Plant Metabolomics Reviews

Subscribe to Plant Metabolomics Reviews feed Plant Metabolomics Reviews
NCBI: db=pubmed; Term=Plant Metabolomics review
Updated: 1 hour 21 min ago

Systems Genetics for Evolutionary Studies.

January 9, 2020 - 5:18am
Icon for Springer Related Articles

Systems Genetics for Evolutionary Studies.

Methods Mol Biol. 2019;1910:635-652

Authors: Prins P, Smant G, Arends D, Mulligan MK, Williams RW, Jansen RC

Abstract
Systems genetics combines high-throughput genomic data with genetic analysis. In this chapter, we review and discuss application of systems genetics in the context of evolutionary studies, in which high-throughput molecular technologies are being combined with quantitative trait locus (QTL) analysis in segregating populations.The recent explosion of high-throughput data-measuring thousands of RNAs, proteins, and metabolites, using deep sequencing, mass spectrometry, chromatin, methyl-DNA immunoprecipitation, etc.-allows the dissection of causes of genetic variation underlying quantitative phenotypes of all types. To deal with the sheer amount of data, powerful statistical tools are needed to analyze multidimensional relationships and to extract valuable information and new modes and mechanisms of changes both within and between species. In the context of evolutionary computational biology, a well-designed experiment and the right population can help dissect complex traits likely to be under selection using proven statistical methods for associating phenotypic variation with chromosomal locations.Recent evolutionary expression QTL (eQTL) studies focus on gene expression adaptations, mapping the gene expression landscape, and, tentatively, define networks of transcripts and proteins that are jointly modulated sets of eQTL networks. Here, we discuss the possibility of introducing an evolutionary "prior" in the form of gene families displaying evidence of positive selection, and using that prior in the context of an eQTL experiment for elucidating host-pathogen protein-protein interactions.Here we review one exemplar evolutionairy eQTL experiment and discuss experimental design, choice of platforms, analysis methods, scope, and interpretation of results. In brief we highlight how eQTL are defined; how they are used to assemble interacting and causally connected networks of RNAs, proteins, and metabolites; and how some QTLs can be efficiently converted to reasonably well-defined sequence variants.

PMID: 31278680 [PubMed - indexed for MEDLINE]

The role of cis-elements in the evolution of crassulacean acid metabolism photosynthesis.

January 8, 2020 - 6:18am

The role of cis-elements in the evolution of crassulacean acid metabolism photosynthesis.

Hortic Res. 2020;7:5

Authors: Chen LY, Xin Y, Wai CM, Liu J, Ming R

Abstract
Crassulacean acid metabolism (CAM) photosynthesis is an innovation of carbon concentrating mechanism that is characterized by nocturnal CO2 fixation. Recent progresses in genomics, transcriptomics, proteomics, and metabolomics of CAM species yielded new knowledge and abundant genomic resources. In this review, we will discuss the pattern of cis-elements in stomata movement-related genes and CAM CO2 fixation genes, and analyze the expression dynamic of CAM related genes in green leaf tissues. We propose that CAM photosynthesis evolved through the re-organization of existing enzymes and associated membrane transporters in central metabolism and stomatal movement-related genes, at least in part by selection of existing circadian clock cis-regulatory elements in their promoter regions. Better understanding of CAM evolution will help us to design crops that can thrive in arid or semi-arid regions, which are likely to expand due to global climate change.

PMID: 31908808 [PubMed]

Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth.

January 8, 2020 - 6:18am

Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth.

Crit Rev Biotechnol. 2020 Jan 06;:1-15

Authors: Asaf S, Numan M, Khan AL, Al-Harrasi A

Abstract
The species belonging to the Sphingomonas genus possess multifaceted functions ranging from remediation of environmental contaminations to producing highly beneficial phytohormones, such as sphingan and gellan gum. Recent studies have shown an intriguing role of Sphingomonas species in the degradation of organometallic compounds. However, the actual biotechnological potential of this genus requires further assessment. Some of the species from the genus have also been noted to improve plant-growth during stress conditions such as drought, salinity, and heavy metals in agricultural soil. This role has been attributed to their potential to produce plant growth hormones e.g. gibberellins and indole acetic acid. However, the current literature is scattered, and some of the important areas, such as taxonomy, phylogenetics, genome mapping, and cellular transport systems, are still being overlooked in terms of elucidation of the mechanisms behind stress-tolerance and bioremediation. In this review, we elucidated the prospective role and function of this genus for improved utilization during environmental biotechnology.

PMID: 31906737 [PubMed - as supplied by publisher]

Is it useful to use several "omics" for obtaining valuable results?

January 8, 2020 - 6:18am
Icon for Springer Related Articles

Is it useful to use several "omics" for obtaining valuable results?

Mol Biol Rep. 2019 Jun;46(3):3597-3606

Authors: Zapalska-Sozoniuk M, Chrobak L, Kowalczyk K, Kankofer M

Abstract
The integration of cell communication and the transfer of signals from stimuli via transcription to translation and further to activation of new protein is crucial for appropriate metabolism and function of living organisms. The overall elucidation and the examination of these complex processes require multistep laboratory approaches in order to obtain results which will not only detect particular stage but also indicate the mechanisms lying upon this process. Such results will be reliable because they will cover multidirectional methods and approaches. The analysis of currently available results already provided with the conclusion that often single omics approach does not correspond with other expected information and may bring misinterpretations. That is why the integration of several "omics" is useful for searching entire explanations and answers as well as appropriate interpretation of obtained complex results. The hypothesis was stated that "from transcriptomics can not be concluded to proteomics". This review focuses on the reasons for the integration of transcriptomic, proteomic and other-omics analysis. Moreover it also describes the examples of clinical meanings and mentions some methods used in these approaches.

PMID: 30989558 [PubMed - indexed for MEDLINE]

Green and White Asparagus (Asparagus officinalis): A Source of Developmental, Chemical and Urinary Intrigue.

December 29, 2019 - 12:18pm
Related Articles

Green and White Asparagus (Asparagus officinalis): A Source of Developmental, Chemical and Urinary Intrigue.

Metabolites. 2019 Dec 25;10(1):

Authors: Pegiou E, Mumm R, Acharya P, de Vos RCH, Hall RD

Abstract
Asparagus (Asparagus officinalis) is one of the world's top 20 vegetable crops. Both green and white shoots (spears) are produced; the latter being harvested before becoming exposed to light. The crop is grown in nearly all areas of the world, with the largest production regions being China, Western Europe, North America and Peru. Successful production demands high farmer input and specific environmental conditions and cultivation practices. Asparagus materials have also been used for centuries as herbal medicine. Despite this widespread cultivation and consumption, we still know relatively little about the biochemistry of this crop and how this relates to the nutritional, flavour, and neutra-pharmaceutical properties of the materials used. To date, no-one has directly compared the contrasting compositions of the green and white crops. In this short review, we have summarised most of the literature to illustrate the chemical richness of the crop and how this might relate to key quality parameters. Asparagus has excellent nutritional properties and its flavour/fragrance is attributed to a set of volatile components including pyrazines and sulphur-containing compounds. More detailed research, however, is needed and we propose that (untargeted) metabolomics should have a more prominent role to play in these investigations.

PMID: 31881716 [PubMed]

Impact of Cocoa Products Intake on Plasma and Urine Metabolites: A Review of Targeted and Non-Targeted Studies in Humans.

December 25, 2019 - 6:18am
Icon for PubMed Central Related Articles

Impact of Cocoa Products Intake on Plasma and Urine Metabolites: A Review of Targeted and Non-Targeted Studies in Humans.

Nutrients. 2019 May 24;11(5):

Authors: Mayorga-Gross AL, Esquivel P

Abstract
Cocoa is continuously drawing attention due to growing scientific evidence suggesting its effects on health. Flavanols and methylxanthines are some of the most important bioactive compounds present in cocoa. Other important bioactives, such as phenolic acids and lactones, are derived from microbial metabolism. The identification of the metabolites produced after cocoa intake is a first step to understand the overall effect on human health. In general, after cocoa intake, methylxanthines show high absorption and elimination efficiencies. Catechins are transformed mainly into sulfate and glucuronide conjugates. Metabolism of procyanidins is highly influenced by the polymerization degree, which hinders their absorption. The polymerization degree over three units leads to biotransformation by the colonic microbiota, resulting in valerolactones and phenolic acids, with higher excretion times. Long term intervention studies, as well as untargeted metabolomic approaches, are scarce. Contradictory results have been reported concerning matrix effects and health impact, and there are still scientific gaps that have to be addresed to understand the influence of cocoa intake on health. This review addresses different cocoa clinical studies, summarizes the different methodologies employed as well as the metabolites that have been identified in plasma and urine after cocoa intake.

PMID: 31137636 [PubMed - indexed for MEDLINE]

Metabolomics: A Way Forward for Crop Improvement.

December 19, 2019 - 8:18am
Related Articles

Metabolomics: A Way Forward for Crop Improvement.

Metabolites. 2019 Dec 14;9(12):

Authors: Razzaq A, Sadia B, Raza A, Khalid Hameed M, Saleem F

Abstract
Metabolomics is an emerging branch of "omics" and it involves identification and quantification of metabolites and chemical footprints of cellular regulatory processes in different biological species. The metabolome is the total metabolite pool in an organism, which can be measured to characterize genetic or environmental variations. Metabolomics plays a significant role in exploring environment-gene interactions, mutant characterization, phenotyping, identification of biomarkers, and drug discovery. Metabolomics is a promising approach to decipher various metabolic networks that are linked with biotic and abiotic stress tolerance in plants. In this context, metabolomics-assisted breeding enables efficient screening for yield and stress tolerance of crops at the metabolic level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC), and direct flow injection (DFI) mass spectrometry, have sped up metabolic profiling. Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants. This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants. Furthermore, the potential of metabolomics-assisted breeding for crop improvement and its future applications in speed breeding are also discussed. Mention has also been made of possible bottlenecks and future prospects of plant metabolomics.

PMID: 31847393 [PubMed]

Synergy and antagonism in natural product extracts: when 1 + 1 does not equal 2.

December 18, 2019 - 8:18am
Icon for Royal Society of Chemistry Icon for PubMed Central Related Articles

Synergy and antagonism in natural product extracts: when 1 + 1 does not equal 2.

Nat Prod Rep. 2019 06 19;36(6):869-888

Authors: Caesar LK, Cech NB

Abstract
Covering: 2000 to 2019 According to a 2012 survey from the Centers for Disease Control and Prevention, approximately 18% of the U.S. population uses natural products (including plant-based or botanical preparations) for treatment or prevention of disease. The use of plant-based medicines is even more prevalent in developing countries, where for many they constitute the primary health care modality. Proponents of the medicinal use of natural product mixtures often claim that they are more effective than purified compounds due to beneficial "synergistic" interactions. A less-discussed phenomenon, antagonism, in which effects of active constituents are masked by other compounds in a complex mixture, also occurs in natural product mixtures. Synergy and antagonism are notoriously difficult to study in a rigorous fashion, particularly given that natural products chemistry research methodology is typically devoted to reducing complexity and identifying single active constituents for drug development. This report represents a critical review with commentary about the current state of the scientific literature as it relates to studying combination effects (including both synergy and antagonism) in natural product extracts. We provide particular emphasis on analytical and Big Data approaches for identifying synergistic or antagonistic combinations and elucidating the mechanisms that underlie their interactions. Specific case studies of botanicals in which synergistic interactions have been documented are also discussed. The topic of synergy is important given that consumer use of botanical natural products and associated safety concerns continue to garner attention by the public and the media. Guidance by the natural products community is needed to provide strategies for effective evaluation of safety and toxicity of botanical mixtures and to drive discovery in botanical natural product research.

PMID: 31187844 [PubMed - indexed for MEDLINE]

Innovative omics-based approaches for prioritisation and targeted isolation of natural products - new strategies for drug discovery.

December 18, 2019 - 8:18am
Icon for Royal Society of Chemistry Related Articles

Innovative omics-based approaches for prioritisation and targeted isolation of natural products - new strategies for drug discovery.

Nat Prod Rep. 2019 06 19;36(6):855-868

Authors: Wolfender JL, Litaudon M, Touboul D, Queiroz EF

Abstract
Covering: 2013 to 2019 The exploration of the chemical diversity of extracts from various biological sources has led to major drug discoveries. Over the past two decades, despite the introduction of advanced methodologies for natural product (NP) research (e.g., dereplication and high content screening), successful accounts of the validation of NPs as lead therapeutic candidates have been limited. In this context, one of the main challenges faced is related to working with crude natural extracts because of their complex composition and the inadequacies of classical bioguided isolation studies given the pace of high-throughput screening campaigns. In line with the development of metabolomics, genomics and chemometrics, significant advances in metabolite profiling have been achieved and have generated high-quality massive genome and metabolome data on natural extracts. The unambiguous identification of each individual NP in an extract using generic methods remains challenging. However, the establishment of structural links among NPs via molecular network analysis and the determination of common features of extract composition have provided invaluable information to the scientific community. In this context, new multi-informational-based profiling approaches integrating taxonomic and/or bioactivity data can hold promise for the discovery and development of new bioactive compounds and return NPs back to an exciting era of development. In this article, we examine recent studies that have the potential to improve the efficiency of NP prioritisation and to accelerate the targeted isolation of key NPs. Perspectives on the field's evolution are discussed.

PMID: 31073562 [PubMed - indexed for MEDLINE]

Reactive oxygen species detection-approaches in plants: insights into genetically encoded FRET-based sensors.

December 15, 2019 - 6:18am
Related Articles

Reactive oxygen species detection-approaches in plants: insights into genetically encoded FRET-based sensors.

J Biotechnol. 2019 Dec 10;:

Authors: Anjum NA, Amreen, Tantray AY, Khan NA, Ahmad A

Abstract
The generation of reactive oxygen species (ROS) (and their reaction products) in abiotic stressed plants can be simultaneous. Hence, it is very difficult to establish individual roles of ROS (and their reaction products) in plants particularly under abiotic stress conditions. It is highly imperative to detect ROS (and their reaction products) and ascertain their role in vivo and also to point their optimal level in order to unveil exact relation of ROS (and their reaction products) with the major components of ROS-controlling systems. Förster Resonance Energy Transfer (FRET) technology enables us with high potential for monitoring and quantification of ROS and redox variations, avoiding some of the obstacles presented by small-molecule fluorescent dyes. This paper aims to: (i) introduce ROS and overview ROS-chemistry and ROS-accrued major damages to major biomolecules; (ii) highlight invasive and non-invasive approaches for the detection of ROS (and their reaction products); (iii) appraise literature available on genetically encoded ROS (and their reaction products)-sensors based on FRET technology, and (iv) enlighten so far unexplored aspects in the current context. The studies integrating the outcomes of the FRET-based ROS-detection approaches with the OMICS (genetics, genomics, proteomics, and metabolomics) would enlighten insights into real-time ROS and redox dynamics, and their signaling at cellular and subcellular levels in living cells.

PMID: 31836526 [PubMed - as supplied by publisher]

Applications of metabolomics in the research of soybean plant under abiotic stress.

December 14, 2019 - 8:19am
Related Articles

Applications of metabolomics in the research of soybean plant under abiotic stress.

Food Chem. 2019 Dec 02;310:125914

Authors: Feng Z, Ding C, Li W, Wang D, Cui D

Abstract
Qualitative and quantitative metabolomics analysis of all small-molecule metabolites in organisms is an emerging omics technology alongside genomics and proteomics. Plant metabolites are extremely diverse both within species and in terms of their physiological function. Plant metabolomics studies use mainly liquid/gas chromatography-mass spectrometry (LC/GC-MS) and nuclear magnetic resonance (NMR) techniques combined with chemometrics and multivariate statistical analysis to analyze plant metabolites, and metabolomics plays a key role in agricultural and food science research. In this review, we discuss the status of metabolomics in soybean in response to abiotic stresses such as drought, heat, salinity, flooding, chilling and heavy metal stresses and analyze the challenges and opportunities. Furthermore, the notable metabolites detected in response to different stresses are summarized to provide a reference for applications of metabolomics in soybean research.

PMID: 31835223 [PubMed - as supplied by publisher]

The dynamic responses of plant physiology and metabolism during environmental stress progression.

December 12, 2019 - 6:18am
Related Articles

The dynamic responses of plant physiology and metabolism during environmental stress progression.

Mol Biol Rep. 2019 Dec 10;:

Authors: Singh AK, Dhanapal S, Yadav BS

Abstract
At adverse environmental conditions, plants produce various kinds of primary and secondary metabolites to protect themselves. Both primary and secondary metabolites play a significant role during the heat, drought, salinity, genotoxic and cold conditions. A multigene response is activated during the progression of these stresses in the plants which stimulate changes in various signaling molecules, amino acids, proteins, primary and secondary metabolites. Plant metabolism is perturbed because of either the inhibition of metabolic enzymes, shortage of substrates, excess demand for specific compounds or a combination of these factors. In this review, we aim to present how plants synthesize different kinds of natural products during the perception of various abiotic stresses. We also discuss how time-scale variable stresses influence secondary metabolite profiles, could be used as a stress marker in plants. This article has the potential to get the attention of researchers working in the area of quantitative trait locus mapping using metabolites as well as metabolomics genome-wide association.

PMID: 31823123 [PubMed - as supplied by publisher]

Pharmacometabonomics: The Prediction of Drug Effects Using Metabolic Profiling.

December 12, 2019 - 6:18am
Related Articles

Pharmacometabonomics: The Prediction of Drug Effects Using Metabolic Profiling.

Handb Exp Pharmacol. 2019 Dec 11;:

Authors: Everett JR

Abstract
Metabonomics, also known as metabolomics, is concerned with the study of metabolite profiles in humans, animals, plants and other systems in order to assess their health or other status and their responses to experimental interventions. Metabonomics is thus widely used in disease diagnosis and in understanding responses to therapies such as drug administration. Pharmacometabonomics, also known as pharmacometabolomics, is a related methodology but with a prognostic as opposed to diagnostic thrust. Pharmacometabonomics aims to predict drug effects including efficacy, safety, metabolism and pharmacokinetics, prior to drug administration, via an analysis of pre-dose metabolite profiles. This article will review the development of pharmacometabonomics as a new field of science that has much promise in helping to deliver more effective personalised medicine, a major goal of twenty-first century healthcare.

PMID: 31823071 [PubMed - as supplied by publisher]

TGFβ-induced metabolic reprogramming during epithelial-to-mesenchymal transition in cancer.

December 12, 2019 - 6:18am
Related Articles

TGFβ-induced metabolic reprogramming during epithelial-to-mesenchymal transition in cancer.

Cell Mol Life Sci. 2019 Dec 10;:

Authors: Hua W, Ten Dijke P, Kostidis S, Giera M, Hornsveld M

Abstract
Metastasis is the most frequent cause of death in cancer patients. Epithelial-to-mesenchymal transition (EMT) is the process in which cells lose epithelial integrity and become motile, a critical step for cancer cell invasion, drug resistance and immune evasion. The transforming growth factor-β (TGFβ) signaling pathway is a major driver of EMT. Increasing evidence demonstrates that metabolic reprogramming is a hallmark of cancer and extensive metabolic changes are observed during EMT. The aim of this review is to summarize and interconnect recent findings that illustrate how changes in glycolysis, mitochondrial, lipid and choline metabolism coincide and functionally contribute to TGFβ-induced EMT. We describe TGFβ signaling is involved in stimulating both glycolysis and mitochondrial respiration. Interestingly, the subsequent metabolic consequences for the redox state and lipid metabolism in cancer cells are found to be in favor of EMT as well. Combined we illustrate that a better understanding of the mechanistic links between TGFβ signaling, cancer metabolism and EMT holds promising strategies for cancer therapy, some of which are already actively being explored in the clinic.

PMID: 31822964 [PubMed - as supplied by publisher]

Advances in molecular biology of Paeonia L.

December 1, 2019 - 8:18am
Related Articles

Advances in molecular biology of Paeonia L.

Planta. 2019 Nov 29;251(1):23

Authors: Fan Y, Wang Q, Dong Z, Yin Y, Teixeira da Silva JA, Yu X

Abstract
Molecular biology can serve as a tool to solve the limitations of traditional breeding and cultivation techniques related to flower patterns, the improvement of flower color, and the regulation of flowering and stress resistance. These characteristics of molecular biology ensured its significant role in improving the efficiency of breeding and germplasm amelioration of Paeonia. This review describes the advances in molecular biology of Paeonia, including: (1) the application of molecular markers; (2) genomics, transcriptomics, proteomics, metabolomics, and microRNA studies; (3) studies of functional genes; and (4) molecular biology techniques. This review also points out select limitations in current molecular biology, analyzes the direction of Paeonia molecular biology research, and provides advice for future research objectives.

PMID: 31784828 [PubMed - in process]

Advances in Understanding the Physiological and Molecular Responses of Sugar Beet to Salt Stress.

November 30, 2019 - 6:17am
Related Articles

Advances in Understanding the Physiological and Molecular Responses of Sugar Beet to Salt Stress.

Front Plant Sci. 2019;10:1431

Authors: Lv X, Chen S, Wang Y

Abstract
Soil salinity is a major environmental stress on crop growth and productivity. A better understanding of the molecular and physiological mechanisms underlying salt tolerance will facilitate efforts to improve crop performance under salinity. Sugar beet is considered to be a salt-tolerant crop, and it is therefore a good model for studying salt acclimation in crops. Recently, many determinants of salt tolerance and regulatory mechanisms have been studied by using physiological and 'omics approaches. This review provides an overview of recent research advances regarding sugar beet response and tolerance to salt stress. We summarize the physiological and molecular mechanisms involved, including maintenance of ion homeostasis, accumulation of osmotic-adjustment substances, and antioxidant regulation. We focus on progress in deciphering the mechanisms using 'omic technologies and describe the key candidate genes involved in sugar beet salt tolerance. Understanding the response and tolerance of sugar beet to salt stress will enable translational application to other crops and thus will have significant impacts on agricultural sustainability and global food security.

PMID: 31781145 [PubMed]

Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato.

November 29, 2019 - 7:17pm
Related Articles

Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato.

Biology (Basel). 2019 Nov 25;8(4):

Authors: Chaudhary J, Khatri P, Singla P, Kumawat S, Kumari A, R V, Vikram A, Jindal SK, Kardile H, Kumar R, Sonah H, Deshmukh R

Abstract
Tomato, one of the most important crops worldwide, has a high demand in the fresh fruit market and processed food industries. Despite having considerably high productivity, continuous supply as per the market demand is hard to achieve, mostly because of periodic losses occurring due to biotic as well as abiotic stresses. Although tomato is a temperate crop, it is grown in almost all the climatic zones because of widespread demand, which makes it challenge to adapt in diverse conditions. Development of tomato cultivars with enhanced abiotic stress tolerance is one of the most sustainable approaches for its successful production. In this regard, efforts are being made to understand the stress tolerance mechanism, gene discovery, and interaction of genetic and environmental factors. Several omics approaches, tools, and resources have already been developed for tomato growing. Modern sequencing technologies have greatly accelerated genomics and transcriptomics studies in tomato. These advancements facilitate Quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). However, limited efforts have been made in other omics branches like proteomics, metabolomics, and ionomics. Extensive cataloging of omics resources made here has highlighted the need for integration of omics approaches for efficient utilization of resources and a better understanding of the molecular mechanism. The information provided here will be helpful to understand the plant responses and the genetic regulatory networks involved in abiotic stress tolerance and efficient utilization of omics resources for tomato crop improvement.

PMID: 31775241 [PubMed]

Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses.

November 28, 2019 - 7:17am
Icon for PubMed Central Related Articles

Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses.

Int J Mol Sci. 2019 Jun 18;20(12):

Authors: Kumar J, Choudhary AK, Gupta DS, Kumar S

Abstract
Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.

PMID: 31216660 [PubMed - indexed for MEDLINE]

Experimental Design and Sample Preparation in Forest Tree Metabolomics.

November 27, 2019 - 8:23am
Related Articles

Experimental Design and Sample Preparation in Forest Tree Metabolomics.

Metabolites. 2019 Nov 22;9(12):

Authors: Rodrigues AM, Ribeiro-Barros AI, António C

Abstract
Appropriate experimental design and sample preparation are key steps in metabolomics experiments, highly influencing the biological interpretation of the results. The sample preparation workflow for plant metabolomics studies includes several steps before metabolite extraction and analysis. These include the optimization of laboratory procedures, which should be optimized for different plants and tissues. This is particularly the case for trees, whose tissues are complex matrices to work with due to the presence of several interferents, such as oleoresins, cellulose. A good experimental design, tree tissue harvest conditions, and sample preparation are crucial to ensure consistency and reproducibility of the metadata among datasets. In this review, we discuss the main challenges when setting up a forest tree metabolomics experiment for mass spectrometry (MS)-based analysis covering all technical aspects from the biological question formulation and experimental design to sample processing and metabolite extraction and data acquisition. We also highlight the importance of forest tree metadata standardization in metabolomics studies.

PMID: 31766588 [PubMed]

Contribution of Berry Polyphenols to the Human Metabolome.

November 24, 2019 - 8:19am
Related Articles

Contribution of Berry Polyphenols to the Human Metabolome.

Molecules. 2019 Nov 20;24(23):

Authors: Chandra P, Rathore AS, Kay KL, Everhart JL, Curtis P, Burton-Freeman B, Cassidy A, Kay CD

Abstract
Diets rich in berries provide health benefits, however, the contribution of berry phytochemicals to the human metabolome is largely unknown. The present study aimed to establish the impact of berry phytochemicals on the human metabolome. A "systematic review strategy" was utilized to characterize the phytochemical composition of the berries most commonly consumed in the USA; (poly)phenols, primarily anthocyanins, comprised the majority of reported plant secondary metabolites. A reference standard library and tandem mass spectrometry (MS/MS) quantitative metabolomics methodology were developed and applied to serum/plasma samples from a blueberry and a strawberry intervention, revealing a diversity of benzoic, cinnamic, phenylacetic, 3-(phenyl)propanoic and hippuric acids, and benzyldehydes. 3-Phenylpropanoic, 2-hydroxybenzoic, and hippuric acid were highly abundant (mean > 1 µM). Few metabolites at concentrations above 100 nM changed significantly in either intervention. Significant intervention effects (P < 0.05) were observed for plasma/serum 2-hydroxybenzoic acid and hippuric acid in the blueberry intervention, and for 3-methoxyphenylacetic acid and 4-hydroxyphenylacetic acid in the strawberry intervention. However, significant within-group effects for change from baseline were prevalent, suggesting that high inter-individual variability precluded significant treatment effects. Berry consumption in general appears to cause a fluctuation in the pools of small molecule metabolites already present at baseline, rather than the appearance of unique berry-derived metabolites, which likely reflects the ubiquitous nature of (poly)phenols in the background diet.

PMID: 31757061 [PubMed - in process]

Pages