Plant Metabolomics Reviews

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Recent breakthroughs in metabolomics promise to reveal the cryptic chemical traits that mediate plant community composition, character evolution and lineage diversification.

February 17, 2018 - 6:51pm
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Recent breakthroughs in metabolomics promise to reveal the cryptic chemical traits that mediate plant community composition, character evolution and lineage diversification.

New Phytol. 2017 May;214(3):952-958

Authors: Sedio BE

Abstract
Contents 952 I. 952 II. 953 III. 955 IV. 956 V. 957 957 References 957 SUMMARY: Much of our understanding of the mechanisms by which biotic interactions shape plant communities has been constrained by the methods available to study the diverse secondary chemistry that defines plant relationships with other organisms. Recent innovations in analytical chemistry and bioinformatics promise to reveal the cryptic chemical traits that mediate plant ecology and evolution by facilitating simultaneous structural comparisons of hundreds of unknown molecules to each other and to libraries of known compounds. Here, I explore the potential for mass spectrometry and nuclear magnetic resonance metabolomics to enable unprecedented tests of seminal, but largely untested hypotheses that propose a fundamental role for plant chemical defenses against herbivores and pathogens in the evolutionary origins and ecological coexistence of plant species diversity.

PMID: 28134431 [PubMed - indexed for MEDLINE]

Advances in computational metabolomics and databases deepen the understanding of metabolisms.

February 8, 2018 - 6:31am

Advances in computational metabolomics and databases deepen the understanding of metabolisms.

Curr Opin Biotechnol. 2018 Jan 29;54:10-17

Authors: Tsugawa H

Abstract
Mass spectrometry (MS)-based metabolomics is the popular platform for metabolome analyses. Computational techniques for the processing of MS raw data, for example, feature detection, peak alignment, and the exclusion of false-positive peaks, have been established. The next stage of untargeted metabolomics would be to decipher the mass fragmentation of small molecules for the global identification of human-, animal-, plant-, and microbiota metabolomes, resulting in a deeper understanding of metabolisms. This review is an update on the latest computational metabolomics including known/expected structure databases, chemical ontology classifications, and mass spectrometry cheminformatics for the interpretation of mass fragmentations and for the elucidation of unknown metabolites. The importance of metabolome 'databases' and 'repositories' is also discussed because novel biological discoveries are often attributable to the accumulation of data, to relational databases, and to their statistics. Lastly, a practical guide for metabolite annotations is presented as the summary of this review.

PMID: 29413746 [PubMed - as supplied by publisher]

Environmental metabolomics with data science for investigating ecosystem homeostasis.

February 7, 2018 - 6:31am

Environmental metabolomics with data science for investigating ecosystem homeostasis.

Prog Nucl Magn Reson Spectrosc. 2018 Feb;104:56-88

Authors: Kikuchi J, Ito K, Date Y

Abstract
A natural ecosystem can be viewed as the interconnections between complex metabolic reactions and environments. Humans, a part of these ecosystems, and their activities strongly affect the environments. To account for human effects within ecosystems, understanding what benefits humans receive by facilitating the maintenance of environmental homeostasis is important. This review describes recent applications of several NMR approaches to the evaluation of environmental homeostasis by metabolic profiling and data science. The basic NMR strategy used to evaluate homeostasis using big data collection is similar to that used in human health studies. Sophisticated metabolomic approaches (metabolic profiling) are widely reported in the literature. Further challenges include the analysis of complex macromolecular structures, and of the compositions and interactions of plant biomass, soil humic substances, and aqueous particulate organic matter. To support the study of these topics, we also discuss sample preparation techniques and solid-state NMR approaches. Because NMR approaches can produce a number of data with high reproducibility and inter-institution compatibility, further analysis of such data using machine learning approaches is often worthwhile. We also describe methods for data pretreatment in solid-state NMR and for environmental feature extraction from heterogeneously-measured spectroscopic data by machine learning approaches.

PMID: 29405981 [PubMed - in process]

Imaging the Unimaginable: Desorption Electrospray Ionization - Imaging Mass Spectrometry (DESI-IMS) in Natural Product Research.

February 2, 2018 - 6:37am
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Imaging the Unimaginable: Desorption Electrospray Ionization - Imaging Mass Spectrometry (DESI-IMS) in Natural Product Research.

Planta Med. 2018 Jan 31;:

Authors: Parrot D, Papazian S, Foil D, Tasdemir D

Abstract
Imaging mass spectrometry (IMS) has recently established itself in the field of "spatial metabolomics." Merging the sensitivity and fast screening of high-throughput mass spectrometry with spatial and temporal chemical information, IMS visualizes the production, location, and distribution of metabolites in intact biological models. Since metabolite profiling and morphological features are combined in single images, IMS offers an unmatched chemical detail on complex biological and microbiological systems. Thus, IMS-type "spatial metabolomics" emerges as a powerful and complementary approach to genomics, transcriptomics, and classical metabolomics studies. In this review, we summarize the current state-of-the-art IMS methods with a strong focus on desorption electrospray ionization (DESI)-IMS. DESI-IMS utilizes the original principle of electrospray ionization, but in this case solvent droplets are rastered and desorbed directly on the sample surface. The rapid and minimally destructive DESI-IMS chemical screening is achieved at ambient conditions and enables the accurate view of molecules in tissues at the µm-scale resolution. DESI-IMS analysis does not require complex sample preparation and allows repeated measurements on samples from different biological sources, including microorganisms, plants, and animals. Thanks to its easy workflow and versatility, DESI-IMS has successfully been applied to many different research fields, such as clinical analysis, cancer research, environmental sciences, microbiology, chemical ecology, and drug discovery. Herein we discuss the present applications of DESI-IMS in natural product research.

PMID: 29388184 [PubMed - as supplied by publisher]

Sunflower Hybrid Breeding: From Markers to Genomic Selection.

February 2, 2018 - 6:37am
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Sunflower Hybrid Breeding: From Markers to Genomic Selection.

Front Plant Sci. 2017;8:2238

Authors: Dimitrijevic A, Horn R

Abstract
In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi, or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare. Integrative approaches combining omic technologies (genomics, transcriptomics, proteomics, metabolomics and phenomics) using bioinformatic tools will facilitate the identification of target genes and markers for complex traits and will give a better insight into the mechanisms behind the traits.

PMID: 29387071 [PubMed]

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

January 25, 2018 - 6:31am
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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 - in process]

Guidelines and recommendations on yeast cell death nomenclature.

January 23, 2018 - 6:57am

Guidelines and recommendations on yeast cell death nomenclature.

Microb Cell. 2018 Jan 01;5(1):4-31

Authors: Carmona-Gutierrez D, Bauer MA, Zimmermann A, Aguilera A, Austriaco N, Ayscough K, Balzan R, Bar-Nun S, Barrientos A, Belenky P, Blondel M, Braun RJ, Breitenbach M, Burhans WC, Büttner S, Cavalieri D, Chang M, Cooper KF, Côrte-Real M, Costa V, Cullin C, Dawes I, Dengjel J, Dickman MB, Eisenberg T, Fahrenkrog B, Fasel N, Fröhlich KU, Gargouri A, Giannattasio S, Goffrini P, Gourlay CW, Grant CM, Greenwood MT, Guaragnella N, Heger T, Heinisch J, Herker E, Herrmann JM, Hofer S, Jiménez-Ruiz A, Jungwirth H, Kainz K, Kontoyiannis DP, Ludovico P, Manon S, Martegani E, Mazzoni C, Megeney LA, Meisinger C, Nielsen J, Nyström T, Osiewacz HD, Outeiro TF, Park HO, Pendl T, Petranovic D, Picot S, Polčic P, Powers T, Ramsdale M, Rinnerthaler M, Rockenfeller P, Ruckenstuhl C, Schaffrath R, Segovia M, Severin FF, Sharon A, Sigrist SJ, Sommer-Ruck C, Sousa MJ, Thevelein JM, Thevissen K, Titorenko V, Toledano MB, Tuite M, Vögtle FN, Westermann B, Winderickx J, Wissing S, Wölfl S, Zhang ZJ, Zhao RY, Zhou B, Galluzzi L, Kroemer G, Madeo F

Abstract
Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cel-lular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the defi-nition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differ-ential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death rou-tines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the au-thors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the pro-gress of this vibrant field of research.

PMID: 29354647 [PubMed]

Impact of Cranberries on Gut Microbiota and Cardiometabolic Health: Proceedings of the Cranberry Health Research Conference 2015.

January 19, 2018 - 6:48am
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Impact of Cranberries on Gut Microbiota and Cardiometabolic Health: Proceedings of the Cranberry Health Research Conference 2015.

Adv Nutr. 2016 Jul;7(4):759S-70S

Authors: Blumberg JB, Basu A, Krueger CG, Lila MA, Neto CC, Novotny JA, Reed JD, Rodriguez-Mateos A, Toner CD

Abstract
Recent advances in cranberry research have expanded the evidence for the role of this Vaccinium berry fruit in modulating gut microbiota function and cardiometabolic risk factors. The A-type structure of cranberry proanthocyanidins seems to be responsible for much of this fruit's efficacy as a natural antimicrobial. Cranberry proanthocyanidins interfere with colonization of the gut by extraintestinal pathogenic Escherichia coli in vitro and attenuate gut barrier dysfunction caused by dietary insults in vivo. Furthermore, new studies indicate synergy between these proanthocyanidins, other cranberry components such as isoprenoids and xyloglucans, and gut microbiota. Together, cranberry constituents and their bioactive catabolites have been found to contribute to mechanisms affecting bacterial adhesion, coaggregation, and biofilm formation that may underlie potential clinical benefits on gastrointestinal and urinary tract infections, as well as on systemic anti-inflammatory actions mediated via the gut microbiome. A limited but growing body of evidence from randomized clinical trials reveals favorable effects of cranberry consumption on measures of cardiometabolic health, including serum lipid profiles, blood pressure, endothelial function, glucoregulation, and a variety of biomarkers of inflammation and oxidative stress. These results warrant further research, particularly studies dedicated to the elucidation of dose-response relations, pharmacokinetic/metabolomics profiles, and relevant biomarkers of action with the use of fully characterized cranberry products. Freeze-dried whole cranberry powder and a matched placebo were recently made available to investigators to facilitate such work, including interlaboratory comparability.

PMID: 27422512 [PubMed - indexed for MEDLINE]

Alternaria Species and Their Associated Mycotoxins.

January 13, 2018 - 6:30am
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Alternaria Species and Their Associated Mycotoxins.

Methods Mol Biol. 2017;1542:13-32

Authors: Pinto VE, Patriarca A

Abstract
The genus Alternaria includes more than 250 species. The traditional methods for identification of Alternaria species are based on morphological characteristics of the reproductive structures and sporulation patterns under controlled culture conditions. Cladistics analyses of "housekeeping genes" commonly used for other genera, failed to discriminate among the small-spored Alternaria species. The development of molecular methods achieving a better agreement with morphological differences is still needed. The production of secondary metabolites has also been used as a means of classification and identification. Alternaria spp. can produce a wide variety of toxic metabolites. These metabolites belong principally to three different structural groups: (1) the dibenzopyrone derivatives, alternariol (AOH), alternariol monomethyl ether (AME), and altenuene (ALT); (2) the perylene derivative altertoxins (ATX-I, ATX-II, and ATX II); and (3) the tetramic acid derivative, tenuazonic acid (TeA). TeA, AOH, AME, ALT, and ATX-I are the main. Certain species in the genus Alternaria produce host-specific toxins (HSTs) that contribute to their pathogenicity and virulence. Alternaria species are plant pathogens that cause spoilage of agricultural commodities with consequent mycotoxin accumulation and economic losses. Vegetable foods infected by Alternaria rot could introduce high amounts of these toxins to the human diet. More investigations on the toxic potential of these toxins and their hazard for human consumption are needed to make a reliable risk assessment of dietary exposure.

PMID: 27924529 [PubMed - indexed for MEDLINE]

[Development of Plant Metabolomics and Medicinal Plant Genomics].

January 10, 2018 - 6:32am
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[Development of Plant Metabolomics and Medicinal Plant Genomics].

Yakugaku Zasshi. 2018;138(1):1-18

Authors: Saito K

Abstract
 A variety of chemicals produced by plants, often referred to as 'phytochemicals', have been used as medicines, food, fuels and industrial raw materials. Recent advances in the study of genomics and metabolomics in plant science have accelerated our understanding of the mechanisms, regulation and evolution of the biosynthesis of specialized plant products. We can now address such questions as how the metabolomic diversity of plants is originated at the levels of genome, and how we should apply this knowledge to drug discovery, industry and agriculture. Our research group has focused on metabolomics-based functional genomics over the last 15 years and we have developed a new research area called 'Phytochemical Genomics'. In this review, the development of a research platform for plant metabolomics is discussed first, to provide a better understanding of the chemical diversity of plants. Then, representative applications of metabolomics to functional genomics in a model plant, Arabidopsis thaliana, are described. The extension of integrated multi-omics analyses to non-model specialized plants, e.g., medicinal plants, is presented, including the identification of novel genes, metabolites and networks for the biosynthesis of flavonoids, alkaloids, sulfur-containing metabolites and terpenoids. Further, functional genomics studies on a variety of medicinal plants is presented. I also discuss future trends in pharmacognosy and related sciences.

PMID: 29311454 [PubMed - in process]

Adulteration of herbal sexual enhancers and slimmers: The wish for better sexual well-being and perfect body can be risky.

January 6, 2018 - 6:29am
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Adulteration of herbal sexual enhancers and slimmers: The wish for better sexual well-being and perfect body can be risky.

Food Chem Toxicol. 2017 Oct;108(Pt B):355-364

Authors: Skalicka-Woźniak K, Georgiev MI, Orhan IE

Abstract
The popularity of herbal medicines and dietary supplements is increasing all over the world due to the many side-effects assigned to synthetic drugs. Herbal remedies should be considered as safe, with no side-effects, but unfortunately, even if they are labelled as natural, large numbers of adulterants, not only with toxic heavy metals but also with undeclared synthetic substances, have been detected up to date. In this review, the most frequent instances of adulteration of herbal medicines and dietary supplements acting as sexual enhancers and slimming products are thoroughly discussed. The great success of synthetic phosphodiesterase type-5 (PDE-5) inhibitory drugs like sildenafil, vardenafil and tadalafil, used for the treatment of erectile dysfunction has made them, as well as their unapproved analogues, popular as adulterants in herbal dietary supplements. The second group among blockbuster products are herbal preparations for slimming purpose, as obesity and gaining weight are major problems worldwide. Here, sibutramine hydrochloride monohydrate, an anti-obesity drug which inhibits serotonergic and noradrenergic reuptake, seems to be the most common adulterant. Together with large numbers of its analogues, thyroid hormones, anorexigens, diuretics, stimulants, and laxative agents are also detected in most of tested diet supplements.

PMID: 27338710 [PubMed - indexed for MEDLINE]

Network pharmacology of cancer: From understanding of complex interactomes to the design of multi-target specific therapeutics from nature.

January 6, 2018 - 6:29am
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Network pharmacology of cancer: From understanding of complex interactomes to the design of multi-target specific therapeutics from nature.

Pharmacol Res. 2016 Sep;111:290-302

Authors: Poornima P, Kumar JD, Zhao Q, Blunder M, Efferth T

Abstract
Despite massive investments in drug research and development, the significant decline in the number of new drugs approved or translated to clinical use raises the question, whether single targeted drug discovery is the right approach. To combat complex systemic diseases that harbour robust biological networks such as cancer, single target intervention is proved to be ineffective. In such cases, network pharmacology approaches are highly useful, because they differ from conventional drug discovery by addressing the ability of drugs to target numerous proteins or networks involved in a disease. Pleiotropic natural products are one of the promising strategies due to their multi-targeting and due to lower side effects. In this review, we discuss the application of network pharmacology for cancer drug discovery. We provide an overview of the current state of knowledge on network pharmacology, focus on different technical approaches and implications for cancer therapy (e.g. polypharmacology and synthetic lethality), and illustrate the therapeutic potential with selected examples green tea polyphenolics, Eleutherococcus senticosus, Rhodiola rosea, and Schisandra chinensis). Finally, we present future perspectives on their plausible applications for diagnosis and therapy of cancer.

PMID: 27329331 [PubMed - indexed for MEDLINE]

Advanced LC-MS-based methods to study the co-occurrence and metabolization of multiple mycotoxins in cereals and cereal-based food.

December 24, 2017 - 6:46am
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Advanced LC-MS-based methods to study the co-occurrence and metabolization of multiple mycotoxins in cereals and cereal-based food.

Anal Bioanal Chem. 2017 Dec 22;:

Authors: Malachová A, Stránská M, Václavíková M, Elliott CT, Black C, Meneely J, Hajšlová J, Ezekiel CN, Schuhmacher R, Krska R

Abstract
Liquid chromatography (LC) coupled with mass spectrometry (MS) is widely used for the determination of mycotoxins in cereals and cereal-based products. In addition to the regulated mycotoxins, for which official control is required, LC-MS is often used for the screening of a large range of mycotoxins and/or for the identification and characterization of novel metabolites. This review provides insight into the LC-MS methods used for the determination of co-occurring mycotoxins with special emphasis on multiple-analyte applications. The first part of the review is focused on targeted LC-MS approaches using cleanup methods such as solid-phase extraction and immunoaffinity chromatography, as well as on methods based on minimum cleanup (quick, easy, cheap, effective, rugged, and safe; QuEChERS) and dilute and shoot. The second part of the review deals with the untargeted determination of mycotoxins by LC coupled with high-resolution MS, which includes also metabolomics techniques to study the fate of mycotoxins in plants.

PMID: 29273904 [PubMed - as supplied by publisher]

Enterohemorrhagic Escherichia coli outwits hosts through sensing small molecules.

December 20, 2017 - 6:48am

Enterohemorrhagic Escherichia coli outwits hosts through sensing small molecules.

Curr Opin Microbiol. 2017 Dec 16;41:83-88

Authors: Carlson-Banning KM, Sperandio V

Abstract
Small molecules help intestinal pathogens navigate the complex human gastrointestinal tract to exploit favorable microhabitats. These small molecules provide spatial landmarks for pathogens to regulate synthesis of virulence caches and are derived from the host, ingested plant and animal material, and the microbiota. Their concentrations and fluxes vary along the length of the gut and provide molecular signatures that are beginning to be explored through metabolomics and genetics. However, while many small molecules have been identified and are reviewed here, there are undoubtedly others that may also profoundly affect how enteric pathogens infect their hosts.

PMID: 29258058 [PubMed - as supplied by publisher]

Recent applications of NMR in food and dietary studies.

December 15, 2017 - 6:26am
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Recent applications of NMR in food and dietary studies.

J Sci Food Agric. 2017 Jan;97(1):33-42

Authors: Ramakrishnan V, Luthria DL

Abstract
Over the last decade, a wide variety of new foods have been introduced into the global marketplace, many with health benefits that exceed those of traditional foods. Simultaneously, a wide range of analytical technologies has evolved that allow greater capability for the determination of food composition. Nuclear magnetic resonance (NMR), traditionally a research tool used for structural elucidation, is now being used frequently for metabolomics and chemical fingerprinting. Its stability and inherent ease of quantification have been exploited extensively to identify and quantify bioactive components in foods and dietary supplements. In addition, NMR fingerprints have been used to differentiate cultivars, evaluate sensory properties of food and investigate the influence of growing conditions on food crops. Here we review the latest applications of NMR in food analysis. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

PMID: 27435122 [PubMed - indexed for MEDLINE]

Post genomics era for orchid research.

December 14, 2017 - 6:46am
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Post genomics era for orchid research.

Bot Stud. 2017 Dec 12;58(1):61

Authors: Tsai WC, Dievart A, Hsu CC, Hsiao YY, Chiou SY, Huang H, Chen HH

Abstract
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing.

PMID: 29234904 [PubMed]

Genomics of Metal Stress-Mediated Signalling and Plant Adaptive Responses in Reference to Phytohormones.

December 6, 2017 - 6:25am
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Genomics of Metal Stress-Mediated Signalling and Plant Adaptive Responses in Reference to Phytohormones.

Curr Genomics. 2017 Dec;18(6):512-522

Authors: Shukla A, Srivastava S, Suprasanna P

Abstract
Introduction: As a consequence of a sessile lifestyle, plants often have to face a number of life threatening abiotic and biotic stresses. Plants counteract the stresses through morphological and physiological adaptations, which are imparted through flexible and well-coordinated network of signalling and effector molecules, where phytohormones play important role. Hormone synthesis, signal transduction, perception and cross-talks create a complex network. Omics approaches, which include transcriptomics, genomics, proteomics and metabolomics, have opened new paths to understand such complex networks.
Objective: This review concentrates on the importance of phytohormones and enzymatic expressions under metal stressed conditions.
Conclusion: This review sheds light on gene expressions involved in plant adaptive and defence responses during metal stress. It gives an insight of genomic approaches leading to identification and functional annotation of genes involved in phytohormone signal transduction and perception. Moreover, it also emphasizes on perception, signalling and cross-talks among various phytohormones and other signalling components viz., Reactive Oxygen Species (ROS) and Reactive Nitrogen Species (RNS).

PMID: 29204080 [PubMed]

More than Pictures: When MS Imaging Meets Histology.

November 29, 2017 - 6:28am
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More than Pictures: When MS Imaging Meets Histology.

Trends Plant Sci. 2016 Aug;21(8):686-698

Authors: Dong Y, Li B, Aharoni A

Abstract
Attaining high-resolution spatial information is a recurrent challenge in biological research, particularly in the case of small-molecule distribution. Mass spectrometry imaging (MSI) is an innovative molecular histology technique that could provide such information. It allows in situ and label-free measurement of both the abundance and distribution of a variety of molecules at the tissue or single cell level. The application of MSI in plant research has received considerable attention; thus, in this review, we describe the current state of MSI in plants. In particular, we present an overview of MSI approaches, highlight the recent technical and methodological developments, and discuss a range of applications contributing to the field of plant science.

PMID: 27155743 [PubMed - indexed for MEDLINE]

Environmental and Endogenous Control of Cortical Microtubule Orientation.

November 29, 2017 - 6:28am
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Environmental and Endogenous Control of Cortical Microtubule Orientation.

Trends Cell Biol. 2016 Jun;26(6):409-19

Authors: Chen X, Wu S, Liu Z, Friml J

Abstract
Plant growth requires a tight coordination of cell shape and anisotropic expansion. Owing to their immobility, plant cells determine body architecture through the orientation of cell division and cell expansion. Microtubule cytoskeleton represents a versatile cellular structure essential for coordinating flexible cell morphogenesis. Previous studies have identified a large number of microtubule-associated regulators that control microtubule dynamics; however, the mechanisms by which microtubule reorientation responds to exogenous and environmental stimuli are largely unknown. In this review, we describe the molecular details of microtubule dynamics that are required for cortical microtubule array pattern formation, and recapitulate current knowledge on the mechanisms by which various environmental and endogenous stimuli control cortical microtubule reorientation.

PMID: 26951762 [PubMed - indexed for MEDLINE]

The application of ion mobility mass spectrometry to metabolomics.

November 22, 2017 - 9:38am

The application of ion mobility mass spectrometry to metabolomics.

Curr Opin Chem Biol. 2017 Nov 18;42:60-66

Authors: Zhang X, Quinn K, Cruickshank-Quinn C, Reisdorph R, Reisdorph N

Abstract
Mass spectrometry-based metabolomics is being increasingly utilized in various research fields including investigating human diseases, nutrition, industrial applications, and plant/natural products studies. Although new analytical approaches have enhanced the performance of metabolomic analyses, significant challenges associated with throughput, metabolome coverage, and compound identification still exist. Ion mobility mass spectrometry offers great potential for improving throughput and depth of coverage in metabolomics experiments. For example, multi-dimensional, structural resolution offered by ion mobility enables improved identification of metabolites and chemical classes. This mini-review discusses the advantages, recent developments and limitations of using ion mobility mass spectrometry as part of a metabolomics workflow.

PMID: 29161611 [PubMed - as supplied by publisher]

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