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Plant Flux analysis

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https://www.readbyqxmd.com/read/28077967/integrated-omics-analyses-reveal-the-details-of-metabolic-adaptation-of-clostridium-thermocellum-to-lignocellulose-derived-growth-inhibitors-released-during-the-deconstruction-of-switchgrass
#1
Suresh Poudel, Richard J Giannone, Miguel Rodriguez, Babu Raman, Madhavi Z Martin, Nancy L Engle, Jonathan R Mielenz, Intawat Nookaew, Steven D Brown, Timothy J Tschaplinski, David Ussery, Robert L Hettich
BACKGROUND: Clostridium thermocellum is capable of solubilizing and converting lignocellulosic biomass into ethanol. Although much of the work-to-date has centered on characterizing this microbe's growth on model cellulosic substrates, such as cellobiose, Avicel, or filter paper, it is vitally important to understand its metabolism on more complex, lignocellulosic substrates to identify relevant industrial bottlenecks that could undermine efficient biofuel production. To this end, we have examined a time course progression of C...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28035269/current-and-future-ozone-risks-to-global-terrestrial-biodiversity-and-ecosystem-processes
#2
REVIEW
Jürg Fuhrer, Maria Val Martin, Gina Mills, Colette L Heald, Harry Harmens, Felicity Hayes, Katrina Sharps, Jürgen Bender, Mike R Ashmore
Risks associated with exposure of individual plant species to ozone (O3) are well documented, but implications for terrestrial biodiversity and ecosystem processes have received insufficient attention. This is an important gap because feedbacks to the atmosphere may change as future O3 levels increase or decrease, depending on air quality and climate policies. Global simulation of O3 using the Community Earth System Model (CESM) revealed that in 2000, about 40% of the Global 200 terrestrial ecoregions (ER) were exposed to O3 above thresholds for ecological risks, with highest exposures in North America and Southern Europe, where there is field evidence of adverse effects of O3, and in central Asia...
December 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28031032/metabolic-model-of-central-carbon-and-energy-metabolisms-of-growing-arabidopsis-thaliana-in-relation-to-sucrose-translocation
#3
Maksim Zakhartsev, Irina Medvedeva, Yury Orlov, Ilya Akberdin, Olga Krebs, Waltraud X Schulze
BACKGROUND: Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of these metabolic and underlying regulatory processes allow a detailed understanding of carbon distribution within the plant and the formation of associated phenotypic traits. Sucrose translocation from 'source' tissues (e.g. mesophyll) to 'sink' tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped into efflux exporters (SWEET family) and proton-symport importers (SUC, STP families)...
December 28, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28024747/greenhouse-gas-footprint-and-the-carbon-flow-associated-with-different-solid-waste-management-strategy-for-urban-metabolism-in-bangladesh
#4
K M Nazmul Islam
Greenhouse gas (GHG) emissions from municipal solid waste (MSW) and associated climate change consequences are gripping attention globally, while MSW management as a vital subsystem of urban metabolism significantly influences the urban carbon cycles. This study evaluates the GHG emissions and carbon flow of existing and proposed MSW management in Bangladesh through scenario analysis, including landfill with landfill gas (LFG) recovery, waste to energy (WtE), and material recovery facility (MRF). The analysis indicates that, scenario H2 and H5 emitted net GHGs -152...
December 23, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/28018381/model-assisted-estimation-of-the-genetic-variability-in-physiological-parameters-related-to-tomato-fruit-growth-under-contrasted-water-conditions
#5
Dario Constantinescu, Mohamed-Mahmoud Memmah, Gilles Vercambre, Michel Génard, Valentina Baldazzi, Mathilde Causse, Elise Albert, Béatrice Brunel, Pierre Valsesia, Nadia Bertin
Drought stress is a major abiotic stress threatening plant and crop productivity. In case of fleshy fruits, understanding mechanisms governing water and carbon accumulations and identifying genes, QTLs and phenotypes, that will enable trade-offs between fruit growth and quality under Water Deficit (WD) condition is a crucial challenge for breeders and growers. In the present work, 117 recombinant inbred lines of a population of Solanum lycopersicum were phenotyped under control and WD conditions. Plant water status, fruit growth and composition were measured and data were used to calibrate a process-based model describing water and carbon fluxes in a growing fruit as a function of plant and environment...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27995647/temporal-development-of-the-barley-leaf-metabolic-response-to-pi-limitation
#6
Ralitza Alexova, Clark J Nelson, A Harvey Millar
The response of plants to Pi limitation involves interplay between root uptake of Pi , adjustment of resource allocation to different plant organs, and increased metabolic Pi use efficiency. To identify potentially novel, early-responding, metabolic hallmarks of Pi limitation in crop plants, we studied the metabolic response of barley leaves over the first 7 days of Pi stress, and the relationship of primary metabolites with leaf Pi levels and leaf biomass. The abundance of leaf Pi , Tyr, and shikimate were significantly different between low Pi and control plants 1 h after transfer of the plants to low Pi ...
December 20, 2016: Plant, Cell & Environment
https://www.readbyqxmd.com/read/27993191/optimizing-led-lighting-for-space-plant-growth-unit-joint-effects-of-photon-flux-density-red-to-white-ratios-and-intermittent-light-pulses
#7
O V Avercheva, Yu A Berkovich, I O Konovalova, S G Radchenko, S N Lapach, E M Bassarskaya, G V Kochetova, T V Zhigalova, O S Yakovleva, I G Tarakanov
The aim of this work were to choose a quantitative optimality criterion for estimating the quality of plant LED lighting regimes inside space greenhouses and to construct regression models of crop productivity and the optimality criterion depending on the level of photosynthetic photon flux density (PPFD), the proportion of the red component in the light spectrum and the duration of the duty cycle (Chinese cabbage Brassica сhinensis L. as an example). The properties of the obtained models were described in the context of predicting crop dry weight and the optimality criterion behavior when varying plant lighting parameters...
November 2016: Life Sciences in Space Research
https://www.readbyqxmd.com/read/27987091/structured-model-and-parameter-estimation-in-plant-cell-cultures-of-thevetia-peruviana
#8
Adriana Villegas, Juan Pablo Arias, Daira Aragón, Silvia Ochoa, Mario Arias
In this work, a mechanistic model for predicting the dynamic behavior of extracellular and intracellular nutrients, biomass production, and the main metabolites involved in the central carbon metabolism in plant cell cultures of Thevetia peruviana is presented. The proposed model is the first mechanistic model implemented for plant cell cultures of this species, and includes 28 metabolites, 33 metabolic reactions, and 61 parameters. Given the over-parametrization of the model, its nonlinear nature and the strong correlation among the effects of the parameters, a parameter estimation routine based on identifiability analysis was implemented...
December 16, 2016: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/27973728/nitrogen-removal-in-myriophyllum-aquaticum-wetland-microcosms-for-swine-wastewater-treatment-15-n-labelled-nitrogen-mass-balance-analysis
#9
Shunan Zhang, Feng Liu, Runlin Xiao, Yang He, Jinshui Wu
BACKGROUND: Ecological treatments are effective for treating agricultural wastewater. In this study, wetland microcosms vegetated with Myriophyllum aquaticum were designed for nitrogen (N) removal from two strengths of swine wastewater, and (15) N-labelled ammonium (NH4(+) -N) was added to evaluate the dominant NH4(+) -N removal pathway. RESULTS: The results showed that 98.8% of NH4(+) -N and 88.3% of TN (TN: 248.6 mg L(-1) ) were removed from low-strength swine wastewater (SW1) after an incubation of 21 days, with corresponding values for high-strength swine wastewater (SW2) being 99...
January 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/27879261/limited-linkages-of-aboveground-and-belowground-phenology-a-study-in-grape
#10
Laura Radville, Taryn L Bauerle, Louise H Comas, Katherine A Marchetto, Alan N Lakso, David R Smart, Richard M Dunst, David M Eissenstat
PREMISE OF THE STUDY: Plant phenology influences resource utilization, carbon fluxes, and interspecific interactions. Although controls on aboveground phenology have been studied to some degree, controls on root phenology are exceptionally poorly understood. METHODS: We used minirhizotrons to examine the timing of grape root production over 5 yr in Fredonia, New York, USA, in a humid continental climate; and over 3 yr in Oakville, California, USA, in a Mediterranean climate...
November 2016: American Journal of Botany
https://www.readbyqxmd.com/read/27829370/drought-stress-in-maize-causes-differential-acclimation-responses-of-glutathione-and-sulfur-metabolism-in-leaves-and-roots
#11
Nisar Ahmad, Mario Malagoli, Markus Wirtz, Ruediger Hell
BACKGROUND: Drought is the most important environmental stress that limits crop yield in a global warming world. Despite the compelling evidence of an important role of oxidized and reduced sulfur-containing compounds during the response of plants to drought stress (e.g. sulfate for stomata closure or glutathione for scavenging of reactive oxygen species), the assimilatory sulfate reduction pathway is almost not investigated at the molecular or at the whole plant level during drought...
November 9, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27821524/left-right-leaf-asymmetry-in-decussate-and-distichous-phyllotactic-systems
#12
Ciera C Martinez, Daniel H Chitwood, Richard S Smith, Neelima R Sinha
Leaves in plants with spiral phyllotaxy exhibit directional asymmetries, such that all the leaves originating from a meristem of a particular chirality are similarly asymmetric relative to each other. Models of auxin flux capable of recapitulating spiral phyllotaxis predict handed auxin asymmetries in initiating leaf primordia with empirically verifiable effects on superficially bilaterally symmetric leaves. Here, we extend a similar analysis of leaf asymmetry to decussate and distichous phyllotaxy. We found that our simulation models of these two patterns predicted mirrored asymmetries in auxin distribution in leaf primordia pairs...
December 19, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27807270/stomatal-design-principles-in-synthetic-and-real-leaves
#13
Maciej A Zwieniecki, Katrine S Haaning, C Kevin Boyce, Kaare H Jensen
Stomata are portals in plant leaves that control gas exchange for photosynthesis, a process fundamental to life on Earth. Gas fluxes and plant productivity depend on external factors such as light, water and CO2 availability and on the geometrical properties of the stoma pores. The link between stoma geometry and environmental factors has informed a wide range of scientific fields-from agriculture to climate science, where observed variations in stoma size and density are used to infer prehistoric atmospheric CO2 content...
November 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/27795326/role-of-o2-in-the-growth-of-rhizobium-leguminosarum-bv-viciae-3841-on-glucose-and-succinate
#14
Rachel M Wheatley, Vinoy K Ramachandran, Barney A Geddes, Benjamin J Perry, Chris K Yost, Philip S Poole
: Insertion sequencing (INSeq) analysis of Rhizobium leguminosarum bv. viciae 3841 (Rlv3841) grown on glucose or succinate at both 21% and 1% O2 was used to understand how O2 concentration alters metabolism. Two transcriptional regulators were required for growth on glucose (pRL120207 [eryD] and RL0547 [phoB]), five were required on succinate (pRL100388, RL1641, RL1642, RL3427, and RL4524 [ecfL]), and three were required on 1% O2 (pRL110072, RL0545 [phoU], and RL4042). A novel toxin-antitoxin system was identified that could be important for generation of new plasmidless rhizobial strains...
January 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/27793154/in-silico-metabolic-network-analysis-of-arabidopsis-leaves
#15
Veronique Beckers, Lisa Maria Dersch, Katrin Lotz, Guido Melzer, Oliver Ernst Bläsing, Regine Fuchs, Thomas Ehrhardt, Christoph Wittmann
BACKGROUND: During the last decades, we face an increasing interest in superior plants to supply growing demands for human and animal nutrition and for the developing bio-based economy. Presently, our limited understanding of their metabolism and its regulation hampers the targeted development of desired plant phenotypes. In this regard, systems biology, in particular the integration of metabolic and regulatory networks, is promising to broaden our knowledge and to further explore the biotechnological potential of plants...
October 29, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27748562/disentangling-the-photochemical-salinity-tolerance-in-aster-tripolium-l-connecting-biophysical-traits-with-changes-in-fatty-acid-composition
#16
B Duarte, M T Cabrita, C Gameiro, A R Matos, R Godinho, J C Marques, I Caçador
A profound analysis of A. tripolium photochemical traits under salinity exposure is lacking in the literature, with very few references focusing on its fatty acid profile role in photophysiology. To address this, the deep photochemical processes were evaluated by Pulse Amplitude Modulated (PAM) Fluorometry coupled with a discrimination of its leaf fatty acid profile. Plants exposed to 125-250 mm NaCl showed higher photochemical light harvesting efficiencies and lower energy dissipation rates. under higher NaCl exposure, there is evident damage of the oxygen evolving complexes (OECs)...
October 17, 2016: Plant Biology
https://www.readbyqxmd.com/read/27735856/understanding-plant-nitrogen-metabolism-through-metabolomics-and-computational-approaches
#17
Perrin H Beatty, Matthias S Klein, Jeffrey J Fischer, Ian A Lewis, Douglas G Muench, Allen G Good
A comprehensive understanding of plant metabolism could provide a direct mechanism for improving nitrogen use efficiency (NUE) in crops. One of the major barriers to achieving this outcome is our poor understanding of the complex metabolic networks, physiological factors, and signaling mechanisms that affect NUE in agricultural settings. However, an exciting collection of computational and experimental approaches has begun to elucidate whole-plant nitrogen usage and provides an avenue for connecting nitrogen-related phenotypes to genes...
October 10, 2016: Plants (Basel, Switzerland)
https://www.readbyqxmd.com/read/27732672/a-resource-allocation-trade-off-between-virulence-and-proliferation-drives-metabolic-versatility-in-the-plant-pathogen-ralstonia-solanacearum
#18
Rémi Peyraud, Ludovic Cottret, Lucas Marmiesse, Jérôme Gouzy, Stéphane Genin
Bacterial pathogenicity relies on a proficient metabolism and there is increasing evidence that metabolic adaptation to exploit host resources is a key property of infectious organisms. In many cases, colonization by the pathogen also implies an intensive multiplication and the necessity to produce a large array of virulence factors, which may represent a significant cost for the pathogen. We describe here the existence of a resource allocation trade-off mechanism in the plant pathogen R. solanacearum. We generated a genome-scale reconstruction of the metabolic network of R...
October 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27725824/recent-developments-in-systems-biology-and-metabolic-engineering-of-plant-microbe-interactions
#19
Vishal Kumar, Mehak Baweja, Puneet K Singh, Pratyoosh Shukla
Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant-microbe interactions using gene editing and system biology tools toward the comprehension in improvement of plant traits...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27649810/differential-expressed-analysis-of-tripterygium-wilfordii-unigenes-involved-in-terpenoid-backbone-biosynthesis
#20
Jing Zhang, Yan-Bo Huo, Yan Liu, Jun-Tao Feng, Zhi-Qing Ma, Chuan-Shu Zhu, Xing Zhang
Tripterygium wilfordii Hook. f. is the traditional medicinal plants in China. Triptolide, wilforgine, and wilforine are the bioactive compounds in T. wilfordii. In this study, the contents of three metabolites and transcription levels of 21 genes involved in three metabolites biosynthesis in T. wilfordii were examined using high-performance liquid chromatography and reverse transcription PCR after application of methyl jasmonate (MeJA) on hairy roots in time course experiment (3-24 h). The results indicated that application of MeJA inhibited triptolide accumulation and promoted wilforgine and wilforine metabolites biosynthesis...
September 21, 2016: Journal of Asian Natural Products Research
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