• Genomics & Informatics
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• 제17권1호
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• pp.2.1-2.12
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• 2019

Chronic obstructive pulmonary disease (COPD) is a type of progressive lung disease, featured by airflow obstruction. Recently, a comprehensive analysis of the transcriptome in lung tissue of COPD patients was performed, but the heterogeneity of the sample was not seriously considered in characterizing the mechanistic dysregulation of COPD. Here, we established a new transcriptome analysis pipeline using a deconvolution process to reduce the heterogeneity and clearly identified that these transcriptome data originated from the mild or moderate stage of COPD patients. Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. Computational protein localization prediction revealed that 19 proteins showing changes in subcellular localization were mostly related to mitochondria, suggesting that mislocalization of mitochondria-targeting proteins plays an important role in COPD pathology. Our extensive evaluation of COPD transcriptome data could provide guidelines for analyzing heterogeneous gene expression profiles and classifying potential candidate genes that are responsible for the pathogenesis of COPD.

• Journal of Plant Biotechnology
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• 제48권3호
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• pp.148-155
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• 2021

Gibberellins (GAs) are essential phytohormones for plant growth that influence developmental processes and crop yields. Recent functional genomic analyses of model plants have yielded good characterizations of the canonical GA signaling pathways and related genes. Although Panax ginseng has long been considered to have economic and medicinal importance, functional genomic studies of the GA signaling pathways in this crucial perennial herb plant have been rarely conducted. Here, we identified and performed functional analysis of the GA signaling-related genes, including PgGID1s, PgSLY1s, and PgRGAs. We confirmed that the physiological role of GA signaling components in P. ginseng was evolutionarily conserved. In addition, the important functional domains and amino acid residues for protein interactions among active GA, GID1, SCF^SLY1, and RGA were also functionally conserved. Prediction and comparison of crystallographic structural similarities between PgGID1s and AtGID1a supported their function as GA receptors. Moreover, the subcellular localization and GA-dependent promotion of DELLA degradation in P. ginseng was similar to the canonical GA signaling pathways in other plants. Finally, we found that overexpression of PgRGA2 and PgSLY1-1 was sufficient to complement the GA-related phenotypes of atgid1a/c double- and rga quintuple-mutants, respectively. This critical information for these GA signaling genes has the potential to facilitate future genetic engineering and breeding of P. ginseng for increased crop yield and production of useful substances.

• Journal of Plant Biotechnology
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• 제48권3호
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• pp.165-172
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• 2021

식물과 동물 모두 단백질체 분석을 위해 계면활성제를 사용하여 단백질을 효과적으로 가용화 하는 것은 매우 중요하다. 여러 계면활성제 중 광분해성의 Azo는 MS 분석에 적합하며 단백질을 효과적으로 잘 가용화 하는 등의 여러 이점을 보여주었다. 그러나 대부분이 동물 단백질체 분석에 적용되어 있었으며 식물 단백질체 분석에의 적용은 미비하였다. 따라서 본 연구에서는 벼 잎의 단백질체 분석을 위한 계면활성제로 Azo를 사용하여 SDS와 비교 분석을 수행하였다. 비표지 단백질체 정량 분석, 단백질 기능 분석, 세포내 단백질체의 위치 확인 분석 및 KEGG 경로 분석을 수행하였으며, 그 결과 SDS와 비교하였을 때 Azo의 단백질 가용화 효율이 전혀 떨어지지 않음을 확인하였다. 이는 앞으로 벼 뿐만 아니라 식물단백질체 분석 시에 광분해성 계면활성제인 Azo의 적용 가능성이 무궁무진함을 의미 한다.