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https://www.readbyqxmd.com/read/29152789/automatic-differential-analysis-of-nmr-experiments-in-complex-samples
#1
Laure Margueritte, Petar Markov, Lionel Chiron, Jean-Philippe Starck, Catherine Vonthron-Sã nà Cheau, Mã Lanie Bourjot, Marc-Andrà Delsuc
Liquid state NMR is a powerful tool for the analysis of complex mixtures of unknown molecules. This capacity has been used in many analytical approaches: metabolomics, identification of active compounds in natural extracts, characterization of species, and such studies require the acquisition of many diverse NMR measurements on series of samples. While acquisition can easily be performed automatically, the number of NMR experiments involved in these studies increases very rapidly and this data avalanche requires to resort to automatic processing and analysis...
November 20, 2017: Magnetic Resonance in Chemistry: MRC
https://www.readbyqxmd.com/read/29152192/close-and-distant-contrasting-the-metabolism-of-two-closely-related-subspecies-of-scots-pine-under-the-effects-of-folivory-and-summer-drought
#2
Albert Rivas-Ubach, Jordi Sardans, José Antonio Hódar, Joan Garcia-Porta, Alex Guenther, Ljiljana Paša-Tolić, Michal Oravec, Otmar Urban, Josep Peñuelas
Metabolomes, as chemical phenotypes of organisms, are likely not only shaped by the environment but also by common ancestry. If this is the case, we expect that closely related species of pines will tend to reach similar metabolomic solutions to the same environmental stressors. We examined the metabolomes of two sympatric subspecies of Pinus sylvestris in Sierra Nevada (southern Iberian Peninsula), in summer and winter and exposed to folivory by the pine processionary moth. The overall metabolomes differed between the subspecies but both tended to respond more similarly to folivory...
November 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29150823/metabolic-dynamics-and-physiological-adaptation-of-panax-ginseng-during-development
#3
Yu-Jin Kim, Sung Chul Joo, Jianxin Shi, Chaoyang Hu, Sheng Quan, Jianping Hu, Johan Sukweenadhi, Padmanaban Mohanan, Deok-Chun Yang, Dabing Zhang
The dynamics of metabolites from leaves to roots of Panax ginseng during development has revealed the tissue-specific and year-specific metabolic networks. Being an essential Oriental medicinal plant, ginseng (Panax ginseng Meyer) is a slow-growing perennial herb-accumulating pharmaceutically active metabolites such as ginsenosides in roots during growth. However, little is known about how ginseng plants survive in the harsh environments such as winter cold and summer heat for a longer period and accumulates those active metabolites as the plant grows...
November 17, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29137184/cell-type-specific-metabolic-flux-analysis-a-challenge-for-metabolic-phenotyping-and-a-potential-solution-in-plants
#4
Merja T Rossi, Monika Kalde, Chaiyakorn Srisakvarakul, Nicholas J Kruger, R George Ratcliffe
Stable isotope labelling experiments are used routinely in metabolic flux analysis (MFA) to determine the metabolic phenotype of cells and tissues. A complication arises in multicellular systems because single cell measurements of transcriptomes, proteomes and metabolomes in multicellular organisms suggest that the metabolic phenotype will differ between cell types. In silico analysis of simulated metabolite isotopomer datasets shows that cellular heterogeneity confounds conventional MFA because labelling data averaged over multiple cell types does not necessarily yield averaged flux values...
November 13, 2017: Metabolites
https://www.readbyqxmd.com/read/29101473/tracking-maize-pollen-development-by-the-leaf-collar-method
#5
Kevin Begcy, Thomas Dresselhaus
An easy and highly reproducible nondestructive method named the Leaf Collar Method is described to identify and characterize the different stages of pollen development in maize. In plants, many cellular events such as meiosis, asymmetric cell division, cell cycle regulation, cell fate determination, nucleus movement, vacuole formation, chromatin condensation and epigenetic modifications take place during pollen development. In maize, pollen development occurs in tassels that are confined within the internal stalk of the plant...
November 4, 2017: Plant Reproduction
https://www.readbyqxmd.com/read/29093742/integrative-field-scale-phenotyping-for-investigating-metabolic-components-of-water-stress-within-a-vineyard
#6
Jorge Gago, Alisdair R Fernie, Zoran Nikoloski, Takayuki Tohge, Sebastiá Martorell, José Mariano Escalona, Miquel Ribas-Carbó, Jaume Flexas, Hipólito Medrano
Background: There is currently a high requirement for field phenotyping methodologies/technologies to determine quantitative traits related to crop yield and plant stress responses under field conditions. Methods: We employed an unmanned aerial vehicle equipped with a thermal camera as a high-throughput phenotyping platform to obtain canopy level data of the vines under three irrigation treatments. High-resolution imagery (< 2.5 cm/pixel) was employed to estimate the canopy conductance (gc ) via the leaf energy balance model...
2017: Plant Methods
https://www.readbyqxmd.com/read/29089961/redox-and-ionic-homeostasis-regulations-against-oxidative-salinity-and-drought-stress-in-wheat-a-systems-biology-approach
#7
REVIEW
Zahid Hussain Shah, Hafiz M Rehman, Tasneem Akhtar, Ihsanullah Daur, Muhammad A Nawaz, Muhammad Q Ahmad, Iqrar A Rana, Rana M Atif, Seung H Yang, Gyuhwa Chung
Systems biology and omics has provided a comprehensive understanding about the dynamics of the genome, metabolome, transcriptome, and proteome under stress. In wheat, abiotic stresses trigger specific networks of pathways involved in redox and ionic homeostasis as well as osmotic balance. These networks are considerably more complicated than those in model plants, and therefore, counter models are proposed by unifying the approaches of omics and stress systems biology. Furthermore, crosstalk among these pathways is monitored by the regulation and streaming of transcripts and genes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29083175/metabolic-fingerprinting-of-dormant-and-active-flower-primordia-of-ribes-nigrum-using-high-resolution-magic-angle-spinning-nmr
#8
Majken Pagter, Christian Clement Yde, Katrine Heinsvig Kjær
Global warming may modify the timing of dormancy release and spring growth of buds of temperate fruit crops. Environmental regulation of the activity-dormancy cycle in perennial plants remains poorly understood at the metabolic level. Especially, the fine-scale metabolic dynamics in the meristematic zone within buds has received little attention. In this work we performed metabolic profiling of intact floral primordia of Ribes nigrum isolated from buds differing in dormancy status using high-resolution magic angle spinning (HR-MAS) NMR...
November 7, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29083151/a-red-algal-bourbonane-sesquiterpene-synthase-defined-by-microgram-scale-nmr-coupled-crystalline-sponge-x-ray-diffraction-analysis
#9
Roland D Kersten, Shoukou Lee, Daishi Fujita, Tomáš Pluskal, Susan Kram, Jennifer E Smith, Takahiro Iwai, Joseph P Noel, Makoto Fujita, Jing-Ke Weng
Sesquiterpene scaffolds are the core backbones of many medicinally and industrially important natural products. A plethora of sesquiterpene synthases, widely present in bacteria, fungi, and plants, catalyze the formation of these intricate structures often with multiple stereocenters starting from linear farnesyl diphosphate substrates. Recent advances in next-generation sequencing and metabolomics technologies have greatly facilitated gene discovery for sesquiterpene synthases. However, a major bottleneck limits biochemical characterization of recombinant sesquiterpene synthases: the absolute structural elucidation of the derived sesquiterpene products...
November 14, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29076119/identification-of-potential-biomarkers-from-aconitum-carmichaelii-a-traditional-chinese-medicine-using-a-metabolomic-approach
#10
Dake Zhao, Yana Shi, Xinyan Zhu, Li Liu, Pengzhang Ji, Chunlin Long, Yong Shen, Edward J Kennelly
Despite their well-known toxicity, Aconitum species are important traditional medicines worldwide. Aconitum carmichaelii, known in Chinese as (fuzi), is an officially recognized traditional Chinese medicine with characteristic analgesic and anti-inflammatory activities, whose principal pharmacological ingredients are considered as aconitine-type diterpene alkaloids. Notwithstanding the long-recorded use of A. carmichaelii in traditional Chinese medicine, no single-entity aconitum alkaloid drug has been developed for clinical use...
October 26, 2017: Planta Medica
https://www.readbyqxmd.com/read/29073064/human-shmt-inhibitors-reveal-defective-glycine-import-as-a-targetable-metabolic-vulnerability-of-diffuse-large-b-cell-lymphoma
#11
Gregory S Ducker, Jonathan M Ghergurovich, Nello Mainolfi, Vipin Suri, Stephanie K Jeong, Sophia Hsin-Jung Li, Adam Friedman, Mark G Manfredi, Zemer Gitai, Hahn Kim, Joshua D Rabinowitz
The enzyme serine hydroxymethyltransferse (SHMT) converts serine into glycine and a tetrahydrofolate-bound one-carbon unit. Folate one-carbon units support purine and thymidine synthesis, and thus cell growth. Mammals have both cytosolic SHMT1 and mitochondrial SHMT2, with the mitochondrial isozyme strongly up-regulated in cancer. Here we show genetically that dual SHMT1/2 knockout blocks HCT-116 colon cancer tumor xenograft formation. Building from a pyrazolopyran scaffold that inhibits plant SHMT, we identify small-molecule dual inhibitors of human SHMT1/2 (biochemical IC50 ∼ 10 nM)...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29066204/morphological-proteomic-and-metabolomic-insight-into-the-effect-of-cerium-dioxide-nanoparticles-to-phaseolus-vulgaris-l-under-soil-or-foliar-application
#12
Hajar Salehi, Abdolkarim Chehregani, Luigi Lucini, Ahmad Majd, Mansour Gholami
Chemically synthesized nanoparticles (NPs) are widely used in industry and concern over their impact on the environment is rising. In this study, greenhouse grown bean (Phaseolus vulgaris L.) plants were treated with CeO2 NPs suspensions at 0, 250, 500, 1000, and 2000mgL(-1) either aerially by spraying or via soil application. At 15days after treatment, plants were analyzed for Ce uptake, morphological and biochemical assays, as well as high-resolution mass spectrometry based metabolomics and proteomics. The results from ICP-MS assays showed a dose dependent absorption, uptake and translocation of Ce through both roots and leaves; Ce content increased from 0...
October 21, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29064449/molecular-affinity-of-mabolo-extracts-to-an-octopamine-receptor-of-a-fruit-fly
#13
Francoise Neil D Dacanay, Ma Carmina Joyce A Ladra, Hiyas A Junio, Ricky B Nellas
Essential oils extracted from plants are composed of volatile organic compounds that can affect insect behavior. Identifying the active components of the essential oils to their biochemical target is necessary to design novel biopesticides. In this study, essential oils extracted from Diospyros discolor (Willd.) were analyzed using gas chromatography mass spectroscopy (GC-MS) to create an untargeted metabolite profile. Subsequently, a conformational ensemble of the Drosophila melanogaster octopamine receptor in mushroom bodies (OAMB) was created from a molecular dynamics simulation to resemble a flexible receptor for docking studies...
October 24, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29052269/control-of-biotin-biosynthesis-in-mycobacteria-by-a-pyruvate-carboxylase-dependent-metabolic-signal
#14
Nathaniel Lazar, Allison Fay, Madhumitha Nandakumar, Kerry E Boyle, Joao Xavier, Kyu Rhee, Michael S Glickman
Biotin is an essential cofactor utilized by all domains of life, but only synthesized by bacteria, fungi and plants, making biotin biosynthesis a target for antimicrobial development. To understand biotin biosynthesis in mycobacteria, we executed a genetic screen in Mycobacterium smegmatis for biotin auxotrophs and identified pyruvate carboxylase (Pyc) as required for biotin biosynthesis. The biotin auxotrophy of the pyc::tn strain is due to failure to transcriptionally induce late stage biotin biosynthetic genes in low biotin conditions...
October 20, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/29047109/metabolic-flux-towards-the-iso-flavonoid-pathway-in-lignin-modified-alfalfa-lines-induces-resistance-against-fusarium-oxysporum-f-sp-medicaginis
#15
Upinder S Gill, Srinivasa R Uppalapati, Lina Gallego-Giraldo, Yasuhiro Ishiga, Richard A Dixon, Kirankumar S Mysore
Downregulation of lignin in alfalfa (Medicago sativa L.) is associated with increased availability of cell wall polysaccharides in plant cells. We tested transgenic alfalfa plants downregulated for Caffeoyl-CoA O-methyltransferase (CCoAOMT) against an economically important fungal disease of alfalfa, Fusarium wilt caused by Fusarium oxysporum f. sp. medicaginis, and found it more resistant to this disease. Transcriptomic and metabolomic analyses indicated that the improved disease resistance against Fusarium wilt is due to increased accumulation and/or spillover of flux towards the (iso)flavonoid pathway...
October 19, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29040673/assimilation-of-omics-strategies-to-study-the-cuticle-layer-and-suberin-lamellae-in-plants
#16
Hagai Cohen, Jedrzej Szymanski, Asaph Aharoni, Eva Dominguez
The assembly of the lipophilic cuticle layer and suberin lamellae, approximately 450 million years ago, was a major evolutionary development that enabled plants to colonize terrestrial habitats. The cuticle layer is composed of cutin polyester and embedded cuticular waxes, whereas the suberin lamellae consist of very long chain fatty acid derivatives, glycerol, and phenolics cross-linked with alkyl ferulate-embedded waxes. Due to their substantial biological roles in plant life, the mechanisms underlying the assembly of these structures have been extensively investigated...
November 9, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29036663/metabolomic-and-biochemical-approaches-link-salicylic-acid-biosynthesis-to-cyanogenesis-in-peach-plants
#17
Pedro Diaz-Vivancos, Agustina Bernal-Vicente, Daniel Cantabella, Cesar Petri, José Antonio Hernández
Despite the long-established importance of salicylic acid (SA) in plant stress responses and other biological processes, its biosynthetic pathways have not been fully characterized. The proposed SA synthesis originates from chorismate by two distinct pathways: isochorismate and phenylalanine (Phe) ammonia-lyase (PAL) pathways. Cyanogenesis is the process related to the release of hydrogen cyanide from endogenous cyanogenic glycosides (CNglcs), and it has been linked to plant plasticity improvement. To date, however, no relationship has been suggested between both pathways...
September 25, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29034954/intergenerational-environmental-effects-functional-signals-in-offspring-transcriptomes-and-metabolomes-after-parental-jasmonic-acid-treatment-in-apomictic-dandelion
#18
Koen J F Verhoeven, Eline H Verbon, Thomas P van Gurp, Carla Oplaat, Julie Ferreira de Carvalho, Alison M Morse, Mark Stahl, Mirka Macel, Lauren M McIntyre
Parental environments can influence offspring traits. However, the magnitude of the impact of parental environments on offspring molecular phenotypes is poorly understood. Here, we test the direct effects and intergenerational effects of jasmonic acid (JA) treatment, which is involved in herbivory-induced defense signaling, on transcriptomes and metabolomes in apomictic common dandelion (Taraxacum officinale). In a full factorial crossed design with parental and offspring JA and control treatments, we performed leaf RNA-seq gene expression analysis, LC-MS metabolomics and total phenolics assays in offspring plants...
October 16, 2017: New Phytologist
https://www.readbyqxmd.com/read/29024237/sterol-content-in-the-artificial-diet-of-mythimna-separata-affects-the-metabolomics-of-arma-chinensis-fallou-as-determined-by-proton-nuclear-magnetic-resonance-spectroscopy
#19
Yi Guo, Chen-Xi Liu, Li-Sheng Zhang, Meng-Qing Wang, Hong-Yin Chen
Insects cannot synthesize sterols and must obtain them from plants. Therefore, reducing plant sterol content or changing sterol type might be an effective pest control strategy. However, the impacts of these changes on pests' natural predators remain unknown. Here, we fed artificial diets with reduced sterol content to Mythimna separata (Walker) (Lepidoptera: Noctuidae) and investigated the effects on its natural predator, Arma chinensis (Fallou) (Hemiptera: Pentatomidae). Reduced sterol content in M. separata (MS1, MS2, and MS5) was achieved by feeding them artificial diets prepared from a feed base subjected to one, two, or five cycles of sterol extractions, respectively...
October 11, 2017: Archives of Insect Biochemistry and Physiology
https://www.readbyqxmd.com/read/28993761/pcr-and-omics-based-techniques-to-study-the-diversity-ecology-and-biology-of-anaerobic-fungi-insights-challenges-and-opportunities
#20
REVIEW
Joan E Edwards, Robert J Forster, Tony M Callaghan, Veronika Dollhofer, Sumit S Dagar, Yanfen Cheng, Jongsoo Chang, Sandra Kittelmann, Katerina Fliegerova, Anil K Puniya, John K Henske, Sean P Gilmore, Michelle A O'Malley, Gareth W Griffith, Hauke Smidt
Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys...
2017: Frontiers in Microbiology
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