Plant Metabolomics Reviews

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Gene Discovery of Characteristic Metabolic Pathways in the Tea Plant (Camellia sinensis) Using 'Omics'-Based Network Approaches: A Future Perspective.

June 20, 2018 - 7:55am
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Gene Discovery of Characteristic Metabolic Pathways in the Tea Plant (Camellia sinensis) Using 'Omics'-Based Network Approaches: A Future Perspective.

Front Plant Sci. 2018;9:480

Authors: Zhang S, Zhang L, Tai Y, Wang X, Ho CT, Wan X

Abstract
Characteristic secondary metabolites, including flavonoids, theanine and caffeine, in the tea plant (Camellia sinensis) are the primary sources of the rich flavors, fresh taste, and health benefits of tea. The decoding of genes involved in these characteristic components is still significantly lagging, which lays an obstacle for applied genetic improvement and metabolic engineering. With the popularity of high-throughout transcriptomics and metabolomics, 'omics'-based network approaches, such as gene co-expression network and gene-to-metabolite network, have emerged as powerful tools for gene discovery of plant-specialized (secondary) metabolism. Thus, it is pivotal to summarize and introduce such system-based strategies in facilitating gene identification of characteristic metabolic pathways in the tea plant (or other plants). In this review, we describe recent advances in transcriptomics and metabolomics for transcript and metabolite profiling, and highlight 'omics'-based network strategies using successful examples in model and non-model plants. Further, we summarize recent progress in 'omics' analysis for gene identification of characteristic metabolites in the tea plant. Limitations of the current strategies are discussed by comparison with 'omics'-based network approaches. Finally, we demonstrate the potential of introducing such network strategies in the tea plant, with a prospects ending for a promising network discovery of characteristic metabolite genes in the tea plant.

PMID: 29915604 [PubMed]

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches.

June 20, 2018 - 7:55am
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Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches.

Front Microbiol. 2018;9:1132

Authors: Malla MA, Dubey A, Yadav S, Kumar A, Hashem A, Abd Allah EF

Abstract
Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

PMID: 29915565 [PubMed]

Metabolomics in Plant Priming Research: The Way Forward?

June 15, 2018 - 8:00am
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Metabolomics in Plant Priming Research: The Way Forward?

Int J Mol Sci. 2018 Jun 13;19(6):

Authors: Tugizimana F, Mhlongo MI, Piater LA, Dubery IA

Abstract
A new era of plant biochemistry at the systems level is emerging, providing detailed descriptions of biochemical phenomena at the cellular and organismal level. This new era is marked by the advent of metabolomics—the qualitative and quantitative investigation of the entire metabolome (in a dynamic equilibrium) of a biological system. This field has developed as an indispensable methodological approach to study cellular biochemistry at a global level. For protection and survival in a constantly-changing environment, plants rely on a complex and multi-layered innate immune system. This involves surveillance of ‘self’ and ‘non-self,’ molecule-based systemic signalling and metabolic adaptations involving primary and secondary metabolites as well as epigenetic modulation mechanisms. Establishment of a pre-conditioned or primed state can sensitise or enhance aspects of innate immunity for faster and stronger responses. Comprehensive elucidation of the molecular and biochemical processes associated with the phenotypic defence state is vital for a better understanding of the molecular mechanisms that define the metabolism of plant⁻pathogen interactions. Such insights are essential for translational research and applications. Thus, this review highlights the prospects of metabolomics and addresses current challenges that hinder the realisation of the full potential of the field. Such limitations include partial coverage of the metabolome and maximising the value of metabolomics data (extraction of information and interpretation). Furthermore, the review points out key features that characterise both the plant innate immune system and enhancement of the latter, thus underlining insights from metabolomic studies in plant priming. Future perspectives in this inspiring area are included, with the aim of stimulating further studies leading to a better understanding of plant immunity at the metabolome level.

PMID: 29899301 [PubMed - in process]

Ethnobotanic, Ethnopharmacologic Aspects and New Phytochemical Insights into Moroccan Argan Fruits.

June 9, 2018 - 7:55am
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Ethnobotanic, Ethnopharmacologic Aspects and New Phytochemical Insights into Moroccan Argan Fruits.

Int J Mol Sci. 2017 Oct 30;18(11):

Authors: Khallouki F, Eddouks M, Mourad A, Breuer A, Owen RW

Abstract
This review summarizes available data on argan fruit botany, geographical distribution, traditional uses, environmental interest, socioeconomic role, phytochemistry, as well as health beneficial effects and examination of future prospects. In particular, ethnomedical uses of argan fruits are carried out throughout Morocco where it has been used against various diseases. Different classes of bioactive compounds have been characterized including essential oils, fatty acids, triacylglycerols, flavonoids and their newly reported acylglycosyl derivatives, monophenols, phenolic acids, cinnamic acids, saponins, triterpenes, phytosterols, ubiquinone, melatonin, new aminophenols along with vitamin E among other secondary metabolites. The latter have already shown a wide spectrum of in vitro, and ex vivo biologicalactivities including antioxidant, anti-inflammatory, anti-diabetic, antihypertensive, anti-hypercholesterolemia, analgesic, antimicrobial, molluscicidal anti-nociceptive and anticancer potential. Argan flesh (pulp) contains a broad spectrum of polyphenolic compounds which may have utility for incorporation into nutraceuticals and cosmeceuticals relevant to the food, cosmetic and health industries. Further research is recommended, especially on the health beneficial effects of the aminophenols.

PMID: 29084170 [PubMed - indexed for MEDLINE]

[Advances on molecular mechanisms of Rehmannia glutinosa consecutive monoculture problem formation in multi-omics era].

June 8, 2018 - 7:52am
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[Advances on molecular mechanisms of Rehmannia glutinosa consecutive monoculture problem formation in multi-omics era].

Zhongguo Zhong Yao Za Zhi. 2017 Feb;42(3):413-419

Authors: Li MJ, Feng FJ, Zhang B, Gu L, Wang FQ, Yang YH, Tian YH, Chen XJ, Zhang ZY

Abstract
Although consecutive monoculture problems have been studied for many years, no effective treatments are currently available. The complexity of systems triggered the formation of consecutive monoculture problems was one major cause. This paper elaborated the physiological and ecological mechanisms of consecutive monoculture problem formation based on the interaction relationship among multiple factors presented in the rhizosphere soil of consecutive monoculture plants. At same time, in this paper the multiple interactions among cultivated medicinal plants, autotoxic allelochemicals and rhizosphere microbial were proposed to be most important causes that derived the formation of consecutive monoculture problem. The paper also highlighted the advantage of 'omics' technologies integrating plant functional genomics and metabolomics as well as microbial macro-omics in understanding the multiple factor interaction under a particular ecological environment. Additionally, taking R. glutinosa as an example, the paper reviewed the molecular mechanism for the formation of R. glutinosa consecutive monoculture problem from the perspective of the accumulation of allelopathic autotoxins, the rhizosphere microecology catastrophe and theresponding of consecutive monoculture plants. Simultaneously, the roles of mutilple 'omics' technologies in comprehending these formation mechanism were described in detail. This paper provides finally a new insight to solve systematically the mechanism of consecutive monoculture problem formation on molecular level.

PMID: 28952242 [PubMed - indexed for MEDLINE]

ER Membrane Lipid Composition and Metabolism: Lipidomic Analysis.

June 7, 2018 - 8:27am
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ER Membrane Lipid Composition and Metabolism: Lipidomic Analysis.

Methods Mol Biol. 2018;1691:125-137

Authors: Fouillen L, Maneta-Peyret L, Moreau P

Abstract
Plant ER membranes are the major site of biosynthesis of several lipid families (phospholipids, sphingolipids, neutral lipids such as sterols and triacylglycerols). The structural diversity of lipids presents considerable challenges to comprehensive lipid analysis. This chapter will briefly review the various biosynthetic pathways and will detail several aspects of the lipid analysis: lipid extraction, handling, separation, detection, identification, and data presentation. The different tools/approaches used for lipid analysis will also be discussed in relation to the studies to be carried out on lipid metabolism and function.

PMID: 29043674 [PubMed - indexed for MEDLINE]

Potential role of CYP1B1 in the development and treatment of metabolic diseases.

June 5, 2018 - 8:13pm
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Potential role of CYP1B1 in the development and treatment of metabolic diseases.

Pharmacol Ther. 2017 Oct;178:18-30

Authors: Li F, Zhu W, Gonzalez FJ

Abstract
Cytochrome P450 1B1 (CYP1B1), a member of CYP superfamily, is expressed in liver and extrahepatic tissues carries out the metabolism of numerous xenobiotics, including metabolic activation of polycyclic aromatic hydrocarbons. Surprisingly, CYP1B1 was also shown to be important in regulating endogenous metabolic pathways, including the metabolism of steroid hormones, fatty acids, melatonin, and vitamins. CYP1B1 and nuclear receptors including peroxisome proliferator-activated receptors (PPARs), estrogen receptor (ER), and retinoic acid receptors (RAR) contribute to the maintenance of the homeostasis of these endogenous compounds. Many natural flavonoids and synthetic stilbenes show inhibitory activity toward CYP1B1 expression and function, notably isorhamnetin and 2,4,3',5'-tetramethoxystilbene. Accumulating evidence indicates that modulation of CYP1B1 can decrease adipogenesis and tumorigenesis, and prevent obesity, hypertension, atherosclerosis, and cancer. Therefore, it may be feasible to consider CYP1B1 as a therapeutic target for the treatment of metabolic diseases.

PMID: 28322972 [PubMed - indexed for MEDLINE]

The Integration of Metabolomics and Next-Generation Sequencing Data to Elucidate the Pathways of Natural Product Metabolism in Medicinal Plants.

May 31, 2018 - 8:33am
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The Integration of Metabolomics and Next-Generation Sequencing Data to Elucidate the Pathways of Natural Product Metabolism in Medicinal Plants.

Planta Med. 2018 May 29;:

Authors: Scossa F, Benina M, Alseekh S, Zhang Y, Fernie AR

Abstract
Plants have always been used as medicines since ancient times to treat diseases. The knowledge around the active components of herbal preparations has remained nevertheless fragmentary: the biosynthetic pathways of many secondary metabolites of pharmacological importance have been clarified only in a few species, while the chemodiversity present in many medicinal plants has remained largely unexplored. Despite the advancements of synthetic biology for production of medicinal compounds in heterologous hosts, the native plant species are often the most reliable and economic source for their production. It thus becomes fundamental to investigate the metabolic composition of medicinal plants to characterize their natural metabolic diversity and to define the biosynthetic routes in planta of important compounds to develop strategies to further increase their content. We present here a number of case studies for selected classes of secondary metabolites and we review their health benefits and the historical developments in their structural elucidation and characterization of biosynthetic genes. We cover the cases of benzoisoquinoline and monoterpenoid indole alkaloids, cannabinoids, caffeine, ginsenosides, withanolides, artemisinin, and taxol; we show how the "early" biochemical or the more recent integrative approaches-based on omics-analyses-have helped to elucidate their metabolic pathways and cellular compartmentation. We also summarize how the knowledge generated about their biosynthesis has been used to develop metabolic engineering strategies in heterologous and native hosts. We conclude that following the advent of novel, high-throughput and cost-effective analytical technologies, the secondary metabolism of medicinal plants can now be examined under the lens of systems biology.

PMID: 29843183 [PubMed - as supplied by publisher]

[Metabolomics research of medicinal plants].

May 31, 2018 - 8:33am
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[Metabolomics research of medicinal plants].

Zhongguo Zhong Yao Za Zhi. 2016 Nov;41(22):4090-4095

Authors: Duan LX, Dai YT, Sun C, Chen SL

Abstract
Metabolomics is the comprehensively study of chemical processes involving small molecule metabolites. It is an important part of systems biology, and is widely applied in complex traditional Chinese medicine(TCM)system. Metabolites biosynthesized by medicinal plants are the effective basis for TCM. Metabolomics studies of medicinal plants will usher in a new period of vigorous development with the implementation of Herb Genome Program and the development of TCM synthetic biology. This manuscript introduces the recent research progresses of metabolomics technology and the main research contents of metabolomics studies for medicinal plants, including identification and quality evaluation for medicinal plants, cultivars breeding, stress resistance, metabolic pathways, metabolic network, metabolic engineering and synthetic biology researches. The integration of genomics, transcriptomics and metabolomics approaches will finally lay foundation for breeding of medicinal plants, R&D, quality and safety evaluation of innovative drug.

PMID: 28933072 [PubMed - indexed for MEDLINE]

Bioinformatics can boost metabolomics research.

May 24, 2018 - 8:31am
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Bioinformatics can boost metabolomics research.

J Biotechnol. 2017 Nov 10;261:137-141

Authors: Meier R, Ruttkies C, Treutler H, Neumann S

Abstract
Metabolomics is the modern term for the field of small molecule research in biology and biochemistry. Currently, metabolomics is undergoing a transition where the classic analytical chemistry is combined with modern cheminformatics and bioinformatics methods, paving the way for large-scale data analysis. We give some background on past developments, highlight current state-of-the-art approaches, and give a perspective on future requirements.

PMID: 28554829 [PubMed - indexed for MEDLINE]

Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia.

May 23, 2018 - 7:53pm
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Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia.

High Throughput. 2018 May 18;7(2):

Authors: Lardi M, Pessi G

Abstract
Biological nitrogen fixation gives legumes a pronounced growth advantage in nitrogen-deprived soils and is of considerable ecological and economic interest. In exchange for reduced atmospheric nitrogen, typically given to the plant in the form of amides or ureides, the legume provides nitrogen-fixing rhizobia with nutrients and highly specialised root structures called nodules. To elucidate the molecular basis underlying physiological adaptations on a genome-wide scale, functional genomics approaches, such as transcriptomics, proteomics, and metabolomics, have been used. This review presents an overview of the different functional genomics approaches that have been performed on rhizobial symbiosis, with a focus on studies investigating the molecular mechanisms used by the bacterial partner to interact with the legume. While rhizobia belonging to the alpha-proteobacterial group (alpha-rhizobia) have been well studied, few studies to date have investigated this process in beta-proteobacteria (beta-rhizobia).

PMID: 29783718 [PubMed]

Use of biomarkers to assess fruit and vegetable intake.

May 23, 2018 - 7:53pm
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Use of biomarkers to assess fruit and vegetable intake.

Proc Nutr Soc. 2017 Aug;76(3):308-315

Authors: Woodside JV, Draper J, Lloyd A, McKinley MC

Abstract
A high intake of fruit and vegetables (FV) has been associated with reduced risk of a number of chronic diseases, including CVD. The aim of this review is to describe the potential use of biomarkers to assess FV intake. Traditional methods of assessing FV intake have limitations, and this is likely to impact on observed associations with disease outcomes and markers of disease risk. Nutritional biomarkers may offer a more objective and reliable method of assessing dietary FV intake. Some single blood biomarkers, such as plasma vitamin C and serum carotenoids, are well established as indicators of FV intake. Combining potential biomarkers of intake may more accurately predict overall FV intake within intervention studies than the use of any single biomarker. Another promising approach is metabolomic analysis of biological fluids using untargeted approaches to identify potential new biomarkers of FV intake. Using biomarkers to measure FV intake may improve the accuracy of dietary assessment.

PMID: 28347371 [PubMed - indexed for MEDLINE]

A Phytochemical-Sensing Strategy Based on Mass Spectrometry Imaging and Metabolic Profiling for Understanding the Functionality of the Medicinal Herb Green Tea.

May 22, 2018 - 7:54am
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A Phytochemical-Sensing Strategy Based on Mass Spectrometry Imaging and Metabolic Profiling for Understanding the Functionality of the Medicinal Herb Green Tea.

Molecules. 2017 Sep 27;22(10):

Authors: Fujimura Y, Miura D, Tachibana H

Abstract
Low-molecular-weight phytochemicals have health benefits and reduce the risk of diseases, but the mechanisms underlying their activities have remained elusive because of the lack of a methodology that can easily visualize the exact behavior of such small molecules. Recently, we developed an in situ label-free imaging technique, called mass spectrometry imaging, for visualizing spatially-resolved biotransformations based on simultaneous mapping of the major bioactive green tea polyphenol and its phase II metabolites. In addition, we established a mass spectrometry-based metabolic profiling technique capable of evaluating the bioactivities of diverse green tea extracts, which contain multiple phytochemicals, by focusing on their compositional balances. This methodology allowed us to simultaneously evaluate the relative contributions of the multiple compounds present in a multicomponent system to its bioactivity. This review highlights small molecule-sensing techniques for visualizing the complex behaviors of herbal components and linking such information to an enhanced understanding of the functionalities of multicomponent medicinal herbs.

PMID: 28953237 [PubMed - indexed for MEDLINE]

Enabling Molecular Technologies for Trait Improvement in Wheat.

May 22, 2018 - 7:54am
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Enabling Molecular Technologies for Trait Improvement in Wheat.

Methods Mol Biol. 2017;1679:3-24

Authors: Bhalla PL, Sharma A, Singh MB

Abstract
Wheat is the major staple food crop and a source of calories for humans worldwide. A steady increase in the wheat production is essential to meet the demands of an ever-increasing global population and to achieve food security. The large size and structurally intricate genome of polyploid wheat had hindered the genomic analysis. However, with the advent of new genomic technologies such as next generation sequencing has led to genome drafts for bread wheat and its progenitors and has paved the way to design new strategies for crop improvement. Here we provide an overview of the advancements made in wheat genomics together with the available "omics approaches" and bioinformatics resources developed for wheat research. Advances in genomic, transcriptomic, and metabolomic technologies are highlighted as options to circumvent existing bottlenecks in the phenotypic and genomic selection and gene transfer. The contemporary reverse genetics approaches, including the novel genome editing techniques to inform targeted manipulation of a single/multiple genes and strategies for generating marker-free transgenic wheat plants, emphasize potential to revolutionize wheat improvement shortly.

PMID: 28913791 [PubMed - indexed for MEDLINE]

Assessing Flux Distribution Associated with Metabolic Specialization of Glandular Trichomes.

May 8, 2018 - 7:52pm
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Assessing Flux Distribution Associated with Metabolic Specialization of Glandular Trichomes.

Trends Plant Sci. 2018 May 04;:

Authors: Zager JJ, Lange BM

Abstract
Many aromatic plants accumulate mixtures of secondary (or specialized) metabolites in anatomical structures called glandular trichomes (GTs). Different GT types may also synthesize different mixtures of secreted metabolites, and this contributes to the enormous chemical diversity reported to occur across species. Over the past two decades, significant progress has been made in characterizing the genes and enzymes that are responsible for the unique metabolic capabilities of GTs in different lineages of flowering plants. Less is known about the processes that regulate flux distribution through precursor pathways toward metabolic end-products. We discuss here the results from a meta-analysis of genome-scale models that were developed to capture the unique metabolic capabilities of different GT types.

PMID: 29735428 [PubMed - as supplied by publisher]

Current Challenges in Plant Eco-Metabolomics.

May 8, 2018 - 7:52pm
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Current Challenges in Plant Eco-Metabolomics.

Int J Mol Sci. 2018 May 06;19(5):

Authors: Peters K, Worrich A, Weinhold A, Alka O, Balcke G, Birkemeyer C, Bruelheide H, Calf OW, Dietz S, Dührkop K, Gaquerel E, Heinig U, Kücklich M, Macel M, Müller C, Poeschl Y, Pohnert G, Ristok C, Rodríguez VM, Ruttkies C, Schuman M, Schweiger R, Shahaf N, Steinbeck C, Tortosa M, Treutler H, Ueberschaar N, Velasco P, Weiß BM, Widdig A, Neumann S, Dam NMV

Abstract
The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant⁻organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.

PMID: 29734799 [PubMed - in process]

Metabolomics 20 years on: What have we learned and what hurdles remain?

May 8, 2018 - 7:52pm
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Metabolomics 20 years on: What have we learned and what hurdles remain?

Plant J. 2018 May 07;:

Authors: Alseekh S, Fernie AR

Abstract
The term metabolome was coined in 1998, by analogy to genome, transcriptome and proteome. The first research papers using the terms metabolomics, metabonomics, metabolic profiling or metabolite profiling were published shortly thereafter. In this short review we reflect on the major achievements brought about by use of these approaches and document knowledge and technology gaps which are currently constraining its further development. Finally, we detail why we think that the time is ripe to refocus our efforts on the understanding of metabolic function. This article is protected by copyright. All rights reserved.

PMID: 29734513 [PubMed - as supplied by publisher]

Review and perspectives on the applications of mass spectrometry imaging under ambient conditions.

April 27, 2018 - 8:29am
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Review and perspectives on the applications of mass spectrometry imaging under ambient conditions.

Rapid Commun Mass Spectrom. 2018 Apr 26;:

Authors: Perez CJ, Bagga AK, Prova SS, Taemeh MY, Ifa DR

Abstract
Ambient MS-based techniques are performed under ambient conditions in which the ionization and desorption occur in the open environment allowing the direct analysis of molecules on surfaces with minimal or no sample preparation. A selected group of ambient MS techniques demonstrate imaging capabilities that can provide information about the localization of molecules on complex sample surfaces such as biological tissues. 2D, 3D, and multimodal imaging have unlocked an array of applications to systematically address complex problems in many areas of research such as drug monitoring, natural products forensics, and cancer diagnostics. In the present review, we summarize recent advances in the field with respect to the implementation of new ambient ionization techniques and current applications in the last 5 years. In more detail, we mainly focus on imaging applications in topics related to animal cells and tissues, single cells, cancer diagnostics and biomarkers, microbial cultures and cocultures, plant and natural product metabolomics, forensic applications. Finally, we discuss new areas of research, future perspectives and the overall direction that the field may take in the years to come.

PMID: 29698560 [PubMed - as supplied by publisher]

Understanding the Molecular Mechanisms of the Interplay Between Herbal Medicines and Gut Microbiota.

April 24, 2018 - 7:56am
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Understanding the Molecular Mechanisms of the Interplay Between Herbal Medicines and Gut Microbiota.

Med Res Rev. 2017 Sep;37(5):1140-1185

Authors: Xu J, Chen HB, Li SL

Abstract
Herbal medicines (HMs) are much appreciated for their significant contribution to human survival and reproduction by remedial and prophylactic management of diseases. Defining the scientific basis of HMs will substantiate their value and promote their modernization. Ever-increasing evidence suggests that gut microbiota plays a crucial role in HM therapy by complicated interplay with HM components. This interplay includes such activities as: gut microbiota biotransforming HM chemicals into metabolites that harbor different bioavailability and bioactivity/toxicity from their precursors; HM chemicals improving the composition of gut microbiota, consequently ameliorating its dysfunction as well as associated pathological conditions; and gut microbiota mediating the interactions (synergistic and antagonistic) between the multiple chemicals in HMs. More advanced experimental designs are recommended for future study, such as overall chemical characterization of gut microbiota-metabolized HMs, direct microbial analysis of HM-targeted gut microbiota, and precise gut microbiota research model development. The outcomes of such research can further elucidate the interactions between HMs and gut microbiota, thereby opening a new window for defining the scientific basis of HMs and for guiding HM-based drug discovery.

PMID: 28052344 [PubMed - indexed for MEDLINE]

The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil.

April 17, 2018 - 7:55am
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The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil.

J Environ Manage. 2018 Apr 13;217:858-870

Authors: Kotoky R, Rajkumari J, Pandey P

Abstract
Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.

PMID: 29660711 [PubMed - as supplied by publisher]

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