Clarification of pathway-specific inhibition by Fourier transform ion cyclotron resonance/mass spectrometry-based metabolic phenotyping studies

We have developed a metabolic profiling scheme based on direct-infusion Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). The scheme consists of: (1) reproducible data collection under optimized FT-ICR/MS analytical conditions; (2) automatic mass-error correction and multivariate analyses for metabolome characterization using a newly developed metabolomics tool (DMASS software); (3) identification of marker metabolite candidates by searching a species-metabolite relationship database, KNApSAcK; and (4) structural analyses by an MS/MS method. The scheme was applied to metabolic phenotyping of Arabidopsis (Arabidopsis thaliana) seedlings treated with different herbicidal chemical classes for pathway-specific inhibitions. Arabidopsis extracts were directly infused into an electrospray ionization source on an FT-ICR/MS system. Acquired metabolomics data were comprised of mass-to-charge ratio values with ion intensity information subjected to principal component analysis, and metabolic phenotypes from the herbicide treatments were clearly differentiated from those of the herbicide-free treatment. From each herbicide treatment, candidate metabolites representing such metabolic phenotypes were found through the KNApSAcK database search. The database search and MS/MS analyses suggested dose-dependent accumulation patterns of specific metabolites including several flavonoid glycosides. The metabolic phenotyping scheme on the basis of FT-ICR/MS coupled with the DMASS program is discussed as a general tool for high throughput metabolic phenotyping studies.     

Predicting medicinal resources in Ranunculaceae family by a combined approach using DNA barcodes and chemical metabolites

Plant taxonomy based on molecular phylogenetic study and/or chemosystematics study has become increasingly important in exploring and utilizing medicinal resources due to the advent of big data era. In this study, we proposed a classifying approach combining DNA and chemical metabolites for the prediction of new medicinal resources. Specifically, we obtained 104 ITS2 barcodes and 847 chemical metabolites from 104 species in Ranunculaceae. Then, phylogenetic tree based on the ITS2 barcode and clustering tree based on structural similarity of metabolites were separately constructed. In addition, we tested the classifying accuracy of the two methods by Baker`s correlation coefficient and the result showed that phylogenetic tree based on the ITS2 barcode was more accurate, giving a higher score of 0.627, whereas clustering tree based on chemical metabolites obtained a lower score of 0.301. Therefore, the natural products of plants might be described using these clades found by ITS2-based methods, and thus new metabolites of plants might be predicted due to the close relationships in a given clade. Using this combined method, 53 plants with structurally similar metabolites were included in 9 plant groups and currently unknown species-metabolite relations were predicted. Finally, 26.92% species in Ranunculaceae were found to contain the predicted metabolites after verification using two alternative KNApSAcKCore and ChEBI databases. As a whole, the combined approach can successfully classify plants and predict specialized natural products based on plant taxa.     

Semantic search among heterogeneous biological databases based on gene ontology

Various biological database systems including datacapture, data storage, data retrieval and other data pro-cessing methods have been developed. These systems havebecome effective tools for today’s genomics and relatedstudies. However, the highly distribu…     

MetaboSearch: tool for mass-based metabolite identification using multiple databases

Searching metabolites against databases according to their masses is often the first step in metabolite identification for a mass spectrometry-based untargeted metabolomics study. Major metabolite databases include Human Metabolome DataBase (HMDB), Madison Metabolomics Consortium Database (MMCD), Metlin, and LIPID MAPS. Since each one of these databases covers only a fraction of the metabolome, integration of the search results from these databases is expected to yield a more comprehensive coverage. However, the manual combination of multiple search results is generally difficult when identification of hundreds of metabolites is desired. We have implemented a web-based software tool that enables simultaneous mass-based search against the four major databases, and the integration of the results. In addition, more complete chemical identifier information for the metabolites is retrieved by cross-referencing multiple databases. The search results are merged based on IUPAC International Chemical Identifier (InChI) keys. Besides a simple list of m/z values, the software can accept the ion annotation information as input for enhanced metabolite identification. The performance of the software is demonstrated on mass spectrometry data acquired in both positive and negative ionization modes. Compared with search results from individual databases, MetaboSearch provides better coverage of the metabolome and more complete chemical identifier information. Availability: The software tool is available at http://omics.georgetown.edu/MetaboSearch.html.     

NMR-based plant metabolomics: where do we stand, where do we go?

NMR-based metabolomics is an important tool for studying biological systems and has been applied in various organisms, including animals, plants and microbes. NMR is able to provide a 'holistic view' of the metabolites under certain conditions, and thus is advantageous for metabolomic studies. To maximize the use of the information obtained, it is also important to create a platform to measure, store and share data. Public databases for storing and sharing information are still lacking for NMR-based metabolomic analysis in plants. Such databases are urgently needed to make metabolic profiling a real omics technology. In addition, to understand metabolic processes in depth, single-cell analysis and the turnover of metabolites in pathways (fluxomics) should be measured.     

拉祜族食疗花卉的研究

对拉祜族的食疗花卉进行了探讨.结果表明,拉祜族有着丰富的食疗花卉知识,其形成有着特殊的医药和文化背景以及朴素的早期传统民族医药特征;拉祜族民间普遍存在的花卉食疗现象,是对其生存空间内现有食物的自然选择结果,是传统知识的积累使然,是在与各民族相互学习交流中得到启迪而加以利用的结果,具有原住民文化特征,是民族文化多样性的重要组成部分.拉祜族食疗花卉约有53种,分别隶属于28个科,较有特色的花卉包括杜鹃花(Rhododendron spp.)、姜花(Alpinia spp.、 Amomum spp.、 Zingiber spp.)、山茶花(Camellia spp.)、蜜蒙花(Buddleja officinalis Maxim.)等.此外还探讨了拉祜族传统文化与当地自然资源及其生物多样性的关系,认为今天拉祜族聚居地还保留有丰富的森林植被和物种,与他们对自然资源的管理与合理使用有着密切的关系.     

药用植物次生代谢的生物学作用及生态环境因子的影响

药用植物的很多有效成分为植物的次生代谢产物,包括生物碱、萜类、酚类、甙类等。这些次生代谢产物在植物的生理调节、自身保护、生存竞争、协调与环境关系等生命活动的许多方面均起着重要作用。各种生态环境因素包括光、温度、土壤、空气以及生物因素均影响到药用植物的次生代谢过程。对药用植物次生代谢成分与生态环境因素的关系进行研究有利于揭示药用植物药用有效成分地域性差异的原因,可为药用植物的育种、栽培提供理论依据。     

Recent and potential developments of biofluid analyses in metabolomics

Metabolomics, one of the ‘omic’ sciences in systems biology, is the global assessment and validation of endogenous small-molecule metabolites within a biologic system. Analysis of these key metabolites in body fluids has become an important role to monitor the state of biological organisms and is a widely used diagnostic tool for disease. A majority of these metabolites are being applied to metabolic profiling of the biological samples, for example, plasma and whole blood, serum, urine, saliva, cerebrospinal fluid, synovial fluid, semen, and tissue homogenates. However, the recognition of the need for a holistic approach to metabolism led to the application of metabolomics to biological fluids for disease diagnostics. A recent surge in metabolomic applications which are probably more accurate than routine clinical practice, dedicated to characterizing the biological fluids. While developments in the analysis of biofluid samples encompassing an important impediment, it must be emphasized that these biofluids are complementary. Metabolomics provides potential advantages that classical diagnostic approaches do not, based on following discovery of a suite of clinically relevant biomarkers that are simultaneously affected by the disease. Emerging as a promising biofocus, metabolomics will drive biofluid analyses and offer great benefits for public health in the long-term.     

Key taste components in two wild edible Boletus mushrooms using widely targeted metabolomics

Compounds from wild edible mushrooms has been reported to exert biological activities and contribute to the different flavors of mushrooms in our diet. Wild edible Boletus mushrooms are popular in Southwest China. In this study, we performed ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) based on widely targeted metabolomics analysis to identify key components. A total of 194 metabolites (113 upregulated, 81 downregulated) divided into 11 groups (49 metabolites in group lipids, 34 in amino acids and derivatives, 30 in organic acids, 18 in phenolic acids, 16 in nucleotides and derivatives, 13 in alkaloids, 6 in flavonoids, 3 in lignans and coumarins, 3 in tannins, 2 in terpenoids, and 20 in others) were found among Boletus bainiugan compared with B. subsplendidus. Through clustering analysis, principal component analysis (PCA), and orthogonal signal correction and partial least squares-discriminant analysis (OPLS-DA), different metabolites from fruiting bodies were clearly identified. Significant differences were observed in the metabolites between Boletus bainiugan and B. subsplendidus. These metabolites are involved in important biological functions. Our results provide new insights into important metabolites and theoretical basis for the taste difference of two wild edible Boletus mushrooms.     

Paleomedicine and the use of plant secondary compounds in the Paleolithic and Early Neolithic

Reconstructing plant use before domestication is challenging due to a lack of evidence. Yet, on the small number of sites with assemblages, the wide range of different plant species cannot be explained simply in terms of nutrition. Assemblages from the Lower Paleolithic to the Early Neolithic were examined to investigate the relative edible and medicinal properties of the plants. The assemblages contain a mixture of edible species, plants that are both edible and medicinal, and plants with only medicinal properties. The proportion of medicinal plants at all sites is well above the natural average and increases over time. Mechanisms for preventing intestinal parasitic infections are common among animals and together with chimpanzees’ preventative and curative self‐medication practices suggest an evolutionary context for this behavior. A broad‐spectrum approach to plant collection is likely to have been in place throughout the Paleolithic driven, in part, by the need for medicinal compounds.     

药用植物内生真菌的多样性及生物功能研究进展

药用植物内生真菌资源丰富,其代谢产物常具有抗肿瘤、抗氧化、抑菌等作用,能产生药用植物生长调节物质及与宿主相同或类似的次生代谢产物,从而成为近年来的研究热点。本文对药用植物内生真菌的分离鉴定、多样性、生物活性及生物学功能等方面进行综述,以期为今后筛选及利用有效的药用植物内生真菌奠定基础。     

浙江瑞安红双林场植物资源及其利用前景

浙江瑞安红双林场共有维管植物167科538属1055种,其中已知有一定利用价值的资源植物715种,隶属于157科429属。按其性质和用途可分为材用植物、药用植物、油脂植物、纤维植物、淀粉植物、食用植物、芳香植物、栲胶植物、保健饮料植物、牧草及饲料植物、保护与改造环境植物、观赏植物、土农药植物、蜜源植物等14类,其中药用植物种类最为丰富。以常见药用植物234种为例,根据植物资源可利用量估量法估量当地植物资源利用前景,结果表明,其中46.2%的常见药用植物可利用量估量值在12以上,可供开发利用。文后提出红双林场植物资源保护与利用建议。     

药用真菌活性次级代谢产物研究

药用真菌作为我国传统中医药体系的重要组成部分,有着悠久的历史。它们能够产生丰富的活性次级代谢产物,具有神经保护、抗肿瘤、降血脂等诸多药效。然而,目前对大部分药用真菌次级代谢产物的化学和生物学研究较少。本课题组主要以抗肿瘤、抗炎、抗菌以及抗病毒等生物活性为指导,选择重要药用真菌进行化学研究,构建我国特色药用真菌代谢产物库。文章主要介绍近4年我们在这方面的研究进展。     

Investigation of species and environmental effects on rhubarb roots metabolome using <Superscript>1</Superscript>H NMR combined with high performance thin layer chromatography

Introduction

The pharmacological activities of medicinal plants are reported to be due to a wide range of metabolites, therein, the concentrations of which are greatly affected by many genetic and/or environmental factors. In this context, a metabolomics approach has been applied to reveal these relationships. The investigation of such complex networks that involve the correlation between multiple biotic and abiotic factors and the metabolome, requires the input of information acquired by more than one analytical platform. Thus, development of new metabolomics techniques or hyphenations is continuously needed.

Objectives

Feasibility of high performance thin-layer chromatography (HPTLC) were investigated as a supplementary tool for medicinal plants metabolomics supporting ¹H nuclear magnetic resonance (¹H NMR) spectroscopy.

Method

The overall metabolic difference of plant material collected from two species (Rheum palmatum and Rheum tanguticum) in different geographical locations and altitudes were analyzed by ¹H NMR- and HPTLC-based metabolic profiling. Both NMR and HPTLC data were submitted to multivariate data analysis including principal component analysis and orthogonal partial least square analysis.

Results

The NMR and HPTLC profiles showed that while chemical variations of rhubarb are in some degree affected by all the factors tested in this study, the most influential factor was altitude of growth. The metabolites responsible for altitude differentiation were chrysophanol, emodin and sennoside A, whereas aloe emodin, catechin, and rhein were the key species-specific markers.

Conclusion

These results demonstrated the potential of HTPLC as a supporting tool for metabolomics due to its high profiling capacity of targeted metabolic groups and preparative capability.

     

Strategies to enhance biologically active-secondary metabolites in cell cultures of Artemisia – current trends

The genus Artemisia has been utilized worldwide due to its immense potential for protection against various diseases, especially malaria. Artemisia absinthium, previously renowned for its utilization in the popular beverage absinthe, is gaining resurgence due to its extensive pharmacological activities. Like A. annua, this species exhibits strong biological activities like antimalarial, anticancer and antioxidant. Although artemisinin was found to be the major metabolite for its antimalarial effects, several flavonoids and terpenoids are considered to possess biological activities when used alone and also to synergistically boost the bioavailability of artemisinin. However, due to the limited quantities of these metabolites in wild plants, in vitro cultures were established and strategies have been adopted to enhance medicinally important secondary metabolites in these cultures. This review elaborates on the traditional medicinal uses of Artemisia species and explains current trends to establish cell cultures of A. annua and A. absinthium for enhanced production of medicinally important secondary metabolites.     

Mass spectrometry methods in metabolomics

The review deals with metabolomics, a new and rapidly growing area directed to the comprehensive analysis of metabolites of biological objects. Metabolites are characterized by various physical and chemical properties, traditionally studied by methods of analytical chemistry focused on certain groups of chemical substances. However, current progress in mass spectrometry has led to formation of rather unified methods, such as metabolic fingerprinting and metabolomic profiling, which allow defining thousands of metabolites in one biological sample and therefore draw “a modern portrait of metabolomics.” This review describes basic characteristics of these methods, ways of metabolite separation, and analysis of metabolites by mass spectrometry. The examples shown in this review, allow to estimate these methods and to compare their advantages and disadvantages. Besides that, we consider the methods, which are of the most frequent use in metabolomics; these include the methods for data processing and the required resources, such as software for mass spectra processing and metabolite search database. In the conclusion, general suggestions for successful metabolomic experiments are given.     

The Investigation on Utilization of Wild Medicinal Plants in Dietary Culture of Quanzhou,Southern Fujian

An ethnobotanical survey on the medicinal plant species marketed in Quanzhou, southern Fujian, was conducted in order to document traditional medicinal knowledge and application of medicinal plants in dietary. In addition to literature review, data was obtained using ethnobotanical tools and methods, including personal interviews during field trips, collecting herbarium specimens, and species identification by cross referencing. The results showed that: 1) There are 148 wild medicinal species, belonging to 56 plant families and 117 genera present in Quanzhou, southern Fujian. Among them, 46 species are edible wild herbs, 37 species are medicinal plants, 38 species are used as tea substituting plants or herbal tea,22 species are wild fruits, 4 species are used as spices and 1 species is used to make bean jelly; 2) The plant families which comprise a major part of the pool are Compositae, Lamiaceae, Rosaceae, Leguminosae, Rubiaceae, Liliaceae, Orchidaceae and Moraceae; 3) This study explored the utilization of the medicinal plants in Quanzhou area, and proposed methods to inherit the culture of using wild plants in dietary, as well as methods to conserve the edible medicinal wild plant resources.     

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. Each PGDB in the BioCyc collection describes the genome and predicted metabolic network of a single organism, inferred from the MetaCyc database, which is a reference source on metabolic pathways from multiple organisms. In addition, each bacterial PGDB includes predicted operons for the corresponding species. The BioCyc collection provides a unique resource for computational systems biology, namely global and comparative analyses of genomes and metabolic networks, and a supplement to the BioCyc resource of curated PGDBs. The Omics viewer available through the BioCyc website allows scientists to visualize combinations of gene expression, proteomics and metabolomics data on the metabolic maps of these organisms. This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways present in these organisms, and the most frequently observed pathways. We seek scientists to adopt and curate individual PGDBs within the BioCyc collection. Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing.     

Extending biochemical databases by metabolomic surveys

Metabolomics can map the large metabolic diversity in species, organs, or cell types. In addition to gains in enzyme specificity, many enzymes have retained substrate and reaction promiscuity. Enzyme promiscuity and the large number of enzymes with unknown enzyme function may explain the presence of a plethora of unidentified compounds in metabolomic studies. Cataloguing the identity and differential abundance of all detectable metabolites in metabolomic repositories may detail which compounds and pathways contribute to vital biological functions. The current status in metabolic databases is reviewed concomitant with tools to map and visualize the metabolome.