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Plant Flux analysis

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https://www.readbyqxmd.com/read/29137184/cell-type-specific-metabolic-flux-analysis-a-challenge-for-metabolic-phenotyping-and-a-potential-solution-in-plants
#1
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/29123533/identifying-developmental-zones-in-maize-lateral-root-cell-length-profiles-using-multiple-change-point-models
#2
Beatriz Moreno-Ortega, Guillaume Fort, Bertrand Muller, Yann Guédon
The identification of the limits between the cell division, elongation and mature zones in the root apex is still a matter of controversy when methods based on cellular features, molecular markers or kinematics are compared while methods based on cell length profiles have been comparatively underexplored. Segmentation models were developed to identify developmental zones within a root apex on the basis of epidermal cell length profiles. Heteroscedastic piecewise linear models were estimated for maize lateral roots of various lengths of both wild type and two mutants affected in auxin signaling (rtcs and rum-1)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29102882/wet-deposition-and-sources-of-inorganic-nitrogen-in-the-three-gorges-reservoir-region-china
#3
Huanbo Wang, Guangming Shi, Mi Tian, Yang Chen, Baoqing Qiao, Liuyi Zhang, Fumo Yang, Leiming Zhang, Qiong Luo
Precipitation samples were collected at five rural and one urban sites in the Three Gorges Reservoir Region (TGR), China from March 2014 to February 2016. The inorganic reactive nitrogen (Nr) contents were analysed to investigate their wet deposition flux, budget, and sources in the area. Annual Nr wet deposition varied from 7.1 to 23.4 kg N ha(-1) yr(-1) over the six sites during the two-year study campaign. The six-site average Nr wet deposition flux was 17.1 and 11.7 kg N ha(-1) yr(-1) in 2014 and 2015, respectively, with 71% from NH4(+) and 29% from NO3(-)...
November 2, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/29094279/high-throughput-transcriptome-analysis-of-coffee-reveals-prehaustorial-resistance-in-response-to-hemileia-vastatrix-infection
#4
Juan Carlos Florez, Luciana Souto Mofatto, Rejane do Livramento Freitas-Lopes, Sávio Siqueira Ferreira, Eunize Maciel Zambolim, Marcelo Falsarella Carazzolle, Laércio Zambolim, Eveline Teixeira Caixeta
We provide a transcriptional profile of coffee rust interaction and identified putative up regulated resistant genes Coffee rust disease, caused by the fungus Hemileia vastatrix, is one of the major diseases in coffee throughout the world. The use of resistant cultivars is considered to be the most effective control strategy for this disease. To identify candidate genes related to different mechanism defense in coffee, we present a time-course comparative gene expression profile of Caturra (susceptible) and Híbrido de Timor (HdT, resistant) in response to H...
November 1, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29083881/organophosphate-triesters-and-diester-degradation-products-in-municipal-sludge-from-wastewater-treatment-plants-in-china-spatial-patterns-and-ecological-implications
#5
Lingfang Fu, Bibai Du, Fei Wang, James C W Lam, Lixi Zeng, Eddy Y Zeng
Little is known about the occurrences, distributions, sources, and potential risks of organophosphate (OP) triesters and diester degradation products in municipal sludge from wastewater treatment plants (WWTPs). In this study, we conducted the first nationwide survey to simultaneously determine a suite of 11 OP triesters and six diester degradation products in sludge from WWTPs across China. All OP triesters were detected and three diesters were identified for the first time in sludge samples. Total concentrations of OP triesters and diester degradation products were in the ranges of 43...
November 14, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29046998/metabolite-profiling-and-associated-gene-expression-reveal-two-metabolic-shifts-during-the-seed-to-seedling-transition-in-arabidopsis-thaliana
#6
Anderson Tadeu Silva, Wilco Ligterink, Henk W M Hilhorst
Metabolic and transcriptomic correlation analysis identified two distinctive profiles involved in the metabolic preparation for seed germination and seedling establishment, respectively. Transcripts were identified that may control metabolic fluxes. The transition from a quiescent metabolic state (dry seed) to the active state of a vigorous seedling is crucial in the plant's life cycle. We analysed this complex physiological trait by measuring the changes in primary metabolism that occur during the transition in order to determine which metabolic networks are operational...
October 18, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29042608/sedum-alfredii-sanramp6-metal-transporter-contributes-to-cadmium-accumulation-in-transgenic-arabidopsis-thaliana
#7
Shuangshuang Chen, Xiaojiao Han, Jie Fang, Zhuchou Lu, Wenmin Qiu, Mingying Liu, Jian Sang, Jing Jiang, Renying Zhuo
The plant natural resistance-associated macrophage protein (Nramp) family plays an important role in tolerance to heavy metal stress. However, few Nramps have been functionally characterized in the heavy metal-accumulating plant Sedum alfredii. Here, Nramp6 was cloned and identified from S. alfredii and its function analyzed in transgenic Arabidopsis thaliana. SaNramp6 cDNA contains an open reading frame of 1, 638 bp encoding 545 amino acids. SaNramp6's expression can be induced by cadmium (Cd) stress, and, after treatment, it peaked at one week and 12 h in the roots and leaves, respectively...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29039014/protocol-for-coexpression-network-construction-and-stress-responsive-expression-analysis-in-brachypodium
#8
Sanchari Sircar, Nita Parekh, Gaurav Sablok
Identifying functionally coexpressed genes and modules has increasingly become important to understand the transcriptional flux and to understand large scale gene association. Application of the graph theory and combination of tools has allowed to understand the genic interaction and to understand the role of hub and non-hub proteins in plant development and its ability to cope with stress. Association genetics has also been coupled with network modules to map these key genes as e-QTLs. High throughput sequencing approaches has revolutionized the mining of the gene behavior and also the association of the genes over time-series...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29030907/macromolecular-rate-theory-mmrt-provides-a-thermodynamics-rationale-to-underpin-the-convergent-temperature-response-in-plant-leaf-respiration
#9
Liyin L Liang, Vickery L Arcus, Mary A Heskel, Odhran S O'Sullivan, Lasantha K Weerasinghe, Danielle Creek, John J G Egerton, Mark G Tjoelker, Owen K Atkin, Louis A Schipper
Temperature is a crucial factor in determining the rates of ecosystem processes, e.g. leaf respiration (R) - the flux of plant respired CO2 from leaves to the atmosphere. Generally, R increases exponentially with temperature and formulations such as the Arrhenius equation are widely used in earth system models. However, experimental observations have shown a consequential and consistent departure from an exponential increase in R. What are the principles that underlie these observed patterns? Here, we demonstrate that macromolecular rate theory (MMRT), based on transition state theory for enzyme-catalyzed kinetics, provides a thermodynamic explanation for the observed departure and the convergent temperature response of R using a global database...
October 14, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28994230/land-use-of-drained-peatlands-greenhouse-gas-fluxes-plant-production-and-economics
#10
Åsa Kasimir, Hongxing He, Jessica Coria, Anna Nordén
Drained peatlands are hotspots for greenhouse gas (GHG) emissions, which could be mitigated by rewetting and land use change. We performed an ecological/economic analysis of rewetting drained fertile peatlands in a hemiboreal climate using different land use strategies over 80 years. Vegetation, soil processes, and total GHG emissions were modeled using the CoupModel for four scenarios: 1) business as usual - Norway spruce with average soil water table of -40 cm; 2) willow with groundwater at -20 cm; 3) reed canary grass with groundwater at -10 cm; and 4) a fully rewetted peatland...
October 10, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28991972/comparison-of-n2o-emissions-and-gene-abundances-between-wastewater-nitrogen-removal-systems
#11
Elizabeth Quinn Brannon, Serena M Moseman-Valtierra, Brittany V Lancellotti, Sara K Wigginton, Jose A Amador, James C McCaughey, George W Loomis
Biological nitrogen removal (BNR) systems are increasingly used in the United States in both centralized wastewater treatment plants (WWTPs) and decentralized advanced onsite wastewater treatment systems (OWTS) to reduce N discharged in wastewater effluent. However, the potential for BNR systems to be sources of nitrous oxide (NO), a potent greenhouse gas, needs to be evaluated to assess their environmental impact. We quantified and compared NO emissions from BNR systems at a WWTP (Field's Point, Providence, RI) and three types of advanced OWTS (Orenco Advantex AX 20, SeptiTech Series D, and Bio-Microbics MicroFAST) in nine Rhode Island residences ( = 3 per type) using cavity ring-down spectroscopy...
September 2017: Journal of Environmental Quality
https://www.readbyqxmd.com/read/28988354/over-expression-of-the-arabidopsis-formate-dehydrogenase-in-chloroplasts-enhances-formaldehyde-uptake-and-metabolism-in-transgenic-tobacco-leaves
#12
Ru Wang, Zhidong Zeng, Hongxia Guo, Hao Tan, Ang Liu, Yan Zhao, Limei Chen
Over-expression of AtFDH controlled by the promoter of Rubisco small subunit in chloroplasts increases formaldehyde uptake and metabolism in tobacco leaves. Our previous study showed that formaldehyde (HCHO) uptake and resistance in tobacco are weaker than in Arabidopsis. Formate dehydrogenase in Arabidopsis (AtFDH) is a key enzyme in HCHO metabolism by oxidation of HCOOH to CO2, which enters the Calvin cycle to be assimilated into glucose. HCHO metabolic mechanism in tobacco differs from that in Arabidopsis...
October 7, 2017: Planta
https://www.readbyqxmd.com/read/28987943/a-standardized-extract-of-butea-monosperma-lam-flowers-suppresses-the-il-1%C3%AE-induced-expression-of-il-6-and-matrix-metalloproteases-by-activating-autophagy-in-human-osteoarthritis-chondrocytes
#13
Mohammad Y Ansari, Nazir M Khan, Tariq M Haqqi
BACKGROUND/OBJECTIVE: Osteoarthritis (OA) is a leading cause of joint dysfunction, disability and poor quality of life in the affected population. The underlying mechanism of joint dysfunction involves increased oxidative stress, inflammation, high levels of cartilage extracellular matrix degrading proteases and decline in autophagy-a mechanism of cellular defense. There is no disease modifying therapies currently available for OA. Different parts of the Butea monosperma (Lam.) plant have widely been used in the traditional Indian Ayurvedic medicine system for the treatment of various human diseases including inflammatory conditions...
October 4, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28985572/post-photosynthetic-carbon-partitioning-to-sugar-alcohols-and-consequences-for-plant-growth
#14
REVIEW
Kathryn Dumschott, Andreas Richter, Wayne Loescher, Andrew Merchant
The occurrence of sugar alcohols is ubiquitous among plants. Physiochemical properties of sugar alcohols suggest numerous primary and secondary functions in plant tissues and are often well documented. In addition to functions arising from physiochemical properties, the synthesis of sugar alcohols may have significant influence over photosynthetic, respiratory, and developmental processes owing to their function as a large sink for photosynthates. Sink strength is demonstrated by the high concentrations of sugar alcohols found in plant tissues and their ability to be readily transported...
October 3, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28977710/multifaceted-plant-responses-to-circumvent-phe-hyperaccumulation-by-downregulation-of-flux-through-the-shikimate-pathway-and-by-vacuolar-phe-sequestration
#15
Joseph H Lynch, Irina Orlova, Chengsong Zhao, Longyun Guo, Rohit Jaini, Hiroshi Maeda, Tariq Akhtar, Junellie Cruz-Lebron, David Rhodes, John Morgan, Guillaume Pilot, Eran Pichersky, Natalia Dudareva
Detrimental effects of hyperaccumulation of the aromatic amino acid phenylalanine (Phe) in animals, known as phenylketonuria, are mitigated by excretion of Phe derivatives; however, how plants endure Phe accumulating conditions in the absence of an excretion system is currently unknown. To achieve Phe hyperaccumulation in a plant system, we simultaneously decreased in petunia flowers expression of all three Phe ammonia lyase (PAL) isoforms that catalyze the non-oxidative deamination of Phe to trans-cinnamic acid, the committed step for the major pathway of Phe metabolism...
October 4, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28939278/engineering-the-biocatalytic-selectivity-of-iridoid-production-in-saccharomyces-cerevisiae
#16
John M Billingsley, Anthony B DeNicola, Joyann S Barber, Man-Cheng Tang, Joe Horecka, Angela Chu, Neil K Garg, Yi Tang
Monoterpene indole alkaloids (MIAs) represent a structurally diverse, medicinally essential class of plant derived natural products. The universal MIA building block strictosidine was recently produced in the yeast Saccharomyces cerevisiae, setting the stage for optimization of microbial production. However, the irreversible reduction of pathway intermediates by yeast enzymes results in a non-recoverable loss of carbon, which has a strong negative impact on metabolic flux. In this study, we identified and engineered the determinants of biocatalytic selectivity which control flux towards the iridoid scaffold from which all MIAs are derived...
September 20, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28871529/assessing-metabolic-flux-in-plants-with-radiorespirometry
#17
Nicholas J Kruger, Shyam K Masakapalli, R George Ratcliffe
Carbohydrates are the dominant respiratory substrate in many plant cells. However, the route of carbohydrate oxidation varies depending on the relative cellular demands for energy, reductant, and precursors for biosynthesis. During these processes individual substrate carbon atoms are differentially released as carbon dioxide by specific reactions in the network, and this can be measured by monitoring the release of (14)CO2 from a range of positionally labeled forms of [(14)C]glucose. Although the relative amounts of carbon dioxide produced from different carbon positions do not allow precise determination of fluxes, they are indicative of the route of carbohydrate utilization...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28822133/isotopically-nonstationary-metabolic-flux-analysis-inst-mfa-of-photosynthesis-and-photorespiration-in-plants
#18
Fangfang Ma, Lara J Jazmin, Jamey D Young, Doug K Allen
Photorespiration is a central component of photosynthesis; however to better understand its role it should be viewed in the context of an integrated metabolic network rather than a series of individual reactions that operate independently. Isotopically nonstationary (13)C metabolic flux analysis (INST-MFA), which is based on transient labeling studies at metabolic steady state, offers a comprehensive platform to quantify plant central metabolism. In this chapter, we describe the application of INST-MFA to investigate metabolism in leaves...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28811563/crosstalk-between-diurnal-rhythm-and-water-stress-reveals-an-altered-primary-carbon-flux-into-soluble-sugars-in-drought-treated-rice-leaves
#19
Seo-Woo Kim, Sang-Kyu Lee, Hee-Jeong Jeong, Gynheung An, Jong-Seong Jeon, Ki-Hong Jung
Plants retain rhythmic physiological responses when adapting to environmental challenges. However, possible integrations between drought conditions and those responses have not received much focus, especially regarding crop plants, and the relationship between abiotic stress and the diurnal cycle is generally not considered. Therefore, we conducted a genome-wide analysis to identify genes showing both diurnal regulation and water-deficiency response in rice (Oryza sativa). Among the 712 drought-responsive genes primary identified, 56...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28795660/systems-and-synthetic-biology-perspective-of-the-versatile-plant-pathogenic-and-polysaccharide-producing-bacterium-xanthomonas-campestris
#20
Sarah Schatschneider, Jessica Schneider, Jochen Blom, Fabien Létisse, Karsten Niehaus, Alexander Goesmann, Frank-Jörg Vorhölter
Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features...
August 10, 2017: Microbiology
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