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plant metabolomics

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https://www.readbyqxmd.com/read/29342073/structure-elucidation-of-unknown-metabolites-in-metabolomics-by-combined-nmr-and-ms-ms-prediction
#1
Rene M Boiteau, David W Hoyt, Carrie D Nicora, Hannah A Kinmonth-Schultz, Joy K Ward, Kerem Bingol
We introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS²), and NMR into a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter out the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture, and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana...
January 17, 2018: Metabolites
https://www.readbyqxmd.com/read/29328914/rewiring-of-the-fruit-metabolome-in-tomato-breeding
#2
Guangtao Zhu, Shouchuang Wang, Zejun Huang, Shuaibin Zhang, Qinggang Liao, Chunzhi Zhang, Tao Lin, Mao Qin, Meng Peng, Chenkun Yang, Xue Cao, Xu Han, Xiaoxuan Wang, Esther van der Knaap, Zhonghua Zhang, Xia Cui, Harry Klee, Alisdair R Fernie, Jie Luo, Sanwen Huang
Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how breeding globally altered fruit metabolite content. Selection for alleles of genes associated with larger fruits altered metabolite profiles as a consequence of linkage with nearby genes...
January 11, 2018: Cell
https://www.readbyqxmd.com/read/29323890/hrmas-nmr-and-mri-spectroscopies-distinguish-metabolome-and-structural-properties-of-maize-seeds-from-plants-treated-with-different-fertilizers-and-arbuscular-mycorrhizal-fungi
#3
Pierluigi Mazzei, Vincenza Cozzolino, Alessandro Piccolo
Both High-Resolution Magic-Angle-Spinning (HRMAS) and Magnetic Resonance Imaging (MRI) NMR spectroscopies were applied here to identify the changes of metabolome, morphology and structural properties induced in seeds (caryopses) of maize plants grown at field level under either mineral or compost fertilization in combination with the inoculation by Arbuscular Mycorrhizal Fungi (AMF). The metabolome of intact caryopses was examined by HRMAS-NMR, while the morphological aspects, endosperm properties and seed water distribution were investigated by MRI...
January 11, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29315593/unraveling-the-metabolic-response-of-brassica-oleracea-exposed-to-xanthomonas-campestris-pv-campestris
#4
María Tortosa, María E Cartea, Víctor M Rodríguez, Pablo Velasco
BACKGROUND: Brassica crops together with cereals represent the basis of world supplies. Due to their importance, the production losses caused by Xanthomonas campestris pv. campestris (Xcc) infection represent a high economic impact. Understanding molecular and biochemical mechanisms of plants is essential to develop resistant crops with durable protection against diseases. In this regard, metabolomics has emerged as a valuable technology to provide an overview of the biological status of a plant exposed to a disease...
January 9, 2018: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/29311454/-development-of-plant-metabolomics-and-medicinal-plant-genomics
#5
Kazuki Saito
 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...
2018: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/29306573/challenges-in-integrating-component-level-technology-and-system-level-information-from-ayurveda-insights-from-nmr-phytometabolomics-and-anti-hiv-potential-of-select-ayurvedic-medicinal-plants
#6
Rama Jayasundar, Somenath Ghatak, Muzamil Ashraf Makhdoomi, Kalpana Luthra, Aruna Singh, Thirumurthy Velpandian
BACKGROUND: Information from Ayurveda meeting the analytical challenges of modern technology is an area of immense relevance. Apart from the cerebral task of bringing together two different viewpoints, the question at the pragmatic level remains 'who benefits whom'. OBJECTIVE: The aim is to highlight the challenges in integration of information (Ayurvedic) and technology using test examples of Nuclear Magnetic Resonance (NMR) metabolomics and anti-HIV-1 potential of select Ayurvedic medicinal plants...
January 3, 2018: Journal of Ayurveda and Integrative Medicine
https://www.readbyqxmd.com/read/29305931/discrimination-of-three-siegesbeckiae-herba-species-using-uplc-qtof-ms-based-metabolomics-approach
#7
Hong-Xun Tao, Wei Xiong, Guan-Ding Zhao, Yu Peng, Zhang-Feng Zhong, Liang Xu, Ran Duan, Karl W K Tsim, Hua Yu, Yi-Tao Wang
The plant origin is one of the most important factors for the quality control of traditional Chinese medicines (TCMs) and highly affected on their safety and effectiveness in clinical applications. Multi-origin has been widely observed for many TCMs. Siegesbeckiae Herba (SH) is a traditional anti-rheumatic TCM which is originated from the plants of Siegesbeckia pubescens Makino (SP), S. orientalis L. (SO), and S. glabrescens Makino (SG). In the present study, an UPLC-QTOF/MS method were validated and successfully applied for the determination of the chemical profiles in the three SH species...
January 3, 2018: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/29301376/sistematx-an-online-web-based-cheminformatics-tool-for-data-management-of-secondary-metabolites
#8
Marcus Tullius Scotti, Chonny Herrera-Acevedo, Tiago Branquinho Oliveira, Renan Paiva Oliveira Costa, Silas Yudi Konno de Oliveira Santos, Ricardo Pereira Rodrigues, Luciana Scotti, Fernando Batista Da-Costa
The traditional work of a natural products researcher consists in large part of time-consuming experimental work, collecting biota to prepare and analyze extracts and to identify innovative metabolites. However, along this long scientific path, much information is lost or restricted to a specific niche. The large amounts of data already produced and the science of metabolomics reveal new questions: Are these compounds known or new? How fast can this information be obtained? To answer these and other relevant questions, an appropriate procedure to correctly store information on the data retrieved from the discovered metabolites is necessary...
January 3, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29298676/a-multi-omics-approach-reveals-function-of-secretory-carrier-associated-membrane-proteins-in-wood-formation-of%C3%A2-%C3%A2-%C3%A2-populus%C3%A2-%C3%A2-%C3%A2-trees
#9
Ogonna Obudulu, Niklas Mähler, Tomas Skotare, Joakim Bygdell, Ilka N Abreu, Maria Ahnlund, Madhavi Latha Gandla, Anna Petterle, Thomas Moritz, Torgeir R Hvidsten, Leif J Jönsson, Gunnar Wingsle, Johan Trygg, Hannele Tuominen
BACKGROUND: Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32-38 kDa proteins that are involved in membrane trafficking. A systems approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. Phenotypic and multi-omics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3; Potri.019G104000). RESULTS: The woody tissues of the transgenic trees displayed increased amounts of both polysaccharides and lignin oligomers, indicating increased deposition of both the carbohydrate and lignin components of the secondary cell walls...
January 3, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29285563/integrated-analysis-of-transcriptomic-and-metabolomic-data-reveals-critical-metabolic-pathways-involved-in-rotenoid-biosynthesis-in-the-medicinal-plant-mirabilis-himalaica
#10
Li Gu, Zhong-Yi Zhang, Hong Quan, Ming-Jie Li, Fang-Yu Zhao, Yuan-Jiang Xu, Jiang Liu, Man Sai, Wei-Lie Zheng, Xiao-Zhong Lan
Mirabilis himalaica (Edgew.) Heimerl is among the most important genuine medicinal plants in Tibet. However, the biosynthesis mechanisms of the active compounds in this species are unclear, severely limiting its application. To clarify the molecular biosynthesis mechanism of the key representative active compounds, specifically rotenoid, which is of special medicinal value for M. himalaica, RNA sequencing and TOF-MS technologies were used to construct transcriptomic and metabolomic libraries from the roots, stems, and leaves of M...
December 28, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29281058/transcriptomic-and-metabolomic-reprogramming-from-roots-to-haustoria-in-the-parasitic-plant-thesium-chinense
#11
Yasunori Ichihashi, Miyako Kusano, Makoto Kobayashi, Kenji Suetsugu, Satoko Yoshida, Takanori Wakatake, Kie Kumaishi, Arisa Shibata, Kazuki Saito, Ken Shirasu
Most of plants show remarkable developmental plasticity in the generation of diverse types of new organs upon external stimuli, allowing them to adapt to their environment. Haustorial formation in parasitic plants is an example of such developmental reprogramming, but its molecular mechanism is largely unknown. In this study, we performed field-omics using transcriptomics and metabolomics to profile the molecular switch occurring in haustorial formation of the root parasitic plant, Thesium chinense, collected from its natural habitat...
December 20, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29277428/complete-pathway-elucidation-and-heterologous-reconstitution-of-rhodiola-salidroside-biosynthesis
#12
Michael P Torrens-Spence, Tomáš Pluskal, Fu-Shuang Li, Valentina Carballo, Jing-Ke Weng
Salidroside is a bioactive tyrosine-derived phenolic natural product found in medicinal plants under the Rhodiola genus. In addition to their anti-fatigue and anti-anoxia roles in traditional medicine, Rhodiola total extract and salidroside have also displayed medicinal properties as anti-cardiovascular diseases and anti-cancer agents. The resulting surge in global demand of Rhodiola plants and salidroside has driven some species close to extinction. Here, we report the full elucidation of Rhodiola salidroside biosynthetic pathway utilizing the first comprehensive transcriptomics and metabolomics datasets for Rhodiola rosea...
December 19, 2017: Molecular Plant
https://www.readbyqxmd.com/read/29274497/a-phylogenomic-analysis-of-lichen-feeding-tiger-moths-uncovers-evolutionary-origins-of-host-chemical-sequestration
#13
Clare H Scott Chialvo, Pablo Chialvo, Jeffrey D Holland, Timothy J Anderson, Jesse W Breinholt, Akito Y Kawahara, Xin Zhou, Shanlin Liu, Jennifer M Zaspel
Host species utilize a variety of defenses to deter feeding, including secondary chemicals. Some phytophagous insects have evolved tolerance to these chemical defenses, and can sequester secondary defense compounds for use against their own predators and parasitoids. While numerous studies have examined plant-insect interactions, little is known about lichen-insect interactions. Our study focused on reconstructing the evolution of lichen phenolic sequestration in the tiger moth tribe Lithosiini (Lepidoptera: Erebidae: Arctiinae), the most diverse lineage of lichen-feeding moths, with 3,000 described species...
December 20, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29273904/advanced-lc-ms-based-methods-to-study-the-co-occurrence-and-metabolization-of-multiple-mycotoxins-in-cereals-and-cereal-based-food
#14
REVIEW
Alexandra Malachová, Milena Stránská, Marta Václavíková, Christopher T Elliott, Connor Black, Julie Meneely, Jana Hajšlová, Chibundu N Ezekiel, Rainer Schuhmacher, Rudolf Krska
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...
December 22, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29247597/metabolic-responses-of-eucalyptus-species-to-different-temperature-regimes
#15
Joao Benhur Mokochinski, Paulo Mazzafera, Alexandra Christine Helena Frankland Sawaya, Roland Mumm, Ric Cornelis Hendricus de Vos, Robert David Hall
Species and hybrids of Eucalyptus are the world's most widely planted hardwood trees. They are cultivated across a wide range of latitudes and therefore environmental conditions. In this context, comprehensive metabolomics approaches have been used to assess how different temperature regimes may affect the metabolism of three species of Eucalyptus, E. dunnii, E. grandis and E. pellita. Young plants were grown for 53 days in the greenhouse and then transferred to growth chambers at 10, 20 or 30°C for another 7 days...
December 16, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/29246190/comparative-metabolite-profiling-of-drought-stress-in-roots-and-leaves-of-seven-triticeae-species
#16
Naimat Ullah, Meral Yüce, Z Neslihan Öztürk Gökçe, Hikmet Budak
BACKGROUND: Drought is a lifestyle disease. Plant metabolomics has been exercised for understanding the fine-tuning of the potential pathways to surmount the adverse effects of drought stress. A broad spectrum of morphological and metabolic responses from seven Triticeae species including wild types with different drought tolerance/susceptibility level was investigated under control and water scarcity conditions. RESULTS: Significant morphological parameters measured were root length, surface area, average root diameter and overall root development...
December 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29240755/integrating-transcriptomics-and-metabolomics-to-characterize-the-regulation-of-epa-biosynthesis-in-response-to-cold-stress-in-seaweed-bangia-fuscopurpurea
#17
Min Cao, Dongmei Wang, Yunxiang Mao, Fanna Kong, Guiqi Bi, Qikun Xing, Zhen Weng
Bangia fuscopurpurea is a traditional mariculture crop having high nutritional value, eicosapntemacnioc acid (EPA) production, and protein content. As an intertidal species, it can tolerate drastic changes in abiotic factors such as temperature, hydration, and light radiation; however, genomic information on the evolutionary aspect and mechanism of EPA enrichment in B. fuscopurpurea and the role of EPA in cold tolerance in this species remain elusive. We conducted transcriptome profile analysis in B. fuscopurpurea to investigate the biological functions of genes associated with resistance to various environment factors...
2017: PloS One
https://www.readbyqxmd.com/read/29238358/characterization-of-the-wheat-leaf-metabolome-during-grain-filling-and-under-varied-n-supply
#18
Elmien Heyneke, Mutsumi Watanabe, Alexander Erban, Guangyou Duan, Peter Buchner, Dirk Walther, Joachim Kopka, Malcolm J Hawkesford, Rainer Hoefgen
Progress in improving crop growth is an absolute goal despite the influence multifactorial components have on crop yield and quality. An Avalon × Cadenza doubled-haploid wheat mapping population was used to study the leaf metabolome of field grown wheat at weekly intervals during the time in which the canopy contributes to grain filling, i.e., from anthesis to 5 weeks post-anthesis. Wheat was grown under four different nitrogen supplies reaching from residual soil N to a luxury over-fertilization (0, 100, 200, and 350 kg N ha-1)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29234904/post-genomics-era-for-orchid-research
#19
REVIEW
Wen-Chieh Tsai, Anne Dievart, Chia-Chi Hsu, Yu-Yun Hsiao, Shang-Yi Chiou, Hsin Huang, Hong-Hwa Chen
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...
December 12, 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/29234472/herpetopanone-a-diterpene-from-herpetosiphon-aurantiacus-discovered-by-isotope-labeling
#20
Xinli Pan, Nicole Domin, Sebastian Schieferdecker, Hirokazu Kage, Martin Roth, Markus Nett
The genome of the predatory bacterium Herpetosiphon aurantiacus 114-95T harbors a number of biosynthesis genes, including four terpene cyclase genes. To identify the terpenes biosynthesized from H. aurantiacus 114-95T, we fed the strain with 13C-labeled glucose and, subsequently, searched for characteristic mass shifts in its metabolome. This approach led to the discovery of a new natural product, of which the isotope pattern is indicative for a diterpene originating from the methylerythritol phosphate pathway...
2017: Beilstein Journal of Organic Chemistry
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