Plant Metabolomics Reviews

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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METHODS: The data was extracted from unpublished theses (Pakistan, China, India and Nepal), and different published research articles confined to pharmacology, phytochemistry and antimicrobial activities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]

Recent advances in matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for in situ analysis of endogenous molecules in plants.

September 12, 2018 - 8:32am
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Recent advances in matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for in situ analysis of endogenous molecules in plants.

Phytochem Anal. 2018 Jul;29(4):351-364

Authors: Qin L, Zhang Y, Liu Y, He H, Han M, Li Y, Zeng M, Wang X

Abstract
INTRODUCTION: Mass spectrometry imaging (MSI) as a label-free and powerful imaging technique enables in situ evaluation of a tissue metabolome and/or proteome, becoming increasingly popular in the detection of plant endogenous molecules.
OBJECTIVE: The characterisation of structure and spatial information of endogenous molecules in plants are both very important aspects to better understand the physiological mechanism of plant organism.
METHODS: Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a commonly-used tissue imaging technique, which requires matrix to assist in situ detection of a variety of molecules on the surface of a tissue section. In previous studies, MALDI-MSI was mostly used for the detection of molecules from animal tissue sections, compared to plant samples due to cell structural limitations, such as plant cuticles, epicuticular waxes, and cell walls. Despite the enormous progress that has been made in tissue imaging, there is still a challenge for MALDI-MSI suitable for the imaging of endogenous compounds in plants.
RESULTS: This review summarises the recent advances in MALDI-MSI, focusing on the application of in situ detection of endogenous molecules in different plant organs, i.e. root, stem, leaf, flower, fruit, and seed.
CONCLUSION: Further improvements on instrumentation sensitivity, matrix selection, image processing and sample preparation will expand the application of MALDI-MSI in plant research.

PMID: 29667236 [PubMed - indexed for MEDLINE]

LC-MS based metabolic and metabonomic studies of Panax ginseng.

September 12, 2018 - 8:32am
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LC-MS based metabolic and metabonomic studies of Panax ginseng.

Phytochem Anal. 2018 Jul;29(4):331-340

Authors: Wu W, Jiao C, Li H, Ma Y, Jiao L, Liu S

Abstract
INTRODUCTION: Panax ginseng has received much attention as a valuable health supplement with medicinal potential. Its chemical diversity and multiple pharmacological properties call for comprehensive methods to better understand the effects of ginseng and ginsenosides. Liquid chromatography-mass spectrometry (LC-MS) based metabonomic approaches just fit the purpose.
OBJECTIVE: Aims to give a review of recent progress on LC-MS based pharmacokinetic, metabolic, and phytochemical metabolomic studies of ginseng, and metabonomic studies of ginseng intervention effects.
METHODS: The review has four sections: the first section discusses metabolic studies of ginsenosides based on LC-MS, the second focuses on ginsenoside-drug interactions and pharmacokinetic interaction between herb compounds based on LC-MS, the third is phytochemical metabolomic studies of ginseng based on LC-MS, and the fourth deals with metabonomic studies of ginseng intervention effects based on LC-MS.
RESULTS: LC-MS based metabonomic research on ginseng include analysis of single ginsenoside and total ginsenosides. The theory of multi-components and multi-targeted mechanisms helps to explain ginseng effects.
CONCLUSION: LC-MS based metabonomics is a promising way to comprehensively assess ginseng. It is valuable for quality control and mechanism studies of ginseng.

PMID: 29460310 [PubMed - indexed for MEDLINE]

Using metabolome data for mathematical modeling of plant metabolic systems.

September 9, 2018 - 8:44am
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Using metabolome data for mathematical modeling of plant metabolic systems.

Curr Opin Biotechnol. 2018 Sep 05;54:138-144

Authors: Hirai MY, Shiraishi F

Abstract
Plant metabolism is characterized by a wide diversity of metabolites, with systems far more complicated than those of microorganisms. Mathematical modeling is useful for understanding dynamic behaviors of plant metabolic systems for metabolic engineering. Time-series metabolome data has great potential for estimating kinetic model parameters to construct a genome-wide metabolic network model. However, data obtained by current metabolomics techniques does not meet the requirement for constructing accurate models. In this article, we highlight novel strategies and algorithms to handle the underlying difficulties and construct dynamic in vivo models for large-scale plant metabolic systems. The coarse but efficient modeling enables the prediction of unknown mechanisms regulating plant metabolism.

PMID: 30195121 [PubMed - as supplied by publisher]

A review of nanoscale LC-ESI for metabolomics and its potential to enhance the metabolome coverage.

September 8, 2018 - 8:35am
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A review of nanoscale LC-ESI for metabolomics and its potential to enhance the metabolome coverage.

Talanta. 2018 May 15;182:380-390

Authors: Chetwynd AJ, David A

Abstract
Liquid chromatography-electrospray ionisation-mass spectrometry (LC-ESI-MS) platforms are widely used to perform high throughput untargeted profiling of biological samples for metabolomics-based approaches. However, these LC-ESI platforms usually favour the detection of metabolites present at relatively high concentrations because of analytical limitations such as ion suppression, thus reducing overall sensitivity. To counter this issue of sensitivity, the latest in terms of analytical platforms can be adopted to enable a greater portion of the metabolome to be analysed in a single analytical run. Here, nanoflow liquid chromatography-nanoelectrospray ionisation (nLC-nESI), which has previously been utilised successfully in proteomics, is explored for use in metabolomic and exposomic research. As a discovery based field, the markedly increased sensitivity of these nLC-nESI platforms offer the potential to uncover the roles played by low abundant signalling metabolites (e.g. steroids, eicosanoids) in health and disease studies, and would also enable an improvement in the detection of xenobiotics present at trace levels in biological matrices to better characterise the chemical exposome. This review aims to give an insight into the advantages associated with nLC-nESI for metabolomics-based approaches. Initially we detail the source of improved sensitivity prior to reviewing the available approaches to achieving nanoflow rates and nanospray ionisation for metabolomics. The robustness of nLC-nESI platforms was then assessed using the literature available from a metabolomic viewpoint. We also discuss the challenging point of sample preparation which needs to be addressed to fully enjoy the benefits of these nLC-nESI platforms. Finally, we assess metabolomic analysis utilising nano scale platforms and look ahead to the future of metabolomics using these new highly sensitive platforms.

PMID: 29501168 [PubMed - indexed for MEDLINE]

Modifications of dietary flavonoids towards improved bioactivity: An update on structure-activity relationship.

September 8, 2018 - 8:35am
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Modifications of dietary flavonoids towards improved bioactivity: An update on structure-activity relationship.

Crit Rev Food Sci Nutr. 2018 Mar 04;58(4):513-527

Authors: Chen L, Teng H, Xie Z, Cao H, Cheang WS, Skalicka-Woniak K, Georgiev MI, Xiao J

Abstract
Over the past two decades, extensive studies have revealed that inflammation represents a major risk factor for various human diseases. Chronic inflammatory responses predispose to pathological progression of chronic illnesses featured with penetration of inflammatory cells, dysregulation of cellular signaling, excessive generation of cytokines, and loss of barrier function. Hence, the suppression of inflammation has the potential to delay, prevent, and to treat chronic diseases. Flavonoids, which are widely distributed in humans daily diet, such as vegetables, fruits, tea and cocoa, among others, are considered as bioactive compounds with anti-inflammatory potential. Modification of flavonoids including hydroxylation, o-methylation, and glycosylation, can alter their metabolic features and affect mechanisms of inflammation. Structure-activity relationships among naturally occurred flavonoids hence provide us with a preliminary insight into their anti-inflammatory potential, not only attributing to the antioxidant capacity, but also to modulate inflammatory mediators. The present review summarizes current knowledge and underlies mechanisms of anti-inflammatory activities of dietary flavonoids and their influences involved in the development of various inflammatory-related chronic diseases. In addition, the established structure-activity relationships of phenolic compounds in this review may give an insight for the screening of new anti-inflammatory agents from dietary materials.

PMID: 27438892 [PubMed - indexed for MEDLINE]

The challenge of the application of 'omics technologies in chemicals risk assessment: Background and outlook.

September 5, 2018 - 8:37am
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The challenge of the application of 'omics technologies in chemicals risk assessment: Background and outlook.

Regul Toxicol Pharmacol. 2017 Dec;91 Suppl 1:S14-S26

Authors: Sauer UG, Deferme L, Gribaldo L, Hackermüller J, Tralau T, van Ravenzwaay B, Yauk C, Poole A, Tong W, Gant TW

Abstract
This survey by the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) highlights that 'omics technologies are generally not yet applied to meet standard information requirements during regulatory hazard assessment. While they are used within weight-of-evidence approaches to investigate substances' modes-of-action, consistent approaches for the generation, processing and interpretation of 'omics data are not applied. To date, no 'omics technology has been standardised or validated. Best practices for performing 'omics studies for regulatory purposes (e.g., microarrays for transcriptome profiling) remain to be established. Therefore, three frameworks for (i) establishing a Good-Laboratory Practice-like context for collecting, storing and curating 'omics data; (ii) 'omics data processing; and (iii) quantitative WoE approaches to interpret 'omics data have been developed, that are presented in this journal supplement. Application of the frameworks will enable between-study comparison of results, which will facilitate the regulatory applicability of 'omics data. The frameworks do not constitute prescriptive protocols precluding any other data analysis method, but provide a baseline for analysis that can be applied to all data allowing ready cross-comparison. Data analysis that does not follow the frameworks can be justified and the resulting data can be compared with the Framework-based common analysis output.

PMID: 28927750 [PubMed - indexed for MEDLINE]

Causes and solutions to "globesity": The new FA(S)T alarming global epidemic.

September 4, 2018 - 7:58am
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Causes and solutions to "globesity": The new FA(S)T alarming global epidemic.

Food Chem Toxicol. 2018 Aug 31;:

Authors: Vasileva LV, Marchev AS, Georgiev MI

Abstract
Diverse groups of factors are leading to increased weight gain and obesity, such as certain genetic phenotypes, neuroendocrine disturbances, the administration of some drugs, behavioral, social and environmental factors. The progressively escalating rates of overweight and obesity worldwide have led to an introduction of a new term "globesity". Excessive accumulation of body fat and especially of visceral adipose tissue is the main predisposing factor for the development of metabolic syndrome and other obesity related co-morbidities. At the present moment only few pharmacotherapeuticals are used for long-term treatment of obesity acting on narrow target spectra, e.g. pancreatic and gastric lipase inhibition, acting as adrenomimetics or activating the satiety centers in hypothalamus. Plant-based medications that accelerate weight loss, proved to be safe, effective and widely available, would be a preferable alternative for anti-obesity treatments. As plant extracts are multi-component systems they could also act by more than one mechanism, including decreased lipid absorption, decreased energy intake, increased energy expenditure, decreased pre-adipocyte differentiation and proliferation, decreased lipogenesis and increased lipolysis. The current review gives a summary of the risk factors for obesity development and its characteristics consequences. Current treatment options, combining lifestyle changes and conventional treatment with commercial anti-obesity drugs have been described as well. Special emphasis on in vitro, in vivo and human studies of potential medicinal plant extracts and phytochemicals, such as polyphenols, terpenoids, alkaloids, saponins, able to modulate the molecular pathways and gene/protein expressions related to obesity have been highlighted.

PMID: 30176311 [PubMed - as supplied by publisher]

Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies.

September 4, 2018 - 7:58am
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Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies.

Mol Nutr Food Res. 2018 Sep 03;:e1800384

Authors: Ulaszewska MM, Weinert CH, Trimigno A, Portmann R, Andres Lacueva C, Badertscher R, Brennan L, Brunius C, Bub A, Capozzi F, Cialiè Rosso M, Cordero CE, Daniel H, Durand S, Egert B, Ferrario PG, Feskens EJM, Franceschi P, Garcia-Aloy M, Giacomoni F, Giesbertz P, González-Domínguez R, Hanhineva K, Hemeryck LY, Kopka J, Kulling S, Llorach R, Manach C, Mattivi F, Migné C, Münger LH, Ott B, Picone G, Pimentel G, Pujos-Guillot E, Riccadonna S, Rist M, Rombouts C, Rubert J, Skurk T, Sri Harsha PSC, Van Meulebroek L, Vanhaecke L, Vázquez-Fresno R, Wishard D, Vergères G

Abstract
The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (FoodBAll) (funded by the European Joint Programming Initiative a Healthy Diet for a Healthy Life (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but, rather, to present a pragmatic guidance on metabolomic methodologies, providing readers with useful "tips and tricks" along the analytical workflow. This article is protected by copyright. All rights reserved.

PMID: 30176196 [PubMed - as supplied by publisher]

A role for ecophysiology in the 'omics' era.

August 10, 2018 - 7:48am

A role for ecophysiology in the 'omics' era.

Plant J. 2018 Aug 09;:

Authors: Flexas J, Gago J

Abstract
Plant Ecophysiology is the study on how Plant Physiology is modulated by the environment. This discipline could have benefited greatly from the development of the different 'omic' technologies (from genomics to metabolomics). Instead, the overall impression is that ecophysiology and 'omics' have developed mostly independent each other. Here we provide a literature analysis over the past twenty years which fully confirms this view. Then, we review a few examples of studies in which ecophysiology and 'omics' studies have combined to different extents to illustrate the potential benefits from their mutualistic interaction. In addition, we debate on the possibilities of working with plants other than Arabidopsis, which is illustrated with some examples of fascinating plants from extreme environments of the world, what we call the 'sherplants'. Finally, we raise a call to both communities (ecophysiology and 'omics') to integrate these disciplines to enter an 'ecophysiolomics era' to maximize our understanding about plant mechanisms from a multidisciplinary approach. This article is protected by copyright. All rights reserved.

PMID: 30091802 [PubMed - as supplied by publisher]

Understanding and exploiting the roles of autophagy in plants through multi-omics approaches.

August 7, 2018 - 7:50am

Understanding and exploiting the roles of autophagy in plants through multi-omics approaches.

Plant Sci. 2018 Sep;274:146-152

Authors: Liu F, Marshall RS, Li F

Abstract
Autophagy is a highly conserved pathway in eukaryotes that promotes nutrient recycling and cellular homeostasis through the degradation of excess or damaged cytoplasmic constituents. In plants, autophagy is increasingly recognized as a key contributor to development, reproduction, metabolism, leaf senescence, endosperm and grain development, pathogen defense, and tolerance to abiotic and biotic stresses. Characterizing the functional transcriptomic, proteomic, and metabolomic networks relating to autophagy in plants subjected to various extra- and intra-cellular stimuli may help to identify components associated with the pathway. As such, the integration of multi-omics approaches (i.e., transcriptomics, proteomics and metabolomics), along with cellular, genetic and functional analyses, could provide a global perspective regarding the effects of autophagy on plant metabolism, development and stress responses. In this mini-review, recent research progress in plant autophagy is discussed, highlighting the importance of high-throughput omics approaches for defining the underpinning molecular mechanisms of autophagy and understanding its associated regulatory network.

PMID: 30080598 [PubMed - in process]

Raising orphans from a metadata morass: A researcher's guide to re-use of public 'omics data.

August 7, 2018 - 7:50am
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Raising orphans from a metadata morass: A researcher's guide to re-use of public 'omics data.

Plant Sci. 2018 Feb;267:32-47

Authors: Bhandary P, Seetharam AS, Arendsee ZW, Hur M, Wurtele ES

Abstract
More than 15 petabases of raw RNAseq data is now accessible through public repositories. Acquisition of other 'omics data types is expanding, though most lack a centralized archival repository. Data-reuse provides tremendous opportunity to extract new knowledge from existing experiments, and offers a unique opportunity for robust, multi-'omics analyses by merging metadata (information about experimental design, biological samples, protocols) and data from multiple experiments. We illustrate how predictive research can be accelerated by meta-analysis with a study of orphan (species-specific) genes. Computational predictions are critical to infer orphan function because their coding sequences provide very few clues. The metadata in public databases is often confusing; a test case with Zea mays mRNA seq data reveals a high proportion of missing, misleading or incomplete metadata. This metadata morass significantly diminishes the insight that can be extracted from these data. We provide tips for data submitters and users, including specific recommendations to improve metadata quality by more use of controlled vocabulary and by metadata reviews. Finally, we advocate for a unified, straightforward metadata submission and retrieval system.

PMID: 29362097 [PubMed - indexed for MEDLINE]

Proteomics survey of Solanaceae family: Current status and challenges ahead.

August 3, 2018 - 8:18am
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Proteomics survey of Solanaceae family: Current status and challenges ahead.

J Proteomics. 2017 Oct 03;169:41-57

Authors: Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R

Abstract
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.

PMID: 28528990 [PubMed - indexed for MEDLINE]

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