• Journal of Ginseng Research
• /
• 제43권1호
• /
• pp.1-9
• /
• 2019

Background: Korean ginseng is an important cash crop in Asian countries. However, plant yield is reduced by pathogens. Among the Ilyonectria radicicola-species complex, I. mors-panacis is responsible for root-rot and replant failure of ginseng in Asia. The development of new methods to reveal the existence of the pathogen before cultivation is started is essential. Therefore, a quantitative real-time polymerase chain reaction method was developed to detect and quantify the pathogen in ginseng soils. Methods: In this study, a species-specific histone H3 primer set was developed for the quantification of I. mors-panacis. The primer set was used on DNA from other microbes to evaluate its sensitivity and selectivity for I. mors-panacis DNA. Sterilized soil samples artificially infected with the pathogen at different concentrations were used to evaluate the ability of the primer set to detect the pathogen population in the soil DNA. Finally, the pathogen was quantified in many natural soil samples. Results: The designed primer set was found to be sensitive and selective for I. mors-panacis DNA. In artificially infected sterilized soil samples, using quantitative real-time polymerase chain reaction the estimated amount of template was positively correlated with the pathogen concentration in soil samples ($R^2=0.95$), disease severity index ($R^2=0.99$), and colony-forming units ($R^2=0.87$). In natural soils, the pathogen was recorded in most fields producing bad yields at a range of $5.82{\pm}2.35pg/g$ to $892.34{\pm}103.70pg/g$ of soil. Conclusion: According to these results, the proposed primer set is applicable for estimating soil quality before ginseng cultivation. This will contribute to disease management and crop protection in the future.

• Asian-Australasian Journal of Animal Sciences
• /
• 제31권6호
• /
• pp.791-797
• /
• 2018

Objective: Trimethylation of histone 3 (H3) at 4th lysine N-termini (H3K4me3) in gene promoter region was the universal marker of active genes specific to cell lineage. On the contrary, coexistence of trimethylation at 27th lysine (H3K27me3) in the same loci-the bivalent H3K4m3/H3K27me3 was known to suspend the gene transcription in germ cells, and could also be inherited to the developed stem cell. In galline species, throughout example of H3K4m3 and H3K27me3 ChIP-seq analysis was still not provided. We therefore designed and demonstrated such procedures using ChIP-seq and mRNA-seq data of chicken follicular mesenchymal cells and male germ cells. Methods: Analytical workflow was designed and provided in this study. ChIP-seq and RNA-seq datasets of follicular mesenchymal cells and male germ cells were acquired and properly preprocessed. Peak calling by Model-based analysis of ChIP-seq 2 was performed to identify H3K4m3 or H3K27me3 enriched regions ($Fold-change{\geq}2$, $FDR{\leq}0.01$) in gene promoter regions. Integrative genomics viewer was utilized for cellular retinoic acid binding protein 1 (CRABP1), growth differentiation factor 10 (GDF10), and gremlin 1 (GREM1) gene explorations. Results: The acquired results indicated that follicular mesenchymal cells and germ cells shared several unique gene promoter regions enriched with H3K4me3 (5,704 peaks) and also unique regions of bivalent H3K4m3/H3K27me3 shared between all cell types and germ cells (1,909 peaks). Subsequent observation of follicular mesenchyme-specific genes-CRABP1, GDF10, and GREM1 correctly revealed vigorous transcriptions of these genes in follicular mesenchymal cells. As expected, bivalent H3K4m3/H3K27me3 pattern was manifested in gene promoter regions of germ cells, and thus suspended their transcriptions. Conclusion: According the results, an example of chicken H3K4m3/H3K27me3 ChIP-seq data analysis was successfully demonstrated in this study. Hopefully, the provided methodology should hereby be useful for galline ChIP-seq data analysis in the future.

• 한국환경성돌연변이발암원학회지
• /
• 제24권4호
• /
• pp.171-179
• /
• 2004

Cytochrome P4503A4(CYP3A4) is the most abundnat CYPs in human liver, comparising approximately 30% of the total liver CYPs contents ans is involbed in the metabolism of more than 60% of currently used therapeutic drugs. The expression of CYP3A4 is induced by a variety of structurally unrelated xonobiotics including the antibiotic rifampicin and endogenous hormones, and might be mediated through steroid and xenobiotic receptor(SXR) system. The molecular mechanisms underlying regulation of CYP3A4 gene expression hae not been understood. In order to gain the insight of the molecular mechanism of CYP3A4 gene expression, study has been undertaken to investigate if the histone deacelylation is involved in the regulation of CYP3A4 gene expression by proximal promoter or not. Also SXR was investigated to see if they were involved in the regulation of CYP3A4 proximal promoter activity. HepG2 or Hena-I cells were transfected with a plasmid containing~1kb of the CYP3A4 proximal promoter region (-863 to +64bp) cloned in front of a reporter gene, luciferase, in the presence or absence of SXR or hER. Transfected cells were treated with CYP3A4 inducers such as rifampicin, PCN and RU 486, or with estradiol, in order to exmine to regulation of CYP3A4 gene expression in the presence or absence of trichostatin A (TSA). In HepG2 cells, CYP3A4 inducers and estradiol increased significantly the luciferase activity by CYP3A4 proximal promoter, only when TSA was co-treated after SXR cotransfection. In the case of Hepa-I cells CYP3A4 inducers and estradiol incressed modestly the luciferase activity when TSA was co-treated, but this increment was not enhanced by SXR cotransfection in contrast to HepG2 cells. Taken together, these results indicated that the inhibition of histone deacetylation was required to SXR-mediated increase in CYP3A4 proximal promoter region when rifampicin, or PCN was treated. Futher a trans-activation by SXR may demand other species-specific transcription factors.

• 생명과학회지
• /
• 제23권5호
• /
• pp.622-628
• /
• 2013

본 연구에서는 마늘에서 유래된 생리활성 물질인 diallyl trisulfide (DATS) 처리에 따른 U937 인체혈구암세포의 증식억제가 apoptosis 및 cell cycle arrest 유발과 관련이 있는지 조사하였다. U937 세포증식은 DATS에 의해 농도 및 시간 의존적으로 감소함을 확인 하였고, 이는 apoptosis에 의한 직접적인 세포죽음과 CDK1 및 cyclin B1의 발현 증가 및 histone H3의 인산화와 연관된 mitotic arrest와 관련이 있음을 알 수 있었다. 또한 DATS 처리 초기에 reactive oxygen species (ROS)의 생성이 매우 증가되었으나, ROS scavenger (N-acetyl-l-cysteine)에 의한 인위적 ROS 생성의 억제는 DATS에 의한 apoptosis 및 mitotic arrest를 완벽하게 차단시켰다. 이는 U937 세포에서 DATS에 의해 유도된 apoptosis 및 mitotic arrest가 ROS에 의해 매개된다는 것을 의미하며, 본 연구의 결과는 DATS가 인체혈구암세포에서 세포증식억제와 관련된 항암기전을 이해할 수 있는 기초자료로서 매우 유용하게 사용될 것이라 생각된다.

• 한국약용작물학회지
• /
• 제26권4호
• /
• pp.302-307
• /
• 2018

Background: A soil-borne pathogenic fungus, Ilyonectria radicicola (Cylindrocarpon destructans) causes root rot on ginseng (Panax ginseng C. A. Meyer) and is known to attack many other plants. The Nectria/Neonectria radicicola complex has been renamed as the I. radicicola complex after analysis of its multi-gene relatedness and morphological characteristics. The fungi in this complex have been reclassified into 16 species under the genus Ilyonectria based on characteristics analysis Methods and Results: To obtain useful data from the Korean ginseng root rot, I. radicicola was isolated from the rhizosphere soils of the chestnut tree. They were identified through a pathogenicity test and a survey of the morphological features. The existence of I. radicicola in soil samples was confirmed by PCR detections using nested PCR with species-specific primer sets. These were subsequenctly isolated on semi-selective media from PCR-positive soils. Genetic analysis of the I. radicicola complex containing these pathogens was done by comparing the DNA sequences of the histone h3 region. These isolates originating from the rhizosphere soils of chestnut constituted a clade with other closely related species or I. radicicola isolates originating from ginseng or other host plants, respectively. Additionally, the pathogenicity tests to analyze the characteristics of these I. radicicola isolates revealed that they caused weakly virulent root rot on ginseng. Conclusions: This is the first study reporting that I. radicicola isolates from chestnut rhizosphere soils can attack ginseng plant in Korea. Thus, these results are expected to provide informations in the selection of suitable fields for ginseng cultivation.