할 것이라고 예상하였다. 결론적으로, 이러한 결과들을 통하여, 뇌에서의 기능과 관련된 인자들과 관련된 바이오마커를 발굴하는 데 중요한 단서를 제공해 줌과 동시에, 우수한 특수 목적견을 선발하는 데 도움을 줄 것이라 기대한다.

• 원예과학기술지
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• 제29권6호
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• pp.633-640
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• 2011

배추는 배추속 식물의 A genome을 대표하는 모델로서 다양한 배추과 작물의 유전학 및 유전체학과 육종연구의 기반이 되는 중요한 작물이다. 최근 들어 배추 유전체 해독이 완료됨에 따라 유전체의 기능 연구가 보다 활발히 진행될 것으로 기대된다. 유전체 정보로부터 유전자의 구조를 예측하고, 기능을 분석하여 프로모터를 포함한 유용 유전자를 개발하기 위한 필수 재료로 이용되는 것이 다양한 조직 또는 실험 처리로부터 생성된 발현 유전자 데이터이다. 2011년 7월 현재 공공 데이터베이스에는 39개의 cDNA library로부터 분석된 147,217개의 배추 발현유전자가 보고되어 있다. 그러나 이들 발현 유전자들은 체계적으로 분석되거나 데이터베이스 형태로 정리되어 있지 않기 때문에 연구자들이 유전자 서열로부터 유용한 정보를 추출하여 사용하기 어려운 문제점이 있다. 따라서 해독 완료된 배추 유전체와 함께 발현 유전자 정보를 보다 잘 활용하기 위하여 배추의 조직 특이적 발현유전자 데이터베이스인 BrTED를 개발하였다. 데이터베이스는 EST 서열 처리-정보 검색 단위와 조직특이성 발현 특성 분석 단위로 이루어져 있으며, 각 정보들은 상호 연결되어 유기적인 검색 환경을 제공하게 하였다. BrTED는 23,962개의 단일 조합 유전자서열을 포함하고 있으며, 각 서열들의 유전자 주석과 암호화하고 있는 단백질의 기능을 동시에 제공한다. 또한 각 단일 조합 유전자서열들의 조직별 발현 특이성을 통계 분석을 통해 조사하여 연구자의 검색 기준에 따라 제공한다. BrTED의 실효성을 검증하기 위하여 데이터베이스를 통해 조직 특이적 발현 유전자 29개를 선발하고, 이들의 발현 특성을 RT-PCR로 확인한 결과, 선발한 유전자 모두 목표한 조직에서 특이적이거나 강한 발현을 보였다. BrTED는 조직 특이적 발현유전자를 신속하게 선발할 수 있는 공공 데이터베이스로서 배추의 기능 유전체 연구뿐만 아니라 근연 배추속 작물의 유전학과 유전체학 연구에 유용한 공공 연구 자원으로 이용될 수 있을 것이다.

• Asian-Australasian Journal of Animal Sciences
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• 제31권6호
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• pp.812-819
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• 2018

Objective: An experiment was conducted to identify and characterize the circular RNA expression and metabolic characteristics in the liver of Jinhua pigs and Landrace pigs. Methods: Three Jinhua pigs and three Landrace pigs respectively at 70-day were slaughtered to collect the liver tissue samples. Immediately after slaughter, blood samples were taken to detect serum biochemical indicators. Total RNA extracted from liver tissue samples were used to prepare the library and then sequence on HiSeq 2500. Bioinformatic methods were employed to analyze sequence data to identify the circRNAs and predict the potential roles of differentially expressed circRNAs between the two breeds. Results: Significant differences in physiological and biochemical traits were observed between growing Jinhua and Landrace pigs. We identified 84,864 circRNA candidates in two breeds and 366 circRNAs were detected as significantly differentially expressed. Their host genes are involved in lipid biosynthetic and metabolic processes according to the gene ontology analysis and associated with metabolic pathways. Conclusion: Our research represents the first description of circRNA profiles in the porcine liver from two divergent phenotype pigs. The predicted miRNA-circRNA interaction provides important basis for miRNA-circRNA relationships in the porcine liver. These data expand the repertories of porcine circRNA and are conducive to understanding the possible molecular mechanisms involved in miRNA and circRNA. Our study provides basic data for further research of the biological functions of circRNAs in the porcine liver.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.131-131
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• 2017

Though the Platycodon grandiflorum, has a broad range of pharmacologic properties, but the mechanisms underlying these effects remain unclear. In order to profile proteins from the nodal segment, callus, root and shoot, high throughput proteome approach was executed in the present study. Two-dimensional gels stained with CBB, a total of 84 differential expressed proteins were confirmed out of 839 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 58 differential expressed protein spots (${\geq}2-fold$) were analyzed using MASCOT search engine according to the similarity of sequences with previously characterized proteins along with the UniProt database. Out of 58 differential expressed protein, 32 protein spots were up-regulated such as ribulose-1,5-bisphosphate carboxylase, endoplasmic oxidoreductin-1, heat stress transcription factor A3, RNA pseudourine synthase 4, cysteine proteinase, GntR family transcriptional regulator, E3 xyloglucan 6-xylosyltransferase, while 26 differential protein spots were down-regulated such as L-ascorbate oxidase precursor, late embryogenesis abundant protein D-34, putative SCO1 protein, oxygen-evolving enhancer protein 3. However, the frequency distribution of identified proteins using iProClass databases, and assignment by function based on gene ontology revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding (17%), transferase activity (14%) and ion binding (12%). Taken together, the protein profile may provide insight clues for better understanding the characteristics of proteins and its metabolic activities in various explants of this essential medicinal plant P. grandiflorum.

• 한국작물학회지
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• 제60권1호
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• pp.97-106
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• 2015

Platycodon grandiflorum, commonly known as Doraji in Korea, has a wide range of pharmacologic properties, such as reducing adiposity and hyperlipidemia, and antiatherosclerotic effects. However, the mechanisms underlying these effects remain unclear. In order to profile proteins from the nodal segment, callus, root and shoot, high throughput proteome approach was executed in the present study. Two dimensional gels stained with CBB, a total of 84 differential expressed proteins were confirmed out of 839 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 58 differential expressed protein spots (${\geq}$ 2-fold) were analyzed using MASCOT search engine according to the similarity of sequences with previously characterized proteins along with the UniProt database. Out of 58 differential expressed protein, 32 protein spots were up-regulated such as ribulose-1,5-bisphosphate carboxylase, endoplasmic oxidoreductin-1, heat stress transcription factor A3, RNA pseudourine synthase 4, cysteine proteinase, GntR family transcriptional regulator, E3 xyloglucan 6-xylosyltransferase, while 26 differential protein spots were down-regulated such as L-ascorbate oxidase precursor, late embryogenesis abundant protein D-34, putative SCO1 protein, oxygen-evolving enhancer protein 3. However, frequency distribution of identified proteins using iProClass databases, and assignment by function based on gene ontology revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding (17%), transferase activity (14%) and ion binding (12%). In that way, the exclusive protein profile may provide insight clues for better understanding the characteristics of proteins and metabolic activity in various explants of the economically important medicinal plant Platycodon grandiflorum.