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plant metabolomics

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https://www.readbyqxmd.com/read/28645179/system-wide-analysis-of-short-term-response-to-high-temperature-in-pinus-radiata
#1
Mónica Escandón, Luis Valledor, Jesús Pascual, Gloria Pinto, María Jesús Cañal, Mónica Meijón
Pinus radiata seedlings, the most widely planted pine species in the world, were exposed to temperatures within a range mimicking future scenarios based on current models of heat increase. The short-term heat response in P. radiata was studied in detail by exploring the metabolome, proteome and targeted transcriptome. The use of complementary mass spectrometry techniques, GC-MS and LC-Orbitrap-MS, together with novel bioinformatics tools allowed the reliable quantification of 2,075 metabolites and 901 protein groups...
June 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28640973/production-of-red-flowered-oilseed-rape-via-the-ectopic-expression-of-orychophragmus-violaceus-ovpap2
#2
Wenqin Fu, Daozong Chen, Qi Pan, Fengfeng Li, Zhigang Zhao, Xianhong Ge, Zaiyun Li
Oilseed rape (Brassica napus L.), which has yellow flowers, is both an important oil crop and a traditional tourism resource in China, whereas the Orychophragmus violaceus, which has purple flowers, likely possesses a candidate gene or genes to alter the flower color of oilseed rape. A previously established B. napus line has a particular pair of O. violaceus chromosomes (M4) and exhibits slightly red petals. In this study, the transcriptomic analysis of M4, B. napus (H3), and O. violaceus with purple petals (OvP) and with white petals (OvW) revealed that most anthocyanin biosynthesis genes were up-regulated in both M4 and OvP...
June 22, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28640868/functional-metabolomics-as-a-tool-to-analyze-mediator-function-and-structure-in-plants
#3
Celine Davoine, Ilka N Abreu, Khalil Khajeh, Jeanette Blomberg, Brendan N Kidd, Kemal Kazan, Peer M Schenk, Lorenz Gerber, Ove Nilsson, Thomas Moritz, Stefan Björklund
Mediator is a multiprotein transcriptional co-regulator complex composed of four modules; Head, Middle, Tail, and Kinase. It conveys signals from promoter-bound transcriptional regulators to RNA polymerase II and thus plays an essential role in eukaryotic gene regulation. We describe subunit localization and activities of Mediator in Arabidopsis through metabolome and transcriptome analyses from a set of Mediator mutants. Functional metabolomic analysis based on the metabolite profiles of Mediator mutants using multivariate statistical analysis and heat-map visualization shows that different subunit mutants display distinct metabolite profiles, which cluster according to the reported localization of the corresponding subunits in yeast...
2017: PloS One
https://www.readbyqxmd.com/read/28639116/integration-of-transcriptomic-and-metabolic-data-reveals-hub-transcription-factors-involved-in-drought-stress-response-in-sunflower-helianthus-annuus-l
#4
Sebastián Moschen, Julio A Di Rienzo, Janet Higgins, Takayuki Tohge, Mutsumi Watanabe, Sergio González, Máximo Rivarola, Francisco García-García, Joaquin Dopazo, H Esteban Hopp, Rainer Hoefgen, Alisdair R Fernie, Norma Paniego, Paula Fernández, Ruth A Heinz
By integration of transcriptional and metabolic profiles we identified pathways and hubs transcription factors regulated during drought conditions in sunflower, useful for applications in molecular and/or biotechnological breeding. Drought is one of the most important environmental stresses that effects crop productivity in many agricultural regions. Sunflower is tolerant to drought conditions but the mechanisms involved in this tolerance remain unclear at the molecular level. The aim of this study was to characterize and integrate transcriptional and metabolic pathways related to drought stress in sunflower plants, by using a system biology approach...
June 21, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28630440/looking-to-nature-for-a-new-concept-in-antimicrobial-treatments-isoflavonoids-from-cytisus-striatus-as-antibiotic-adjuvants-against-mrsa
#5
Ana Cristina Abreu, Aline Coqueiro, Andi R Sultan, Nicole Lemmens, Hye Kyong Kim, Robert Verpoorte, Willem J B van Wamel, Manuel Simões, Young Hae Choi
The spread of multidrug-resistant Staphylococcus aureus strains, including methicillin-resistant S. aureus (MRSA), has shortened the useful life of anti-staphylococcal drugs enormously. Two approaches can be followed to address this problem: screening various sources for new leads for antibiotics or finding ways to disable the resistance mechanisms to existing antibiotics. Plants are resistant to most microorganisms, but despite extensive efforts to identify metabolites that are responsible for this resistance, no substantial progress has been made...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28629120/metabolomics-characterization-of-two-apocynaceae-plants-catharanthus-roseus-and-vinca-minor-using-gc-ms-and-lc-ms-methods-in-combination
#6
Qi Chen, Xueyan Lu, Xiaorui Guo, Qingxi Guo, Dewen Li
Catharanthus roseus (C. roseus) and Vinca minor (V. minor) are two common important medical plants belonging to the family Apocynaceae. In this study, we used non-targeted GC-MS and targeted LC-MS metabolomics to dissect the metabolic profile of two plants with comparable phenotypic and metabolic differences. A total of 58 significantly different metabolites were present in different quantities according to PCA and PLS-DA score plots of the GC-MS analysis. The 58 identified compounds comprised 16 sugars, eight amino acids, nine alcohols and 18 organic acids...
June 17, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28628666/the-effector-avrrxo1-phosphorylates-nad-in-planta
#7
Teja Shidore, Corey D Broeckling, Jay S Kirkwood, John J Long, Jiamin Miao, Bingyu Zhao, Jan E Leach, Lindsay R Triplett
Gram-negative bacterial pathogens of plants and animals employ type III secreted effectors to suppress innate immunity. Most characterized effectors work through modification of host proteins or transcriptional regulators, although a few are known to modify small molecule targets. The Xanthomonas type III secreted avirulence factor AvrRxo1 is a structural homolog of the zeta toxin family of sugar-nucleotide kinases that suppresses bacterial growth. AvrRxo1 was recently reported to phosphorylate the central metabolite and signaling molecule NAD in vitro, suggesting that the effector might enhance bacterial virulence on plants through manipulation of primary metabolic pathways...
June 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28626037/autopolyploidization-geographic-origin-and-metabolome-evolution-in-arabidopsis-thaliana
#8
Fredd Vergara, Bart Rymen, Ayuko Kuwahara, Yuji Sawada, Muneo Sato, Masami Y Hirai
PREMISE OF THE STUDY: Autopolyploidy, or whole-genome duplication, is a recurrent phenomenon in plant evolution. Its existence can be inferred from the presence of massive levels of genetic redundancy revealed by comparative plant phylogenomics. Whole-genome duplication is theoretically associated with evolutionary novelties such as the development of new metabolic reactions and therefore contributes to the evolution of new plant metabolic profiles. However, very little is yet known about the impact of autopolyploidy on the metabolism of recently formed autopolyploids...
June 16, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28620397/metabolome-dynamics-of-smutted-sugarcane-reveals-mechanisms-involved-in-disease-progression-and-whip-emission
#9
Patricia D C Schaker, Leila P Peters, Thais R Cataldi, Carlos A Labate, Camila Caldana, Claudia B Monteiro-Vitorello
Sugarcane smut disease, caused by the biotrophic fungus Sporisorium scitamineum, is characterized by the development of a whip-like structure from the plant meristem. The disease causes negative effects on sucrose accumulation, fiber content and juice quality. The aim of this study was to exam whether the transcriptomic changes already described during the infection of sugarcane by S. scitamineum result in changes at the metabolomic level. To address this question, an analysis was conducted during the initial stage of the interaction and through disease progression in a susceptible sugarcane genotype...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28617451/biological-and-chemical-strategies-for-exploring-inter-and-intra-kingdom-communication-mediated-via-bacterial-volatile-signals
#10
Mohamed A Farag, Geun Cheol Song, Yong-Soon Park, Bianca Audrain, Soohyun Lee, Jean-Marc Ghigo, Joseph W Kloepper, Choong-Min Ryu
Airborne chemical signals emitted by bacteria influence the behavior of other bacteria and plants. We present an overview of in vitro methods for evaluating bacterial and plant responses to bacterial volatile compounds (BVCs). Three types of equipment have been used to physically separate the bacterial test strains from either other bacterial strains or plants (in our laboratory we use either Arabidopsis or tobacco plant seedlings): a Petri dish containing two compartments (BI Petri dish); two Petri dishes connected with tubing; and a microtiter-based assay...
July 2017: Nature Protocols
https://www.readbyqxmd.com/read/28612345/metabolome-comparison-of-bioactive-and-inactive-rhododendron-extracts-and-identification-of-an-antibacterial-cannabinoid-s-from-rhododendron-collettianum
#11
Inamullah Hakeem Said, Ahmed Rezk, Ishtiaq Hussain, Anne Grimbs, Abhinandan Shrestha, Hartwig Schepker, Klaudia Brix, Matthias S Ullrich, Nikolai Kuhnert
INTRODUCTION: The science of metabolomics offers the possibility to measure full secondary plant metabolomes with limited experimental effort to allow identification of metabolome differences using principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) of liquid chromatography mass spectrometry (LC-MS) data. OBJECTIVE: To demonstrate a bioinformatics driven hypothesis generator for identification of biologically active compounds in plant crude extracts, which is validated by activity guided fractionation...
June 13, 2017: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/28612342/effect-of-glycine-nitrogen-on-lettuce-growth-under-soilless-culture-a-metabolomics-approach-to-identify-the-main-changes-occurred-in-plant-primary-and-secondary-metabolism
#12
Xiao Yang, Lei Feng, Li Zhao, Xiaosong Liu, Danial Hassani, Danfeng Huang
BACKGROUND: Lettuce is a significant source of antioxidants and bioactive compounds. Nitrate is a cardinal fertilizer in horticulture and influences vegetable yield and quality; however, the negative effects of nitrate on the biosynthesis of flavonoids require further study. It is expected that using fertilizers containing organic N could promote the synthesis of health-promoting compounds. RESULTS: Lettuces were hydroponically cultured in media containing 9 mM nitrate or 9 mM glycine for 4 weeks...
June 14, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28605387/a-simple-fractionated-extraction-method-for-the-comprehensive-analysis-of-metabolites-lipids-and-proteins-from-a-single-sample
#13
Mohamed Salem, Michal Bernach, Krzysztof Bajdzienko, Patrick Giavalisco
Understanding of complex biological systems requires the measurement, analysis and integration of multiple compound classes of the living cell, usually determined by transcriptomic, proteomic, metabolomics and lipidomic measurements. In this protocol, we introduce a simple method for the reproducible extraction of metabolites, lipids and proteins from biological tissues using a single aliquot per sample. The extraction method is based on a methyl tert-butyl ether: methanol: water system for liquid: liquid partitioning of hydrophobic and polar metabolites into two immiscible phases along with the precipitation of proteins and other macromolecules as a solid pellet...
June 1, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28594267/a-plant-pathogenic-bacterium-exploits-the-tricarboxylic-acid-cycle-metabolic-pathway-of-its-insect-vector
#14
Nabil Killiny, Yasser Nehela, Faraj Hijaz, Christopher I Vincent
Huanglongbing in citrus is caused by a phloem-limited, uncultivable, gram-negative α-proteobacterium, Candidatus Liberibacter asiaticus (CLas). CLas is transmitted by the phloem-sucking insect, Diaphorina citri (Hemiptera: Liviidae), in a persistent, circulative, and propagative manner. In this study, we investigated the metabolomic and respiration rates changes in D. citri upon infection with CLas using gas chromatography-mass spectrometry (GC-MS) and gas exchange analysis. The level of glycine, L-serine, L-threonine, and gamma-amino butyric acid were higher in CLas-infected D...
June 8, 2017: Virulence
https://www.readbyqxmd.com/read/28590463/prediction-and-association-mapping-of-agronomic-traits-in-maize-using-multiple-omic-data
#15
Y Xu, C Xu, S Xu
Genomic selection holds a great promise to accelerate plant breeding via early selection before phenotypes are measured, and it offers major advantages over marker-assisted selection for highly polygenic traits. In addition to genomic data, metabolome and transcriptome are increasingly receiving attention as new data sources for phenotype prediction. We used data available from maize as a model to compare the predictive abilities of three different omic data sources using eight representative methods for six traits...
June 7, 2017: Heredity
https://www.readbyqxmd.com/read/28588481/medicinally-used-asarum-species-high-resolution-lc-ms-analysis-of-aristolochic-acid-analogs-and-in-vitro-toxicity-screening-in-hk-2-cells
#16
Johanna Michl, Olusheyi Bello, Geoffrey C Kite, Monique S J Simmonds, Michael Heinrich
Species of Asarum are used in traditional Chinese medicine and, similar to members of the genus Aristolochia, they contain aristolochic acid analogs (AAAs). These compounds are known for their nephrotoxic and carcinogenic effects. So far, the phytochemistry and nephrotoxicity of species of Asarum is not well studied. A high-resolution LC-MS-based metabolomic approach was used to study the phytochemical variation in medicinally used Asarum species. The cytotoxicity of the samples was assessed using human kidney (HK-2) cells...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28586477/affinity-purification-with-metabolomic-and-proteomic-analysis-unravels-diverse-roles-of-nucleoside-diphosphate-kinases
#17
Marcin Luzarowski, Monika Kosmacz, Ewelina Sokolowska, Weronika Jasinska, Lothar Willmitzer, Daniel Veyel, Aleksandra Skirycz
Interactions between metabolites and proteins play an integral role in all cellular functions. Here we describe an affinity purification (AP) approach in combination with LC/MS-based metabolomics and proteomics that allows, to our knowledge for the first time, analysis of protein-metabolite and protein-protein interactions simultaneously in plant systems. More specifically, we examined protein and small-molecule partners of the three (of five) nucleoside diphosphate kinases present in the Arabidopsis genome (NDPK1-NDPK3)...
June 6, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28584907/acute-psychoactive-and-toxic-effects-of-d-metel-on-mice-explained-by-1-h-nmr-based-metabolomics-approach
#18
Yonghong Fu, Zhihong Si, Pumin Li, Minghui Li, He Zhao, Lei Jiang, Yuexiao Xing, Wei Hong, Lingyu Ruan, Jun-Song Wang
Datura metel L. (D. metel) is one well-known folk medical herb with wide application and also the most abused plants all over the world, mainly for spiritual or religious purpose, over-dosing of which often produces poisonous effects. In this study, mice were orally administered with the extract of D. metel once a day at doses for 10 mg/kg and 40 mg/kg for consecutive 4 days, (1)H NMR based metabolomics approach aided with histopathological inspection and biochemical assays were used for the first time to study the psychoactive and toxic effects of D...
June 5, 2017: Metabolic Brain Disease
https://www.readbyqxmd.com/read/28584146/a-targeted-metabolomics-analysis-identifies-intestinal-microbiota-derived-urinary-biomarkers-of-colonization-resistance-in-antibiotic-treated-mice
#19
Mark E Obrenovich, Mary Ann Tima, Alex Polinkovsky, Renliang Zhang, Steven N Emancipator, Curtis J Donskey
Antibiotics excreted into the intestinal tract may disrupt the microbiota that provide colonization resistance against enteric pathogens and alter normal metabolic functions of the microbiota. Many of the bacterial metabolites produced in the intestinal tract are absorbed systemically and excreted in urine. Here, we used a mouse model to test the hypothesis that alterations in levels of targeted bacterial metabolites in urine specimens could provide useful biomarkers indicating disrupted or intact colonization resistance...
June 5, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28580581/comparison-of-partial-least-squares-and-random-forests-for-evaluating-relationship-between-phenolics-and-bioactivities-of-neptunia-oleracea
#20
Soo Yee Lee, Ahmed Mediani, Maulidiani, Alfi Khatib, Intan Safinar Ismail, Norhasnida Zawawi, Faridah Abas
BACKGROUND: Neptunia oleracea is a plant consumed as vegetable and used as folk remedy for several diseases. Herein, two regression models (partial least square, PLS and random forest, RF) in metabolomics approach were compared and applied for the evaluation of relationship between phenolics and bioactivities of N. oleracea. In addition, the effects of different extraction conditions on the phenolic constituents were also assessed by pattern recognition analysis. RESULTS: Comparison of the PLS and RF showed that RF exhibited poorer generalization and hence poorer predictive performance...
June 5, 2017: Journal of the Science of Food and Agriculture
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