Hub genes and sub‐networks of stoma‐related genes in Hylocereus undatus through trypsin treatment during storage revealed by transcriptomic analysis

2020 ◽  
Author(s):  
Xin Li ◽  
Bairu Li ◽  
Suixia Guan ◽  
Luning Cai ◽  
Pang Xinyue
Keyword(s):  
Transcriptomic Analysis ◽  
Trypsin Treatment ◽  
Hub Genes ◽  
Hylocereus Undatus

scholarly journals Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Xin Li ◽  
Xueru Liu ◽  
Xinyue Pang ◽  
Yong Yin ◽  
Huichun Yu ◽  
...  
Keyword(s):  
Transcriptomic Analysis ◽  
Trypsin Treatment ◽  
Hub Genes ◽  
Ros Metabolism ◽  
Hylocereus Undatus ◽  
Superoxide Scavenger

scholarly journals Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage

2019 ◽  
Author(s):  
Xin Li ◽  
Liu Xueru ◽  
Pang Xinyue ◽  
Yin Yong ◽  
Yu Huichun ◽  
...  
Keyword(s):  
Active Oxygen Species ◽  
Membrane Lipid ◽  
Regulatory Mechanisms ◽  
Trypsin Treatment ◽  
Fruit Storage ◽  
Protein Protein Interaction ◽  
Ros Metabolism ◽  
Malondialdehyde Content ◽  
Hylocereus Undatus ◽  
Related Proteins

Abstract Background It was demonstrated in our previous research that trypsin scavenges superoxide anions. In this study, the mechanisms of storage quality improvement by trypsin were evaluated in H. undatus .Results Trypsin significantly delayed the weight loss and decreased the levels of ROS and membrane lipid peroxidation. Transcriptome profiles of H. undatus treated with trypsin revealed the pathways and regulatory mechanisms of ROS genes that were up- or downregulated following trypsin treatment by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses. The current results showed that through the regulation of the expression of hub redox enzymes, especially thioredoxin-related proteins, trypsin can maintain low levels of endogenous active oxygen species, reduce malondialdehyde content and delay fruit aging. In addition, the results of protein-protein interaction networks suggested that the downregulated NAD(P)H and lignin pathways might be the key regulatory mechanisms governed by trypsin.Conclusions Trypsin significantly prolonged the storage life of H. undatus through regulatory on the endogenous ROS metabolism. As a new biopreservative, trypsin is highly efficient, safe and economical. Therefore, trypsin possesses technical feasibility for the quality control of fruit storage.

scholarly journals Transcriptomic analysis of tumor tissues and organoids reveals the crucial genes regulating the proliferation of lung adenocarcinoma

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Xiao Ma ◽  
Su Yang ◽  
Hesheng Jiang ◽  
Yujie Wang ◽  
Zhen Xiang
Keyword(s):  
Network Analysis ◽  
Lung Adenocarcinoma ◽  
Signaling Pathways ◽  
Signaling Pathway ◽  
Cell Lines ◽  
Cancer Biology ◽  
Transcriptomic Analysis ◽  
Hub Genes ◽  
Prognostic Analysis ◽  
Tumor Tissues

Abstract Background Accumulative evidence shows that an organoid is a more practical and reliable tool in cancer biology research. This study aimed to identify and validate crucial genes involved in non-small cell lung cancer carcinogenesis and development using the transcriptomic analysis of tumor tissues and organoids. Methods Gene set enrichment analysis (GSEA) of tumor tissues, tumor organoids, and normal tissues was performed to reveal the similar and different mechanisms involved in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) carcinogenesis and progression. Differentially expressed gene analysis, prognostic analysis, and gene co-expression network analysis were further used to identify hub genes involved in LUAD and LUSC carcinogenesis and development. Finally, LUAD cell lines and organoids were used to validate these findings. Results GSEA analysis was performed to reveal the similar mechanisms involved in LUAD and LUSC carcinogenesis and development, such as P53 signaling pathway, base mismatch repair, DNA replication, cAMP signaling pathway and PPAR pathway. However, comparing with LUSC organoids, LUAD organoids showed downregulation of immune-related pathways, inflammation-related pathways, MAPK signaling pathways, and Rap1 signaling pathways, although these pathways were downregulated in LUAD and LUSC tissues by comparing with normal lung tissues. Further gene co-expression network analysis and prognostic analysis indicated CDK1, CCNB2, and CDC25A as the hub tumor-promoting genes in LUAD but not in LUSC, which were further validated in other datasets. Using LUAD cell lines and organoid models, CDK1 and CCNB2 knockdown were found to suppress LUAD proliferation. However, CDC25A knockdown did not inhibit LUAD cell line proliferation but could effectively suppress LUAD organoid growth, indicating that an organoid could be used as an effective tool to study cancer biology in LUAD. Conclusions The results revealed CDK1, CCNB2, and CDC25A as the hub genes involved in LUAD carcinogenesis and development, which could be used as the potential biomarkers and targets for LUAD.

Transcriptomic analysis reveals key genes associated with the biosynthesis regulation of phenolics in fresh-cut pitaya fruit (Hylocereus undatus)

2021 ◽  
Vol 181 ◽  
pp. 111684
Author(s):  
Xiaoan Li ◽  
Bingru Li ◽  
Dedong Min ◽  
Nana Ji ◽  
Xinhua Zhang ◽  
...  
Keyword(s):  
Transcriptomic Analysis ◽  
Fresh Cut ◽  
Key Genes ◽  
Hylocereus Undatus ◽  
Biosynthesis Regulation

Transcriptomic analysis reveals key genes related to antioxidant mechanisms of Hylocereus undatus quality improvement by trypsin during storage

2019 ◽  
Vol 10 (12) ◽  
pp. 8116-8128 ◽  
Author(s):  
Xin Li ◽  
Xueru Liu ◽  
Yong Yin ◽  
Huichun Yu ◽  
Min Zhang ◽  
...  
Keyword(s):  
Antioxidant Enzymes ◽  
Quality Improvement ◽  
Transcriptomic Analysis ◽  
Ppi Network ◽  
Storage Quality ◽  
System P ◽  
Key Genes ◽  
Hylocereus Undatus ◽  
Antioxidant Mechanisms

The synergistic effect of trypsin with antioxidant enzymes can improve the storage quality of H. undatus. Transcriptomic analysis and PPI network indicated that CAT is the key one among the enzymes of the complicated antioxidant system.

scholarly journals Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage

2020 ◽  
Author(s):  
Xin Li ◽  
Liu Xueru ◽  
Pang Xinyue ◽  
Yin Yong ◽  
Yu Huichun ◽  
...  
Keyword(s):  
Active Oxygen Species ◽  
Membrane Lipid ◽  
Regulatory Mechanisms ◽  
Trypsin Treatment ◽  
Fruit Storage ◽  
Protein Protein Interaction ◽  
Ros Metabolism ◽  
Malondialdehyde Content ◽  
Hylocereus Undatus ◽  
Related Proteins

Abstract Background: It was demonstrated in our previous research that trypsin scavenges superoxide anions. In this study, the mechanisms of storage quality improvement by trypsin were evaluated in H. undatus. Results: Trypsin significantly delayed the weight loss and decreased the levels of ROS and membrane lipid peroxidation. Transcriptome profiles of H. undatus treated with trypsin revealed the pathways and regulatory mechanisms of ROS genes that were up- or downregulated following trypsin treatment by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses. The current results showed that through the regulation of the expression of hub redox enzymes, especially thioredoxin-related proteins, trypsin can maintain low levels of endogenous active oxygen species, reduce malondialdehyde content and delay fruit aging. In addition, the results of protein-protein interaction networks suggested that the downregulated NAD(P)H and lignin pathways might be the key regulatory mechanisms governed by trypsin.Conclusions: Trypsin significantly prolonged the storage life of H. undatus through regulatory on the endogenous ROS metabolism. As a new biopreservative, trypsin is highly efficient, safe and economical. Therefore, trypsin possesses technical feasibility for the quality control of fruit storage.

scholarly journals Transcriptomic Analysis Reveals Cu/Zn SODs Acting as Hub Genes of SODs in Hylocereus undatus Induced by Trypsin during Storage

Antioxidants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 162 ◽  
Author(s):  
Xinyue Pang ◽  
Xinling Li ◽  
Xueru Liu ◽  
Luning Cai ◽  
Bairu Li ◽  
...  
Keyword(s):  
Metal Ion ◽  
Antioxidant Activities ◽  
Defense Responses ◽  
Transcriptomic Analysis ◽  
Scale Free ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Free Network ◽  
Hylocereus Undatus

It has been revealed by us that superoxide scavenging is a new activity of trypsin. In this study, the synergistic mechanisms of trypsin and superoxide dismutases (SODs) were evaluated in Hylocereus undatus (pitaya). Trypsin significantly improved the storage quality of H. undatus, including weight loss impediment and decrease of cellular injury. The regulatory mechanisms of 16 SOD genes by trypsin were revealed using transcriptomic analysis on H. undatus. Results revealed that important physiological metabolisms, such as antioxidant activities or metal ion transport were induced, and defense responses were inhibited by trypsin. Furthermore, the results of protein–protein interaction (PPI) networks showed that besides the entire ROS network, the tiny SODs sub-network was also a scale-free network. Cu/Zn SODs acted as the hub that SODs synergized with trypsin during the storage of H. undatus.

scholarly journals Genome-wide transcriptomic analysis of a desert willow, Salix psammophila, reveals the function of hub genes SpMDP1 and SpWRKY33 in drought tolerance

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Huixia Jia ◽  
Jin Zhang ◽  
Jianbo Li ◽  
Pei Sun ◽  
Yahong Zhang ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Transcriptomic Analysis ◽  
Hub Genes ◽  
Genome Wide

scholarly journals Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage

2020 ◽  
Author(s):  
Xin Li ◽  
Liu Xueru ◽  
Pang Xinyue ◽  
Yin Yong ◽  
Yu Huichun ◽  
...  
Keyword(s):  
Active Oxygen Species ◽  
Membrane Lipid ◽  
Regulatory Mechanisms ◽  
Trypsin Treatment ◽  
Fruit Storage ◽  
Protein Protein Interaction ◽  
Ros Metabolism ◽  
Malondialdehyde Content ◽  
Hylocereus Undatus ◽  
Related Proteins

Abstract Background: It was demonstrated in our previous research that trypsin scavenges superoxide anions. In this study, the mechanisms of storage quality improvement by trypsin were evaluated in H. undatus. Results: Trypsin significantly delayed the weight loss and decreased the levels of ROS and membrane lipid peroxidation. Transcriptome profiles of H. undatus treated with trypsin revealed the pathways and regulatory mechanisms of ROS genes that were up- or downregulated following trypsin treatment by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses. The current results showed that through the regulation of the expression of hub redox enzymes, especially thioredoxin-related proteins, trypsin can maintain low levels of endogenous active oxygen species, reduce malondialdehyde content and delay fruit aging. In addition, the results of protein-protein interaction networks suggested that the downregulated NAD(P)H and lignin pathways might be the key regulatory mechanisms governed by trypsin.Conclusions: Trypsin significantly prolonged the storage life of H. undatus through regulatory on the endogenous ROS metabolism. As a new biopreservative, trypsin is highly efficient, safe and economical. Therefore, trypsin possesses technical feasibility for the quality control of fruit storage.

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