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Article ; Online: Pan-Genomic and Transcriptomic Analyses of Marine Pseudoalteromonas agarivorans Hao 2018 Revealed Its Genomic and Metabolic Features

Yuhao Jv / Chenxiang Xi / Yanqiu Zhao / Wei Wang / Yiling Zhang / Kai Liu / Wenlin Liu / Kai Shan / Chunlei Wang / Ruiwen Cao / Cunxi Dai / Yiting Jv / Wenxing Zhu / Haiyong Wang / Qiuxia He / Lujiang Hao

Marine Drugs, Vol 20, Iss 248, p

2022 Volume 248

Abstract: The genomic and carbohydrate metabolic features of Pseudoalteromonas agarivorans Hao 2018 ( P ... agarivorans Hao 2018) were investigated through pan-genomic and transcriptomic analyses, and key enzyme genes ... with the stationary phase (24 h), strain P. agarivorans Hao 2018 had upregulated expression of genes related ...

Abstract	The genomic and carbohydrate metabolic features of Pseudoalteromonas agarivorans Hao 2018 ( P. agarivorans Hao 2018) were investigated through pan-genomic and transcriptomic analyses, and key enzyme genes that may encode the process involved in its extracellular polysaccharide synthesis were screened. The pan-genome of the P. agarivorans strains consists of a core-genome containing 2331 genes, an accessory-genome containing 956 genes, and a unique-genome containing 1519 genes. Clusters of Orthologous Groups analyses showed that P. agarivorans harbors strain-specifically diverse metabolisms, probably representing high evolutionary genome changes. The Kyoto Encyclopedia of Genes and Genomes and reconstructed carbohydrate metabolic pathways displayed that P. agarivorans strains can utilize a variety of carbohydrates, such as d -glucose, d -fructose, and d -lactose. Analyses of differentially expressed genes showed that compared with the stationary phase (24 h), strain P. agarivorans Hao 2018 had upregulated expression of genes related to the synthesis of extracellular polysaccharides in the logarithmic growth phase (2 h), and that the expression of these genes affected extracellular polysaccharide transport, nucleotide sugar synthesis, and glycosyltransferase synthesis. This is the first investigation of the genomic and metabolic features of P. agarivorans through pan-genomic and transcriptomic analyses, and these intriguing discoveries provide the possibility to produce novel marine drug lead compounds with high biological activity.
Keywords	Pseudoalteromonas agarivorans ; pan-genome ; genomic and metabolic features ; KEGG analysis ; transcriptome analysis ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Effect of Different Initial Fermentation pH on Exopolysaccharides Produced by Pseudoalteromonas agarivorans Hao 2018 and Identification of Key Genes Involved in Exopolysaccharide Synthesis via Transcriptome Analysis

Ju, Yuhao / Shan, Kai / Liu, Wenlin / Xi, Chenxiang / Zhang, Yiling / Wang, Wei / Wang, Chunlei / Cao, Ruiwen / Zhu, Wenxing / Wang, Haiyong / Zhao, Yanqiu / Hao, Lujiang

Marine drugs. 2022 Jan. 20, v. 20, no. 2

2022

Abstract: ... monosaccharide composition, and antioxidant activity of the EPSs of Pseudoalteromonas agarivorans Hao 2018 ... In addition, the transcriptome sequence of P. agarivorans Hao 2018 under different initial fermentation pH ...

Abstract	Exopolysaccharides (EPSs) are carbohydrate polymers produced and secreted by microorganisms. In a changing marine environment, EPS secretion can reduce damage from external environmental disturbances to microorganisms. Meanwhile, EPSs have promising application prospects in the fields of food, cosmetics, and pharmaceuticals. Changes in external environmental pH have been shown to affect the synthesis of EPSs in microorganisms. In this study, we analyzed the effects of different initial fermentation pHs on the production, monosaccharide composition, and antioxidant activity of the EPSs of Pseudoalteromonas agarivorans Hao 2018. In addition, the transcriptome sequence of P. agarivorans Hao 2018 under different initial fermentation pH levels was determined. GO and KEGG analyses showed that the differentially expressed genes were concentrated in the two-component regulatory system and bacterial chemotaxis pathways. We further identified the expression of key genes involved in EPS synthesis during pH changes. In particular, the expression of genes encoding the glucose/galactose MFS transporter, phosphomannomutase, and mannose-1-phosphate guanylyltransferase was upregulated when the environmental pH increased, thus promoting EPS synthesis. This study not only contributes to elucidating the environmental adaptation mechanisms of P. agarivorans, but also provides important theoretical guidance for the directed development of new products using biologically active polysaccharides.
Keywords	Pseudoalteromonas ; antioxidant activity ; chemotaxis ; cosmetics ; drugs ; exopolysaccharides ; fermentation ; galactose ; gene expression regulation ; glucose ; marine environment ; pH ; phosphomannomutase ; secretion ; transcriptome ; transcriptomics
Language	English
Dates of publication	2022-0120
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2175190-0
ISSN	1660-3397
ISSN	1660-3397
DOI	10.3390/md20020089
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Effect of Different Initial Fermentation pH on Exopolysaccharides Produced by Pseudoalteromonas agarivorans Hao 2018 and Identification of Key Genes Involved in Exopolysaccharide Synthesis via Transcriptome Analysis

Yuhao Ju / Kai Shan / Wenlin Liu / Chenxiang Xi / Yiling Zhang / Wei Wang / Chunlei Wang / Ruiwen Cao / Wenxing Zhu / Haiyong Wang / Yanqiu Zhao / Lujiang Hao

Marine Drugs, Vol 20, Iss 89, p

2022 Volume 89

Abstract	Exopolysaccharides (EPSs) are carbohydrate polymers produced and secreted by microorganisms. In a changing marine environment, EPS secretion can reduce damage from external environmental disturbances to microorganisms. Meanwhile, EPSs have promising application prospects in the fields of food, cosmetics, and pharmaceuticals. Changes in external environmental pH have been shown to affect the synthesis of EPSs in microorganisms. In this study, we analyzed the effects of different initial fermentation pHs on the production, monosaccharide composition, and antioxidant activity of the EPSs of Pseudoalteromonas agarivorans Hao 2018. In addition, the transcriptome sequence of P. agarivorans Hao 2018 under different initial fermentation pH levels was determined. GO and KEGG analyses showed that the differentially expressed genes were concentrated in the two-component regulatory system and bacterial chemotaxis pathways. We further identified the expression of key genes involved in EPS synthesis during pH changes. In particular, the expression of genes encoding the glucose/galactose MFS transporter, phosphomannomutase, and mannose-1-phosphate guanylyltransferase was upregulated when the environmental pH increased, thus promoting EPS synthesis. This study not only contributes to elucidating the environmental adaptation mechanisms of P. agarivorans , but also provides important theoretical guidance for the directed development of new products using biologically active polysaccharides.
Keywords	marine bacteria ; structural analysis ; transcriptome sequence ; KEGG analysis ; GO analysis ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Yin-Chen-Hao-Tang alleviates biliary obstructive cirrhosis in rats by inhibiting biliary epithelial cell proliferation and activation.

Wang, Bing / Sun, Ming-Yu / Long, Ai-Hua / Cao, Hong-Yan / Ren, Shuang / Bian, Yan-Qin / Lu, Xiong / Gu, Hong-Tu / Liu, Cheng-Hai / Liu, Ping

Pharmacognosy magazine

2015 Volume 11, Issue 42, Page(s) 417–425

Abstract: Background: Yin-Chen-Hao-Tang (YCHT) consists of three aqueous extracts from Artemisia capillaris ...

Abstract	Background: Yin-Chen-Hao-Tang (YCHT) consists of three aqueous extracts from Artemisia capillaris, Gardenia sp., and prepared Rheum rhabarbarum (rhubarb) (3:2:1). YCHT is characterized by its anti-inflammatory properties in liver regulation and relief of jaundice. We aimed to study the effects and mechanisms of action of YCHT on biliary obstructive cirrhosis. Materials and methods: Secondary biliary fibrosis was induced in rats by bile duct ligation (BDL) and scission. One week after BDL, rats were randomly divided into a saline-treated BDL or YCHT-treated BDL group for 4 weeks. Liver function and hepatic hydroxyproline (Hyp) content were assessed. Types I and IV collagen (Col-IV), laminin, fibronectin, alpha smooth muscle actin (α-SMA), and proliferating cell nuclear antigen protein and messenger ribonucleic acid (mRNA) expression were assessed with immunohistochemistry and real-time polymerase chain reaction. Results: In the YCHT-treated BDL group, serum total bilirubin, total bile acids, aspartate aminotransferase, alanine aminotransferase, and γ-glutamyl transferase were lower than those in the sham-operated BDL group. The proliferation of bile ducts in hepatic tissues and the Hyp content and Col deposition were also significantly lower than those in control rats. In addition, α-SMA and Col-IV staining was less obvious, and mRNA expression of Procol-α1 (IV), platelet derived growth factor subunit B (PDGF)-B, connective tissue growth factor, and transforming growth factor-beta in proliferative biliary epithelial cells (BECs) in the YCHT-treated BDL group was significantly lower than those in controls. Conclusions: YCHT effectively reduces the formation of biliary obstructive cirrhosis mainly via inhibition of BEC proliferation by down-regulation of PDGF-B mRNA expression, inhibition of BEC profibrogenic paracrines, and the epithelial-mesenchymal transition pathological process.
Language	English
Publishing date	2015-01-29
Publishing country	India
Document type	Journal Article
ZDB-ID	2274976-7
ISSN	0976-4062 ; 0973-1296
ISSN (online)	0976-4062
ISSN	0973-1296
DOI	10.4103/0973-1296.153098
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Development and Application of an UHPLC-MS/MS Method for Comparative Pharmacokinetic Study of Eight Major Bioactive Components from Yin Chen Hao Tang in Normal and Acute Liver Injured Rats.

Wang, Yun / Xing, Xinrui / Cao, Yan / Zhao, Liang / Sun, Sen / Chen, Yang / Chai, Yifeng / Chen, Si / Zhu, Zhenyu

Evidence-based complementary and alternative medicine : eCAM

2018 Volume 2018, Page(s) 3239785

Abstract: Yin Chen Hao Tang (YCHT) is one of the most famous hepatoprotective herbal formulas in China ...

Abstract	Yin Chen Hao Tang (YCHT) is one of the most famous hepatoprotective herbal formulas in China, but its pharmacokinetic investigation in model rats has been rarely conducted. In this study, the hepatic injury model was caused by intraperitoneal injections of carbon tetrachloride (CCl
Language	English
Publishing date	2018-11-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2171158-6
ISSN	1741-4288 ; 1741-427X
ISSN (online)	1741-4288
ISSN	1741-427X
DOI	10.1155/2018/3239785
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Article: Corrigendum to "Development and Application of an UHPLC-MS/MS Method for Comparative Pharmacokinetic Study of Eight Major Bioactive Components from Yin Chen Hao Tang in Normal and Acute Liver Injured Rats".

Wang, Yun / Xing, Xinrui / Cao, Yan / Zhao, Liang / Sun, Sen / Chen, Yang / Chai, Yifeng / Chen, Si / Zhu, Zhenyu

Evidence-based complementary and alternative medicine : eCAM

2018 Volume 2018, Page(s) 3024841

Abstract: This corrects the article DOI: 10.1155/2018/3239785.]. ...

Abstract	[This corrects the article DOI: 10.1155/2018/3239785.].
Language	English
Publishing date	2018-12-16
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	2171158-6
ISSN	1741-4288 ; 1741-427X
ISSN (online)	1741-4288
ISSN	1741-427X
DOI	10.1155/2018/3024841
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Article ; Online: Development and Application of an UHPLC-MS/MS Method for Comparative Pharmacokinetic Study of Eight Major Bioactive Components from Yin Chen Hao Tang in Normal and Acute Liver Injured Rats

Yun Wang / Xinrui Xing / Yan Cao / Liang Zhao / Sen Sun / Yang Chen / Yifeng Chai / Si Chen / Zhenyu Zhu

Evidence-Based Complementary and Alternative Medicine, Vol

2018 Volume 2018

Abstract: Yin Chen Hao Tang (YCHT) is one of the most famous hepatoprotective herbal formulas in China ...

Abstract	Yin Chen Hao Tang (YCHT) is one of the most famous hepatoprotective herbal formulas in China, but its pharmacokinetic investigation in model rats has been rarely conducted. In this study, the hepatic injury model was caused by intraperitoneal injections of carbon tetrachloride (CCl4), and YCHT was orally administered to the model and normal rats. An ultrahigh performance liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS) method was established to analyze the plasma pharmacokinetics of eight major bioactive ingredients from YCHT in both the normal and liver injured rats. The calibration curves presented good linearity (r > 0.9981) in the concentration range. The relative standard deviation (RSD%) of inter- and intraday precision was within 9.55%, and the accuracy (RE%) ranged from -10.72% to 2.46%. The extraction recovery, matrix effect, and stability were demonstrated to be within acceptable ranges. The lower limit of detection (LLOD) and lower limit of quantitation (LLOQ) were around 0.1 ng/mL and 0.5 ng/mL, respectively, which were much lower than those in other related researches. Results reveal that there are significant differences in the pharmacokinetics of scoparone, geniposide, rhein, aloe-emodin, physcion, and chrysophanol in hepatic injured rats as compared to those in control except for scopoletin and emodin. Our experimental results provide a meaningful reference for the clinical dosage of YCHT in treating liver disorders, and the improvement of LLOD and LLOQ can also broaden the range of our method’s application, which is very suitable for quantitating these eight compounds with low levels.
Keywords	Other systems of medicine ; RZ201-999
Subject code	610
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Analysis of the constituents in the rat plasma after oral administration of Yin Chen Hao Tang by UPLC/Q-TOF-MS/MS.

Wang, Xijun / Sun, Wenjun / Sun, Hui / Lv, Haitao / Wu, Zeming / Wang, Ping / Liu, Lian / Cao, Hongxin

Journal of pharmaceutical and biomedical analysis

2008 Volume 46, Issue 3, Page(s) 477–490

Abstract: ... of Yin Chen Hao Tang (YCHT), a traditional Chinese medical formula, has been established. The UPLC/MS ...

Abstract	A UPLC/Q-TOF-MS/MS method for analyzing the constituents in rat plasma after oral administration of Yin Chen Hao Tang (YCHT), a traditional Chinese medical formula, has been established. The UPLC/MS fingerprints of the samples were established first in vitro and in vivo, with 45 compounds in YCHT and 21 compounds in rat plasma after oral administration of YCHT were detected. Of the 45 detected compounds in vitro, 30 were identified, and all of the 21 compounds detected in rat plasma were identified either by comparing the retention time and mass spectrometry data with that of reference compounds or by mass spectrometry analysis and retrieving the reference literatures. Of the identified 21 compounds in rat plasma, 19 were the original form of compounds absorbed from the 45 detected compounds in vitro, 2 were the metabolites of the compounds existed in YCHT. It is concluded that a rapid and validated method has been developed based on UPLC-MS/MS, which shows high sensitivity and resolution that is more suitable for identifying the bioactive constituents in plasma after oral administration of Chinese herbal medicines, and provides helpful chemical information for further pharmacology and active mechanism research on the Chinese medical formula.
MeSH term(s)	Administration, Oral ; Animals ; Chromatography, High Pressure Liquid/methods ; Drugs, Chinese Herbal/analysis ; Drugs, Chinese Herbal/pharmacokinetics ; Male ; Medicine, Chinese Traditional ; Rats ; Rats, Wistar ; Sensitivity and Specificity ; Spectrometry, Mass, Electrospray Ionization/methods
Chemical Substances	Drugs, Chinese Herbal
Language	English
Publishing date	2008-02-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	604917-5
ISSN	1873-264X ; 0731-7085
ISSN (online)	1873-264X
ISSN	0731-7085
DOI	10.1016/j.jpba.2007.11.014
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Article: Effects of different compounding of formulae on content of gardenoside in Yin Chen Hao decoction.

Liang, Guangyi / Cao, Peixue / Chai, Li / Xian, Furong / Li, Xia

Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan

2002 Volume 22, Issue 1, Page(s) 55–60

Abstract: ... combinations of the ingredients and refined single Chinese drug granules in Yin Chen Hao Decoction compound ...

Abstract	In order to observe the effects of the ground and intact Zhi Zi (Fructus Gardeniae) and different combinations of the ingredients and refined single Chinese drug granules in Yin Chen Hao Decoction compound prescription on the contents of gardenoside (an effective component of the prescription), the contents of gardenoside were determined with reversed phase high performance liquid chromatography (HPLC), with acetonitrile-water (15:85) as mobile phase, at wave length 238 nm. The results indicated that the gardenoside-decocted-out rates in the decoctions prepared by different combinations of the ingredients with the ground Zhi Zi (Fructus Gardeniae) all were higher significantly than those in the decoction with intact Zhi Zi (Fructus Gardeniae), and generally, different combinations of the ingredients in the decoction had only little effect on the gardenoside-decocted-out rate.
MeSH term(s)	Chromatography, High Pressure Liquid/methods ; Drug Compounding ; Drugs, Chinese Herbal/chemistry ; Iridoids ; Pyrans/analysis ; Technology, Pharmaceutical
Chemical Substances	Drugs, Chinese Herbal ; Iridoids ; Pyrans ; gardenoside (INE79XNR2C)
Language	English
Publishing date	2002-03
Publishing country	China
Document type	Comparative Study ; Journal Article
ZDB-ID	603186-9
ISSN	0254-6272 ; 0255-2922
ISSN (online)	0254-6272
ISSN	0255-2922
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Article: Simultaneous determination of 6,7-dimethylesculetin and geniposide in rat plasma and its application to pharmacokinetic studies of Yin Chen Hao Tang preparation.

Wang, Xijun / Lv, Haitao / Sun, Hui / Sun, Wenjun / Liu, Lian / Wang, Ping / Cao, Hongxin

Arzneimittel-Forschung

2008 Volume 58, Issue 7, Page(s) 336–341

Abstract: ... demonstrated for the pharmacokinetic study of a Traditional Chinese Medicine formula of Yin Chen Hao Tang ...

Abstract	A method for the rapid and simultaneous determination of 6,7-dimethylesculetin (CAS 120-08-1) and geniposide (CAS 24512-63-8) in rat plasma has been developed, using validated high performance liquid chromatography (HPLC) with solid phase extraction (SPE). The HPLC analysis was performed on a commercially available column (200 mm x 4.6 mm, 5 microm) with acetonitrile-methanol-0.1% aqueous formic acid as mobile phase and the UV detection at 343 nm and 238 nm for 6,7-dimethylesculetin and geniposide, respectively. The calibration curves for 6,7-dimethylesculetin and geniposide were linear over the range 0.4-25.6 microg/mL and 1.12-71.68 microg/mL, respectively. The lower limits of quantitation were 0.40 microg/ mL and 1.12 microg/mL, and the lower limits of detection were 0.06 microg/mL and 0.09 microg/ mL, respectively. The intra-day and inter-day precision for 6,7-dimethylesculetin and geniposide were < 5%, whereas the absolute recovery percentages were > 74%. A successful application of the developed HPLC analysis was demonstrated for the pharmacokinetic study of a Traditional Chinese Medicine formula of Yin Chen Hao Tang preparation.
MeSH term(s)	Algorithms ; Animals ; Calibration ; Chromatography, High Pressure Liquid ; Coumarins/blood ; Coumarins/pharmacokinetics ; Drugs, Chinese Herbal ; Half-Life ; Iridoids/blood ; Iridoids/pharmacokinetics ; Male ; Rats ; Rats, Wistar ; Reproducibility of Results
Chemical Substances	Coumarins ; Drugs, Chinese Herbal ; Iridoids ; geniposide (145295QLXY) ; scoparone (H5841PDT4Y)
Language	English
Publishing date	2008
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	502081-5
ISSN	1616-7066 ; 0004-4172
ISSN (online)	1616-7066
ISSN	0004-4172
DOI	10.1055/s-0031-1296516
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