Plant Metabolomics Reviews

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Multifaceted Interactions Between Endophytes and Plant: Developments and Prospects.

December 1, 2018 - 7:17pm
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Multifaceted Interactions Between Endophytes and Plant: Developments and Prospects.

Front Microbiol. 2018;9:2732

Authors: Khare E, Mishra J, Arora NK

Abstract
Microbial endophytes are present in all known plant species. The ability to enter and thrive in the plant tissues makes endophytes unique, showing multidimensional interactions within the host plant. Several vital activities of the host plant are known to be influenced by the presence of endophytes. They can promote plant growth, elicit defense response against pathogen attack, and can act as remediators of abiotic stresses. To date, most of the research has been done assuming that the interaction of endophytes with the host plant is similar to the plant growth-promoting (PGP) microbes present in the rhizosphere. However, a new appreciation of the difference of the rhizosphere environment from that of internal plant tissues is gaining attention. It would be interesting to explore the impact of endosymbionts on the host's gene expression, metabolism, and other physiological aspects essential in conferring resistance against biotic and abiotic stresses. A more intriguing and inexplicable issue with many endophytes that has to be critically evaluated is their ability to produce host metabolites, which can be harnessed on a large scale for potential use in diverse areas. In this review, we discuss the concept of endophytism, looking into the latest insights related to the multifarious interactions beneficial for the host plant and exploring the importance of these associations in agriculture and the environment and in other vital aspects such as human health.

PMID: 30498482 [PubMed]

Rice Secondary Metabolites: Structures, Roles, Biosynthesis, and Metabolic Regulation.

November 30, 2018 - 6:48pm
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Rice Secondary Metabolites: Structures, Roles, Biosynthesis, and Metabolic Regulation.

Molecules. 2018 Nov 27;23(12):

Authors: Wang W, Li Y, Dang P, Zhao S, Lai D, Zhou L

Abstract
Rice (Oryza sativa L.) is an important food crop providing energy and nutrients for more than half of the world population. It produces vast amounts of secondary metabolites. At least 276 secondary metabolites from rice have been identified in the past 50 years. They mainly include phenolic acids, flavonoids, terpenoids, steroids, alkaloids, and their derivatives. These metabolites exhibit many physiological functions, such as regulatory effects on rice growth and development, disease-resistance promotion, anti-insect activity, and allelopathic effects, as well as various kinds of biological activities such as antimicrobial, antioxidant, cytotoxic, and anti-inflammatory properties. This review focuses on our knowledge of the structures, biological functions and activities, biosynthesis, and metabolic regulation of rice secondary metabolites. Some considerations about cheminformatics, metabolomics, genetic transformation, production, and applications related to the secondary metabolites from rice are also discussed.

PMID: 30486426 [PubMed - in process]

Metabolomic and biotechnological approaches to determine therapeutic potential of Withania somnifera (L.) Dunal: A review.

November 24, 2018 - 7:13am
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Metabolomic and biotechnological approaches to determine therapeutic potential of Withania somnifera (L.) Dunal: A review.

Phytomedicine. 2018 Nov 15;50:127-136

Authors: Tripathi N, Shrivastava D, Ahmad Mir B, Kumar S, Govil S, Vahedi M, Bisen PS

Abstract
BACKGROUND: Withania somnifera, a high value medicinal plant is a major source of pharmaceutically important active compounds withanolides. Withania somnifera has been used in ayurveda as health restorative and anabolic agent besides having anti-arthritic, antidepressant, anti-microbial, anti-inflammatory, anti-diabetic, anti-stress, neuroprotective and cardio-protective activities.
HYPOTHESIS/PURPOSE: The mining of the compound(s) of interest offers opportunity to identify desired attributes in the therapeutic area of interest. Metabolomic has become an important tool in the field of pharmacological and functional genomics of medicinal plants. The analysis supports the information regarding differential outline of the gene expression for increasing important withanolides viz. withanolide A and withaferin A in W. somnifera.
STUDY DESIGN: The bioinformatics and biotechnological approaches viz. tissue culture, genetic transformation, genomic, transcriptomic, proteomic, gene mining and metabolomic studies have opened new windows about engineering of withanolide production.
METHODS: Target and network analysis for maximum therapeutic potential of Withania somnifera have been determined by employing Genemania software for finding interactions among various human genes that are being affected by active constituents.
RESULTS: Some of the major bioactive compounds of Withania somnifera have been discussed on protein-protein, protein-DNA and genetic interactions with respect to gene and protein expression data, protein domains, metabolic profiling, root organ culture, genetic transformation and phenotypic screening profiles CONCLUSION: The implementation of latest bioinformatic tools in combination with biotechnological techniques for breeding platforms are important in conservation of medicinal plant species in danger. The current review is based on molecular and in vitro methodologies employed in W. somnifera for accepting their importance in the improvement of this valuable medicinal species.

PMID: 30466971 [PubMed - in process]

The guard cell ionome: Understanding the role of ions in guard cell functions.

November 21, 2018 - 7:16am
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The guard cell ionome: Understanding the role of ions in guard cell functions.

Prog Biophys Mol Biol. 2018 Nov 17;:

Authors: Misra BB, Reichman SM, Chen S

Abstract
The plant ionome is critical for growth, productivity, defense, and it eventually affects food quantity and quality. Located on the leaf surface, stomatal guard cells are critical gatekeepers for water, gas, and pathogens. Insights form ionomics (metallomics) is imperative as we enter an omics-driven systems biology era where an understanding of guard cell function and physiology is advanced through efforts in genomics, transcriptomics, proteomics, and metabolomics. While the roles of major cations (K, Ca) and anions (Cl) are well known in guard cell function, the related physiology, movement and regulation of trace elements, metal ions, and heavy metals are poorly understood. The majority of the information on the role of trace elements in guard cells emanates from classical feeding experiments, field or in vitro fortification, micropropagation, and microscopy studies, while novel insights are available from metal ion transporter and ion channel studies. Given the rejuvenated and recent interest in the constantly changing ionome in plant mineral balance and eventually in human nutrition and health, we have looked into the far from established guard cell ionome in lieu of the modern omics era of high throughput research endeavors. Newer technologies and tools i.e., high resolution mass spectrometry, advanced imaging, and phenomics are now available to delve into the guard cell ionomes. In this review, research efforts on guard cell ionomes were collated and categorized, and we highlight the underlying role of the largely unknown ionome in guard cell function towards a systems physiology aspects of understanding of plant health and productivity.

PMID: 30458181 [PubMed - as supplied by publisher]

Accelerating metabolite identification in natural product research: toward an ideal combination of LC-HRMS/MS and NMR profiling, in silico databases and chemometrics.

November 21, 2018 - 7:16am
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Accelerating metabolite identification in natural product research: toward an ideal combination of LC-HRMS/MS and NMR profiling, in silico databases and chemometrics.

Anal Chem. 2018 Nov 19;:

Authors: Wolfender JL, Nuzillard JM, van der Hooft JJJ, Renault JH, Bertrand S

Abstract
The rapid innovations in metabolite profiling, bioassays and chemometrics have led to a paradigm shift in natural product (NP) research. Indeed, having partial or full structure information about possibly "all" specialized metabolites and an estimation of their levels in plants or microorganisms provides a way to perform pharmacognostic or chemical ecology investigations from a new and holistic perspective. The increasing amount of accurate metabolome data that can be acquired on massive sample sets, notably through data-dependent LC-HRMS/MS and NMR profiling, allows the mapping of natural extracts at an unprecedented level of precision. Most progress made recently in accelerating metabolite identification has been pushed by the need for metabolomics to have tools that provide a confident annotation of the biomarkers highlighted as the results of data mining through multivariate analysis, often on important datasets of complex samples. Historically, NP chemists have been involved in the unambiguous full de novo identification of unknown compounds from complex natural biological matrices. This process is classically performed by the tedious isolation of pure bioactive NPs through comprehensive bioactivity-guided isolation workflows involving orthogonal chromatographic steps at the preparative level. Increasingly advanced metabolomics metabolite profiling methods are of strategic importance in dereplication workflows in NP research as well as for the full metabolome composition assignment of relevant organisms from both drug discovery and chemical ecology perspectives. In this review, we describe the latest developments in metabolite profiling by both LC-MS and NMR-based methods and related databases from a natural product chemist perspective. We assess the current possibilities and limits of such methods and the workflows for manual and automated NP annotations by equally treating the MS and NMR approaches that are both key for the "as confident as possible" NP annotation in crude natural extracts. We also propose future lines of development in the field that are important for NP research but are also generally needed for metabolite annotation in metabolomics because NPs represent perfect candidate compounds for identification due to their intrinsic structural complexity and chemodiversity across organisms. This review does not aim to provide a comprehensive survey of all metabolite profiling applications made in NP research to date. Typical case studies are discussed, and an update of a selection of the latest advanced original studies and numerous specialized reviews is made with links to tools and DBs regarded as useful for their current or future usage in NP research. Evaluations of what can be readily implemented and what is still required for confident NP structural elucidation are made, especially concerning access to generic structural and spectral DBs as well as the use of orthogonal detection methods for improved confidence in metabolite annotation.

PMID: 30453740 [PubMed - as supplied by publisher]

Thermodynamic buffering, stable non-equilibrium and establishment of the computable structure of plant metabolism.

November 18, 2018 - 6:41am
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Thermodynamic buffering, stable non-equilibrium and establishment of the computable structure of plant metabolism.

Prog Biophys Mol Biol. 2018 Nov 13;:

Authors: Igamberdiev AU, Kleczkowski LA

Abstract
The equilibria of coenzyme nucleotides and substrates established in plant cells generate simple rules that govern the plant metabolome and provide optimal conditions for the non-equilibrium fluxes of major metabolic processes such as ATP synthesis, CO2 fixation, and mitochondrial respiration. Fast and abundant enzymes, such as adenylate kinase, carbonic anhydrase or malate dehydrogenase, provide constant substrate flux for these processes. These "buffering" enzymes follow the Michaelis-Menten (MM) kinetics and operate near equilibrium. The non-equilibrium "engine" enzymes, such as ATP synthase, Rubisco or the respiratory complexes, follow the modified version of MM kinetics due to their high concentration and low concentration of their substrates. The equilibrium reactions serve as control gates for the non-equilibrium flux through the engine enzymes establishing the balance of the fluxes of load and consumption of metabolic components. Under the coordinated operation of buffering and engine enzymes, the concentrations of free and Mg-bound adenylates and of free Mg2+ are set, serving as feedback signals from the adenylate metabolome. Those are linked to various cell energetics parameters, including membrane potentials. Also, internal levels of reduced and oxidized pyridine nucleotides are established in the coordinated operation of malate dehydrogenase and respiratory components, with proton concentration as a feedback from pyridine nucleotide pools. Non-coupled pathways of respiration serve to equilibrate the levels of pyridine nucleotides, adenylates, and as a pH stat. This stable non-equilibrium organizes the fluxes of energy spatially and temporally, controlling the rates of major metabolic fluxes that follow thermodynamically and kinetically defined computational principles.

PMID: 30444975 [PubMed - as supplied by publisher]

Tools and Resources for Metabolomics Research Community: A 2017-2018 update.

November 18, 2018 - 6:41am
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Tools and Resources for Metabolomics Research Community: A 2017-2018 update.

Electrophoresis. 2018 Nov 16;:

Authors: Misra BB, Mohapatra S

Abstract
The veracity at which mass spectrometry (MS) and nuclear magnetic resonance (NMR)-based platforms generate metabolomics datasets for both research and clinical facilities to address challenges in biomedical to agricultural sciences is under appreciated. Thus, metabolomics efforts spanning microbe, environment, plant, animal and human systems, have led to a continual and concomitant growth of the in silico resources for analysis and interpretation of these datasets. These software tools, resources, and databases drive the field forward to help keep pace with the amount of data being generated and the sophisticated and diverse analytical platforms that are being used to generate metabolomics data. To address challenges in data pre-processing, metabolite annotation, statistical interrogation, visualization, interpretation, and integration, the metabolomics and informatics community comes up with hundreds of tools every year to tackle these challenges. The purpose of the present review is to provide a brief and useful summary of more than 95 metabolomics tools, software, and databases that were either developed or significantly improved during 2017-2018. We see this review help readers, developers, and researchers to obtain an informed access to these thorough list of resources for further improvisation, implementation, and application in due course of time. This article is protected by copyright. All rights reserved.

PMID: 30443919 [PubMed - as supplied by publisher]

Current trends to comprehend lipid metabolism in diatoms.

November 10, 2018 - 7:25am
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Current trends to comprehend lipid metabolism in diatoms.

Prog Lipid Res. 2018 04;70:1-16

Authors: Zulu NN, Zienkiewicz K, Vollheyde K, Feussner I

Abstract
Diatoms are the most dominant phytoplankton species in oceans and they continue to receive a great deal of attention because of their significant contributions in ecosystems and the environment. Due to triacylglycerol (TAG) profiles that are abundant in medium-chain fatty acids, diatoms have emerged to be better feed stocks for biofuel production, in comparison to the commonly studied green microalgal species (chlorophytes). Importantly, diatoms are also known for their high levels of the essential ω3 fatty acids, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and are considered to be a promising alternative source of these components. The two most commonly exploited diatoms include Thalassiosira pseudonana and Phaeodactylum tricornutum. Although obvious similarities between diatoms and chlorophytes exist, there are some substantial differences in their lipid metabolism. This review provides an overview on lipid metabolism in diatoms, with P. tricornutum as the most explored model. Special emphasis is placed on the synthesis and incorporation of very long chain ω3 fatty acids into lipids. Furthermore, current approaches including genetic engineering and biotechnological methods aimed at improving and maximizing lipid production in P. tricornutum are also discussed.

PMID: 29524459 [PubMed - indexed for MEDLINE]

Application of Proteomics Technologies in Oil Palm Research.

October 28, 2018 - 8:06am
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Application of Proteomics Technologies in Oil Palm Research.

Protein J. 2018 Oct 26;:

Authors: Lau BYC, Othman A, Ramli US

Abstract
Proteomics technologies were first applied in the oil palm research back in 2008. Since proteins are the gene products that are directly correspond to phenotypic traits, proteomic tools hold a strong advantage above other molecular tools to comprehend the biological and molecular mechanisms in the oil palm system. These emerging technologies have been used as non-overlapping tools to link genome-wide transcriptomics and metabolomics-based studies to enhance the oil palm yield and quality through sustainable plant breeding. Many efforts have also been made using the proteomics technologies to address the oil palm's Ganoderma disease; the cause and management. At present, the high-throughput screening technologies are being applied to identify potential biomarkers involved in metabolism and cellular development through determination of protein expression changes that correlate with oil production and disease. This review highlights key elements in proteomics pipeline, challenges and some examples of their implementations in plant studies in the context of oil palm in particular. We foresee that the proteomics technologies will play more significant role to address diverse issues related to the oil palm in the effort to improve the oil crop.

PMID: 30367348 [PubMed - as supplied by publisher]

Contribution of Untargeted Metabolomics for Future Assessment of Biotech Crops.

October 27, 2018 - 7:40am
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Contribution of Untargeted Metabolomics for Future Assessment of Biotech Crops.

Trends Plant Sci. 2018 Oct 22;:

Authors: Christ B, Pluskal T, Aubry S, Weng JK

Abstract
The nutritional value and safety of food crops are ultimately determined by their chemical composition. Recent developments in the field of metabolomics have made it possible to characterize the metabolic profile of crops in a comprehensive and high-throughput manner. Here, we propose that state-of-the-art untargeted metabolomics technology should be leveraged for safety assessment of new crop products. We suggest generally applicable experimental design principles that facilitate the efficient and rigorous identification of both intended and unintended metabolic alterations associated with a newly engineered trait. Our proposition could contribute to increased transparency of the safety assessment process for new biotech crops.

PMID: 30361071 [PubMed - as supplied by publisher]

Biosynthesis and regulation of cyanogenic glycoside production in forage plants.

October 24, 2018 - 7:40am
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Biosynthesis and regulation of cyanogenic glycoside production in forage plants.

Appl Microbiol Biotechnol. 2018 Jan;102(1):9-16

Authors: Sun Z, Zhang K, Chen C, Wu Y, Tang Y, Georgiev MI, Zhang X, Lin M, Zhou M

Abstract
The natural products cyanogenic glycosides (CNglcs) are present in various forage plant species including Sorghum spp., Trifolium spp., and Lotus spp. The release of toxic hydrogen cyanide (HCN) from endogenous CNglcs, which is known as cyanogenesis, leads to a serious problem for animal consumption while as defensive secondary metabolites, CNglcs play multiple roles in plant development and responses to adverse environment. Therefore, it is highly important to fully uncover the molecular mechanisms of CNglc biosynthesis and regulation to manipulate the contents of CNglcs in forage plants for fine-tuning the balance between defensive responses and food safety. This review summarizes recent studies on the production, function, polymorphism, and regulation of CNglcs in forage plants, aiming to provide updated knowledge on the ways to manipulate CNglcs for further beneficial economic effects.

PMID: 29022076 [PubMed - indexed for MEDLINE]

Opportunities for green microextractions in comprehensive two-dimensional gas chromatography / mass spectrometry-based metabolomics - A review.

October 18, 2018 - 8:55am
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Opportunities for green microextractions in comprehensive two-dimensional gas chromatography / mass spectrometry-based metabolomics - A review.

Anal Chim Acta. 2018 Dec 21;1040:1-18

Authors: de Souza JRB, Dias FFG, Caliman JD, Augusto F, Hantao LW

Abstract
Microextractions have become an attractive class of techniques for metabolomics. The most popular technique is solid-phase microextraction that revolutionized the field of modern sample preparation in the early nineties. Ever since this milestone, microextractions have taken on many principles and formats comprising droplets, fibers, membranes, needles, and blades. Sampling devices may be customized to impart exhaustive or equilibrium-based characteristics to the extraction method. Equilibrium-based approaches may rely on additional methods for calibration, such as diffusion-based or on-fiber kinetic calibration to improve bioanalysis. In addition, microextraction-based methods may enable minimally invasive sampling protocols and measure the average free concentration of analytes in heterogeneous multiphasic biological systems. On-fiber derivatization has evidenced new opportunities for targeted and untargeted analysis in metabolomics. All these advantages have highlighted the potential of microextraction techniques for in vivo and on-site sampling and sample preparation, while many opportunities are still available for laboratory protocols. In this review, we outline and discuss some of the most recent applications using microextractions techniques for comprehensive two-dimensional gas chromatography-based metabolomics, including potential research opportunities.

PMID: 30327098 [PubMed - in process]

Elucidating Bacterial Gene Functions in the Plant Microbiome.

October 12, 2018 - 8:00am
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Elucidating Bacterial Gene Functions in the Plant Microbiome.

Cell Host Microbe. 2018 Oct 10;24(4):475-485

Authors: Levy A, Conway JM, Dangl JL, Woyke T

Abstract
There is a growing appreciation for the important roles microorganisms play in association with plants. Microorganisms are drawn to distinct plant surfaces by the nutrient-rich microenvironment, and in turn some of these colonizing microbes provide mutualistic benefits to their host. The development of plant probiotics to increase crop yield and provide plant resistance against biotic and abiotic stresses, while minimizing chemical inputs, would benefit from a deeper mechanistic understanding of plant-microbe interaction. Technological advances in molecular biology and high-throughput -omics provide stepping stones to the elucidation of critical microbiome gene functions that aid in improving plant performance. Here, we review -omics-based approaches that are propelling forward the current understanding of plant-associated bacterial gene functions, and describe how these technologies have helped unravel key bacterial genes and pathways that mediate pathogenic, beneficial, and commensal host interactions.

PMID: 30308154 [PubMed - in process]

Botany, ethnomedicines, phytochemistry and pharmacology of Himalayan paeony (Paeonia emodi Royle.).

October 3, 2018 - 8:48am
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Botany, ethnomedicines, phytochemistry and pharmacology of Himalayan paeony (Paeonia emodi Royle.).

J Ethnopharmacol. 2018 Jun 28;220:197-219

Authors: Ahmad M, Malik K, Tariq A, Zhang G, Yaseen G, Rashid N, Sultana S, Zafar M, Ullah K, Khan MPZ

Abstract
ETHNOPHARMACOLOGICAL RELEVANCE: Himalayan paeony (Paeonia emodi Royle.) is an important species used to treat various diseases. This study aimed to compile the detailed traditional medicinal uses, phytochemistry, pharmacology and toxicological investigations on P. emodi. This study also highlights taxonomic validity, quality of experimental designs and shortcomings in previously reported information on Himalayan paeony.
METHODS: The data was extracted from unpublished theses (Pakistan, China, India and Nepal), and different published research articles confined to pharmacology, phytochemistry and antimicrobial activities using different databases through specific keywords. The relevant information regarding medicinal uses, taxonomic/common names, part used, collection and identification source, authentication, voucher specimen number, plant extracts and their characterization, isolation and identification of phytochemicals, methods of study in silico, in vivo or in vitro, model organism used, dose and duration, minimal active concentration, zone of inhibition (antimicrobial study), bioactive compound(s), mechanism of action on single or multiple targets, and toxicological information.
RESULTS: P. emodi is reported for diverse medicinal uses with pharmacological properties like antioxidant, nephroprotective, lipoxygenase inhibitory, cognition and oxidative stress release, cytotoxic, anti-inflammatory, antiepileptic, anticonvulsant, haemaglutination, alpha-chymotrypsin inhibitory, hepatoprotective, hepatic chromes and pharmacokinetics of carbamazepine expression, β-glucuronidase inhibitory, spasmolytic and spasmogenic, and airway relaxant. Data confined to its taxonomic validity, shows 10% studies with correct taxonomic name while 90% studies with incorrect taxonomic, pharmacopeial and common names. The literature reviewed, shows lack of collection source (11 reports), without proper source of identification (15 reports), 33 studies without voucher specimen number, 26 reports lack information on authentic herbarium submission and most of the studies (90%) without validation of taxonomic names using recognized databases. In reported methods, 67% studies without characterization of extracts, 25% lack proper dose, 40% without duration and 31% reports lack information on proper controls. Similarly, only 18% studies reports active compound(s) responsible for pharmacological activities, 14% studies show minimal active concentration, only 2.5% studies report mechanism of action on target while none of the reports mentioned in silico approach.
CONCLUSION: P. emodi is endemic to Himalayan region (Pakistan, China, India and Nepal) with diverse traditional therapeutic uses. Majority of reviewed studies showed confusion in its taxonomic validity, incomplete methodologies and ambiguous findings. Keeping in view the immense uses of P. emodi in various traditional medicinal systems, holistic pharmacological approaches in combination with reverse pharmacology, system biology, and "omics" technologies are recommended to improve the quality of research which leads to natural drug discovery development at global perspectives.

PMID: 29625273 [PubMed - indexed for MEDLINE]

Application of metabolomics to drug discovery and understanding the mechanisms of action of medicinal plants with anti-tuberculosis activity.

October 2, 2018 - 8:09pm
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Application of metabolomics to drug discovery and understanding the mechanisms of action of medicinal plants with anti-tuberculosis activity.

Clin Transl Med. 2018 Oct 01;7(1):29

Authors: Tuyiringire N, Tusubira D, Munyampundu JP, Tolo CU, Muvunyi CM, Ogwang PE

Abstract
Human tuberculosis (TB) is amongst the oldest and deadliest human bacterial diseases that pose major health, social and economic burden at a global level. Current regimens for TB treatment are lengthy, expensive and ineffective to emerging drug resistant strains. Thus, there is an urgent need for identification and development of novel TB drugs and drug regimens with comprehensive and specific mechanisms of action. Many medicinal plants are traditionally used for TB treatment. While some of their phytochemical composition has been elucidated, their mechanisms of action are not well understood. Insufficient knowledge on Mycobacterium tuberculosis (M.tb) biology and the complex nature of its infection limit the effectiveness of current screening-based methods used for TB drug discovery. Nonetheless, application of metabolomics tools within the 'omics' approaches, could provide an alternative method of elucidating the mechanism of action of medicinal plants. Metabolomics aims at high throughput detection, quantification and identification of metabolites in biological samples. Changes in the concentration of specific metabolites in a biological sample indicate changes in the metabolic pathways. In this paper review and discuss novel methods that involve application of metabolomics to drug discovery and the understanding of mechanisms of action of medicinal plants with anti-TB activity. Current knowledge on TB infection, anti-TB drugs and mechanisms of action are also included. We further highlight metabolism of M. tuberculosis and the potential drug targets, as well as current approaches in the development of anti-TB drugs.

PMID: 30270413 [PubMed]

Stable Isotope Composition of Metal Elements in Biological Samples as Tracers for Element Metabolism.

October 2, 2018 - 8:09pm
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Stable Isotope Composition of Metal Elements in Biological Samples as Tracers for Element Metabolism.

Anal Sci. 2018;34(6):645-655

Authors: Tanaka YK, Hirata T

Abstract
Stable isotope composition varies due to different reactivity or mobility among the isotopes. Various pioneering studies revealed that isotope fractionation is common for many elements, and it is now widely recognized that the stable isotope compositions of biometals can be used as new tracers for element metabolism. In this review, we summarize the recently published isotope compositions of iron (Fe), copper (Cu), zinc (Zn), and calcium (Ca) in various biological samples, including tissues from plants, animals, and humans. Discussions were carried out with respect to age, sex, organ, and the presence or absence of particular diseases for animals and humans. For Fe and Cu isotopes, changes in oxidation states generate large isotopic fractionation through the metabolism of those elements. Isotope composition of Zn greatly fractionates among tissues even without changes in oxidation state. Isotopic composition of Ca is a powerful tracer for the metabolism of Ca in bones. The review results suggest that the stable isotope compositions of the biometals can be used as effective markers for diagnostics of various kinds of diseases related to metabolic disorders.

PMID: 29887552 [PubMed - indexed for MEDLINE]

Plant-Derived Polyphenols in Human Health: Biological Activity, Metabolites and Putative Molecular Targets.

October 2, 2018 - 8:09pm
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Plant-Derived Polyphenols in Human Health: Biological Activity, Metabolites and Putative Molecular Targets.

Curr Drug Metab. 2018;19(4):351-369

Authors: Olivares-Vicente M, Barrajon-Catalan E, Herranz-Lopez M, Segura-Carretero A, Joven J, Encinar JA, Micol V

Abstract
BACKGROUND: Hibiscus sabdariffa, Lippia citriodora, Rosmarinus officinalis and Olea europaea, are rich in bioactive compounds that represent most of the phenolic compounds' families and have exhibited potential benefits in human health. These plants have been used in folk medicine for their potential therapeutic properties in human chronic diseases. Recent evidence leads to postulate that polyphenols may account for such effects. Nevertheless, the compounds or metabolites that are responsible for reaching the molecular targets are unknown.
OBJECTIVE: data based on studies directly using complex extracts on cellular models, without considering metabolic aspects, have limited applicability. In contrast, studies exploring the absorption process, metabolites in the blood circulation and tissues have become essential to identify the intracellular final effectors that are responsible for extracts bioactivity. Once the cellular metabolites are identified using high-resolution mass spectrometry, docking techniques suppose a unique tool for virtually screening a large number of compounds on selected targets in order to elucidate their potential mechanisms.
RESULTS: we provide an updated overview of the in vitro and in vivo studies on the toxicity, absorption, permeability, pharmacokinetics and cellular metabolism of bioactive compounds derived from the abovementioned plants to identify the potential compounds that are responsible for the observed health effects.
CONCLUSION: we propose the use of targeted metabolomics followed by in silico studies to virtually screen identified metabolites on selected protein targets, in combination with the use of the candidate metabolites in cellular models, as the methods of choice for elucidating the molecular mechanisms of these compounds.

PMID: 29468962 [PubMed - indexed for MEDLINE]

Metabolomics in the Clinic: A Review of the Shared and Unique Features of Untargeted Metabolomics for Clinical Research and Clinical Testing.

September 23, 2018 - 8:59am
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Metabolomics in the Clinic: A Review of the Shared and Unique Features of Untargeted Metabolomics for Clinical Research and Clinical Testing.

J Mass Spectrom. 2018 Sep 22;:

Authors: Kennedy AD, Wittmann BM, Evans AM, Miller LAD, Toal DR, Lonergan S, Elsea SH, Pappan KL

Abstract
Metabolomics is the untargeted measurement of the metabolome, which is comprised of the complement of small molecules detected in a biological sample. As such, metabolomic analysis produces a global biochemical phenotype. It is a technology that has been utilized in the research setting for over a decade. The metabolome is directly linked to and is influenced by genetics, epigenetics, environmental factors and the microbiome - all of which affect health. Metabolomics can be applied to human clinical diagnostics and to other fields such as veterinary medicine, nutrition, exercise, physiology, agriculture/plant biochemistry, and toxicology. Applications of metabolomics in clinical testing are emerging, but several aspects of its use as a clinical test differ from applications focused on research or biomarker discovery and need to be considered for metabolomics clinical test data to have optimum impact, be meaningful, and be used responsibly. In this review, we deconstruct aspects and challenges of metabolomics for clinical testing by illustrating the significance of test design, accurate and precise data acquisition, quality control, data processing, n-of-1 comparison to a reference population, and biochemical pathway analysis. We describe how metabolomics technology is integral to defining individual biochemical phenotypes, elaborates on human health and disease, and fits within the precision medicine landscape. Finally, we conclude by outlining some future steps needed to bring metabolomics into the clinical space and to be recognized by the broader medical and regulatory fields.

PMID: 30242936 [PubMed - as supplied by publisher]

CE-MS for metabolomics: developments and applications in the period 2016-2018.

September 21, 2018 - 8:04am
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CE-MS for metabolomics: developments and applications in the period 2016-2018.

Electrophoresis. 2018 Sep 19;:

Authors: Ramautar R, Somsen GW, de Jong GJ

Abstract
In the field of metabolomics, capillary electrophoresis-mass spectrometry (CE-MS) is now recognized as a strong analytical technique for the analysis of (highly) polar and charged metabolites in a wide range of biological samples. Over the past few years, significant attention has been paid to the design and improvement of CE-MS approaches for (large-scale) metabolic profiling studies and for establishing protocols in order to further expand the role of CE-MS in metabolomics. In this paper, which is a follow-up of a previous review paper covering the years 2014-2016 (Electrophoresis 2017, 38, 190-202), main advances in CE-MS approaches for metabolomics studies are outlined covering the literature from July 2016 to June 2018. Aspects like developments in interfacing designs and data analysis tools for improving the performance of CE-MS for metabolomics are discussed. Representative examples highlight the utility of CE-MS in the fields of biomedical, clinical, microbial and plant metabolomics. A complete overview of recent CE-MS-based metabolomics studies is given in a table, which provides information on sample type and pretreatment, capillary coatings and MS detection mode. Finally, some general conclusions and perspectives are given. This article is protected by copyright. All rights reserved.

PMID: 30232802 [PubMed - as supplied by publisher]

Breakthroughs in the health effects of plant food bioactives: a perspective on microbiomics, nutri(epi)genomics, and metabolomics.

September 14, 2018 - 8:02am
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Breakthroughs in the health effects of plant food bioactives: a perspective on microbiomics, nutri(epi)genomics, and metabolomics.

J Agric Food Chem. 2018 Sep 13;:

Authors: Bayram B, Gonzalez-Sarrias A, Istas G, Garcia-Aloy M, Morand C, Tuohy K, Garcia-Villalba R, Mena P

Abstract
Plant bioactive compounds consumed as part of our diet are able to influence human health. They include secondary metabolites like (poly)phenols, carotenoids, glucosinolates, alkaloids, and terpenes. Although much knowledge has been gained, there is still need for studies unravelling the effects of plant bioactives on cardiometabolic health at individual level, using cutting-edge high resolution and data-rich holistic approaches. The aim of this perspective paper is to review the prospects of microbiomics, nutrigenomics and nutriepigenomics, and metabolomics to assess the response to plant bioactive consumption while considering inter-individual variability. Insights for future research in the field towards personalized nutrition are discussed.

PMID: 30208704 [PubMed - as supplied by publisher]

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