Untargeted profiling of field cultivated bush tea (Athrixia phylicoides DC.) based on metabolite analysis

A viral development of statistical data processing, computing capabilities, chromatography-mass spectrometry, and omics technologies (technologies based on the achievements of genomics, transcriptomics, proteomics, metabolomics) in recent decades has not led to formation of a unified protocol for untargeted profiling. Systematic errors reduce the reproducibility and reliability of the obtained results, and at the same time hinder consolidation and analysis of data gained in large-scale multi-day experiments. We propose an algorithm for conducting omics profiling to identify potential markers in the samples of complex composition and present the case study of urine samples obtained from different clinical groups of patients. Profiling was carried out by the method of liquid chromatography mass spectrometry. The markers were selected using methods of multivariate analysis including machine learning and feature selection. Testing of the approach was performed using an independent dataset by clustering and projection on principal components.

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Faculty Opinions recommendation of Global metabolite analysis of yeast: evaluation of sample preparation methods.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1029141.343568 ◽

2005 ◽

Author(s):

Oliver Fiehn

Keyword(s):

Sample Preparation ◽

Metabolite Analysis ◽

Preparation Methods ◽

Sample Preparation Methods

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Faculty Opinions recommendation of Integrated proteome and metabolite analysis of the de-etiolation process in plastids from rice (Oryza sativa L.).

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.721312405.793515226 ◽

2016 ◽

Author(s):

Dario Leister

Keyword(s):

Oryza Sativa ◽

Oryza Sativa L ◽

Metabolite Analysis

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Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass

Biotechnology for Biofuels ◽

10.1186/s13068-021-01950-w ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

James Kirby ◽

Gina M. Geiselman ◽

Junko Yaegashi ◽

Joonhoon Kim ◽

Xun Zhuang ◽

...

Keyword(s):

Lignocellulosic Biomass ◽

Copy Number ◽

Mevalonate Pathway ◽

Mevalonate Kinase ◽

Metabolite Analysis ◽

Lignocellulosic Hydrolysate ◽

Microbial Conversion ◽

Lignocellulosic Hydrolysates ◽

Lignocellulosic Feedstocks ◽

Fuels And Chemicals

Abstract Background Mitigation of climate change requires that new routes for the production of fuels and chemicals be as oil-independent as possible. The microbial conversion of lignocellulosic feedstocks into terpene-based biofuels and bioproducts represents one such route. This work builds upon previous demonstrations that the single-celled carotenogenic basidiomycete, Rhodosporidium toruloides, is a promising host for the production of terpenes from lignocellulosic hydrolysates. Results This study focuses on the optimization of production of the monoterpene 1,8-cineole and the sesquiterpene α-bisabolene in R. toruloides. The α-bisabolene titer attained in R. toruloides was found to be proportional to the copy number of the bisabolene synthase (BIS) expression cassette, which in turn influenced the expression level of several native mevalonate pathway genes. The addition of more copies of BIS under a stronger promoter resulted in production of α-bisabolene at 2.2 g/L from lignocellulosic hydrolysate in a 2-L fermenter. Production of 1,8-cineole was found to be limited by availability of the precursor geranylgeranyl pyrophosphate (GPP) and expression of an appropriate GPP synthase increased the monoterpene titer fourfold to 143 mg/L at bench scale. Targeted mevalonate pathway metabolite analysis suggested that 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMGR), mevalonate kinase (MK) and phosphomevalonate kinase (PMK) may be pathway bottlenecks are were therefore selected as targets for overexpression. Expression of HMGR, MK, and PMK orthologs and growth in an optimized lignocellulosic hydrolysate medium increased the 1,8-cineole titer an additional tenfold to 1.4 g/L. Expression of the same mevalonate pathway genes did not have as large an impact on α-bisabolene production, although the final titer was higher at 2.6 g/L. Furthermore, mevalonate pathway intermediates accumulated in the mevalonate-engineered strains, suggesting room for further improvement. Conclusions This work brings R. toruloides closer to being able to make industrially relevant quantities of terpene from lignocellulosic biomass.

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Ketamine for Refractory Chronic Migraine: an Observational Pilot Study and Metabolite Analysis

The Journal of Clinical Pharmacology ◽

10.1002/jcph.1920 ◽

2021 ◽

Author(s):

Eric S. Schwenk ◽

Marc C. Torjman ◽

Ruin Moaddel ◽

Jacqueline Lovett ◽

Daniel Katz ◽

...

Keyword(s):

Pilot Study ◽

Chronic Migraine ◽

Metabolite Analysis ◽

Refractory Chronic Migraine

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De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

BMC Genomics ◽

10.1186/s12864-021-07715-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yu-Fu Gao ◽

Dong-Hui Zhao ◽

Jia-Qi Zhang ◽

Jia-Shuo Chen ◽

Jia-Lin Li ◽

...

Keyword(s):

Differentially Expressed Genes ◽

De Novo ◽

Regulatory Genes ◽

Differentially Expressed ◽

Anthocyanin Synthesis ◽

Leaf Color ◽

Metabolite Analysis ◽

Color Formation ◽

Content Change ◽

Final Color

Abstract Background Leaf color is an important ornamental trait of colored-leaf plants. The change of leaf color is closely related to the synthesis and accumulation of anthocyanins in leaves. Acer pseudosieboldianum is a colored-leaf tree native to Northeastern China, however, there was less knowledge in Acer about anthocyanins biosynthesis and many steps of the pathway remain unknown to date. Results Anthocyanins metabolite and transcript profiling were conducted using HPLC and ESI-MS/MS system and high-throughput RNA sequencing respectively. The results demonstrated that five anthocyanins were detected in this experiment. It is worth mentioning that Peonidin O-hexoside and Cyanidin 3, 5-O-diglucoside were abundant, especially Cyanidin 3, 5-O-diglucoside displayed significant differences in content change at two periods, meaning it may be play an important role for the final color. Transcriptome identification showed that a total of 67.47 Gb of clean data were obtained from our sequencing results. Functional annotation of unigenes, including comparison with COG and GO databases, yielded 35,316 unigene annotations. 16,521 differentially expressed genes were identified from a statistical analysis of differentially gene expression. The genes related to leaf color formation including PAL, ANS, DFR, F3H were selected. Also, we screened out the regulatory genes such as MYB, bHLH and WD40. Combined with the detection of metabolites, the gene pathways related to anthocyanin synthesis were analyzed. Conclusions Cyanidin 3, 5-O-diglucoside played an important role for the final color. The genes related to leaf color formation including PAL, ANS, DFR, F3H and regulatory genes such as MYB, bHLH and WD40 were selected. This study enriched the available transcriptome information for A. pseudosieboldianum and identified a series of differentially expressed genes related to leaf color, which provides valuable information for further study on the genetic mechanism of leaf color expression in A. pseudosieboldianum.

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