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Unknown,Transcriptomics,Genomics,Proteomics

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Anti-Stress Effect of Red Ginseng via Repression of PADI4 by ER-beta Stimulation

ABSTRACT: Ginseng has been used for anti-stress agents, and its active ingredient, ginsenoside, has similar structure with estrogen. In this study, effects of red ginseng (RG) on gene expressions in immobilization (IMO) stressed mice brain was analyzed by system biology.

ORGANISM(S): Mus musculus

SUBMITTER: Choi Sangdun

PROVIDER: E-MTAB-856 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Systems biology analysis of Korean red ginseng effects on Immobilization stressed mice brain

Project description:Here we present molecular mechanisms of Korean red ginseng (KRG) on immobilization stresses Keywords: stress response Mice were divided into three groups (3 mice / group): control, stress + no treat, and stress + Korean Red Ginseng (KRG, 100 mg). Stress + KRG group were given KRG 100 mg orally for 7 days and then exposed to immobilization stress for 45 min. stress + no treat group were administrated with phosphate buffer saline (d-PBS, pH 7.4) together with IMO stress for 45 min.

2010-05-15 | E-GEOD-12656 | biostudies-arrayexpress

De novo sequencing and analysis of the Panax ginseng transcriptome in the leaf-expansion period

Project description:In order to analyze the transcriptome of ginseng root during leaf-expansion period and discover the genes during development, a cDNA sample was prepared from the leaf-expansion period of ginseng root and sequenced using the Illumina sequencing platform.The transcriptomic sequencing technology was set up the first time for five years the transcription of the ginseng root in the leaf-expansion period.

2013-06-15 | E-MTAB-974 | biostudies-arrayexpress

Transcriptional profiling by high throughput sequencing of Panax ginseng C.A. Meyer leaf and stem transcriptomes during the leaf-expansion period.

Project description:In order to research the ginseng leaf-stem gene expression profiles of and dig out its function genes in the leaf-expansion period, the transcriptomic sequencing technology was set up the first time for five years the transcription of the Panax ginseng leaf-stem in the leaf-expansion period.

2012-07-31 | E-MTAB-937 | biostudies-arrayexpress

Analysis of Panax ginseng secreted proteins under salt stress

Project description:Salt stress is one of the major abiotic stresses affecting the yield of ginseng (Panax ginseng C. A. Meyer). The objective of this study was to identify proteins of ginseng, which is responsive in salt stress. In this direction, ginseng plants of different growth stages (3, 4 and 5 years), were grown in the hydroponic conditions and exposed to 5 ds/m salt concentration. The secreted proteins, collected from the water, at 0, 24, 72 and 120 hours after exposure were used for the proteome analysis using shotgun approaches. Through the shotgun proteomics, a total of 155 and 88 secreted proteins were identified by searching in two RNA-sequencing (RNA-seq) database, respectively.

2022-11-17 | PXD010322 | Pride

Transcript profiles of the flowering period Panax ginseng C.A. Meyer root and analysis the gene function

Project description:Panax ginseng C.A. Meyer is one of the most popular medicinal herbs. In order to research the genes that related to the flowering period of ginseng, and find out the antifungal proteins and transcription factors that combat various biotic and abiotic stress, a cDNA sample was prepared from the flowering period ginseng root of a five-year-old plant and sequenced using the Illumina sequencing platform. In this study, we produced nearly 40 million sequencing reads. These reads were assembled into 134,045 contigs using Trinity software (mean size: 282 bp). Based on a similarity search with known proteins, we identified 79,307 sequences with a cut-off E-value of 10-5. Assembled sequences were then annotated using gene ontology (GO) terms, clusters of orthologous group (COG) classifications and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways respectively.

2014-07-25 | E-MTAB-1239 | biostudies-arrayexpress

Label-free quantitative proteomic approach to investigate the effect of heat stress on Panax ginseng leaves

Project description:Ginseng is one of the well-known medicinal plants, exhibiting diverse medicinal effects. Its roots possess anticancer and anti-aging properties and are being used in the medical systems of East Asian countries. Ginseng is grown in low-light and low-temperature conditions and its growth is strongly inhibited at temperatures above 25 ℃. However, the molecular responses of ginseng to heat stress are currently poorly understood, especially at protein level. Therefore, here we utilized a shotgun proteomics approach to investigate the effect of heat stress on ginseng leaves. Total proteins were isolated from control (25 ℃) and ginseng plants exposed to 35 ℃ for 1 and 3 days and subjected to in-solution trypsin digestion. A total of 3,359 ginseng proteins were identified when searched in an in-house developed RNA-seq (PAC-BIO) database.

2018-12-11 | PXD009124 | Pride

Proteomic analysis of Panax ginseng leaves subjected to salinity stress

Project description:Ginseng is an important crop in East Asia due to its medicinal and nutritional benefits originating from ingredients such as the ginsenosides. Numerous researches have been directed to cultivate ginseng with high yield especially targeting its growth and development for protection against abiotic stresses, which are affecting both the yield and quality. Particularly, salinity has been characterized as a major abiotic stressor that affects the annual yield of ginseng. Therefore, to characterize the salt-responsive proteins in the ginseng plant, ginseng leaves were harvested post-treatment with salt in a time-dependent manner. Utilizing a label-free quantitative proteome analysis approach, this study identified a total of 2,484 proteins. Among them, 468 proteins showed a significant modulation in their abundance among ginseng leaf samples at 4 different time points (0, 24, 72, 96 h) following salt stress. Further functional classification revealed that catalase-peroxidase 2, voltage-gated potassium channel subunit beta-2, fructose-1,6-bisphosphatase class 1, and chlorophyll a-b binding protein associated proteins accumulated in response to the salt stress. Of these, glycosyl hydrolase 17 (GH17) showed similar abundance profiles at both the transcript and proteome level. Therefore, for further understanding of GH17 underlying salt stress response mechanism, GH17 overexpressing transgenic Arabidopsis were generated. In response to salt stress, transgenic plants uncovered a tolerance phenotype without compromising plant growth. The proteome alterations in response to salt stress presented here resulted in identifying a protein GH17 with a potential key role in salt-stressed ginseng.

2023-03-11 | PXD038524 | Pride

Optimization of Protein Isolation and Label–free Quantitative Proteomic Analysis in Four Different Tissues of Korean Ginseng

Project description:Korean ginseng is one of the most valuable medicinal plants worldwide. Yet, our understanding of ginseng proteomics is largely limited due to difficulties in extraction and resolution of ginseng proteins because of the presence of natural contaminants such as polysaccharides, phenols, and glycosides. Here, we compared four different protein extraction methods, namely, TCA/acetone, TCA/acetone–MeOH/chloroform, Phenol–TCA/acetone, and Phenol–MeOH/chloroform methods. Consequently, the TCA/acetone–MeOH/chloroform method displayed the highest extraction efficiency, thus it was used for the comparative proteome profiling of leaf, root, shoot, and fruit by a label–free quantitative proteomics approach. This approach led to the identification of 2,604 significantly modulated proteins among four tissues. We could pinpoint differential pathways and proteins associated with ginsenoside biosynthesis including the methylerythritol 4–phosphate (MEP) pathway, the mevalonate (MVA) pathway, UDP–glycosyltransferases (UGTs), and oxidoreductases (CYP450s). The current study reports an efficient and reproducible method for the isolation of proteins from a wide range of ginseng tissues and provides a detailed organ–based proteome map and a more comprehensive view of enzymatic alterations in ginsenoside biosynthesis.

2021-09-07 | PXD022914 | Pride

Characterization of hyperglycemia due to sub-chronic administration of red ginseng extract via comparative global proteomic analysis

Project description:Ginseng (Panax ginseng Meyer) is commonly used as an herbal remedy worldwide. Few studies have explored the possible physiological changes in the liver although patients often self-medicate with ginseng preparations, which may lead to exceeding the recommended dose for long-term administration. Here, we analyzed changes in the hepatic proteins of mouse livers using quantitative proteomics after sub-chronic administration of Korean red ginseng (KRG) extract (control group and 0.5, 1.0, and 2.0 g/kg KRG) using tandem mass tag (TMT) 6‐plex technology. The 1.0 and 2.0 g/kg KRG groups exhibited signs of liver injury, including increased levels of aspartate transaminase (AST) and alanine aminotransferase (ALT) in the serum. Furthermore, serum glucose levels were significantly higher following KRG administration compared with the control group. Based on the upregulated proteins found in the proteomic analysis, we found that increased cystathionin beta-synthase (CBS) and cystathionine gamma-lyase (CSE) levels promoted greater hydrogen sulfide (HRR2RRS) synthesis in the liver. This investigation provides novel evidence that14T sub-chronic administration of 4T14TKRG can elevate HRR2RRS production by increasing protein expression of CBS and CSE in the liver.

2021-09-10 | PXD023731 | Pride

Analysis of differential genetic expression by dietary intervention using moderate-carbohydrate restriction diet (MCD) in B16F10 xenografted mouse model.

Project description:We performed survival analysis of control and MCD groups, and explored underlying tumor suppression mechanisms after dietary intervention, focused on alterations in the energy-dependent signaling pathways, histone modifications, and global gene expression differences on cDNA microarray study. Illumina arrays: Five- week- old male C57BL6 mice were randomly divided into two groups and fed control diet (control group, LabDiet, Brentwood, MO, USA) or moderate restriced carbohydrate diet formula (MCD, Treat group) in a specific pathogen free zone. All procedures were approved by the institutional animal use and care committee. Following a preliminary feeding of each diet formula for one week, 1 × 106 B16F10 cells (suspended with 100 μl of PBS) were subcutaneously injected into the back of the mice. After 2 weeks of diet supplementation, all mice were sacrificed. Tumor tissue was excised for cDNA microarray. Agilent arrays: Five- week- old male C57BL6 mice were randomly divided into two groups and fed control diet (control group, LabDiet, Brentwood, MO, USA) or moderate restriced carbohydrate diet formula (MCD, Treat group) in a specific pathogen free zone. All procedures were approved by the institutional animal use and care committee. Following a preliminary feeding of each diet formula for one week, 1 × 106 B16F10 cells (suspended with 100 μl of PBS) were subcutaneously injected into the back of the mice. After 2 weeks of diet supplementation, all mice were sacrificed. Tumor tissue was excised for chip-on-chip microarray.

2012-03-21 | E-GEOD-36633 | biostudies-arrayexpress

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