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Flux analysis

I R MacDonald, O Garcia-Pineda, A Beet, S Daneshgar Asl, L Feng, G Graettinger, D French-McCay, J Holmes, C Hu, F Huffer, I Leifer, F Muller-Karger, A Solow, M Silva, G Swayze
When wind speeds are 2-10 m s(-1), reflective contrasts in the ocean surface make oil slicks visible to synthetic aperture radar (SAR) under all sky conditions. Neural network analysis of satellite SAR images quantified the magnitude and distribution of surface oil in the Gulf of Mexico from persistent, natural seeps and from the Deepwater Horizon (DWH) discharge. This analysis identified 914 natural oil seep zones across the entire Gulf of Mexico in pre-2010 data. Their ∼0.1 µm slicks covered an aggregated average of 775 km(2)...
December 2015: Journal of Geophysical Research. Oceans
Eric H Wilson, Sushil K Atreya, Ralf I Kaiser, Paul R Mahaffy
Recent observations of the Martian surface by the Phoenix lander and the Sample Analysis at Mars indicate the presence of perchlorate (ClO4(-)). The abundance and isotopic composition of these perchlorates suggest that the mechanisms responsible for their formation in the Martian environment may be unique in our solar system. With this in mind, we propose a potential mechanism for the production of Martian perchlorate: the radiolysis of the Martian surface by galactic cosmic rays, followed by the sublimation of chlorine oxides into the atmosphere and their subsequent synthesis to form perchloric acid (HClO4) in the atmosphere, and the surface deposition and subsequent mineralization of HClO4 in the regolith to form surface perchlorates...
August 2016: Journal of Geophysical Research. Planets
Akos A Gerencser, Shona A Mookerjee, Martin Jastroch, Martin D Brand
Analysis of the cellular mechanisms of metabolic disorders, including type 2 diabetes mellitus, is complicated by the large number of reactions and interactions in metabolic networks. Metabolic control analysis with appropriate modularization is a powerful method for simplifying and analyzing these networks. To analyze control of cellular energy metabolism in adherent cell cultures of the INS-1832/13 pancreatic β-cell model we adapted our microscopy assay of absolute mitochondrial membrane potential (ΔψM) to a fluorescence microplate reader format, and applied it in conjunction with cell respirometry...
October 20, 2016: Biochimica et Biophysica Acta
Andrew J Loder, Yejun Han, Aaron B Hawkins, Hong Lian, Gina L Lipscomb, Gerrit J Schut, Matthew W Keller, Michael W W Adams, Robert M Kelly
The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle fixes CO2 in extremely thermoacidophilic archaea and holds promise for metabolic engineering because of its thermostability and potentially rapid pathway kinetics. A reaction kinetics model was developed to examine the biological and biotechnological attributes of the 3HP/4HB cycle as it operates in Metallosphaera sedula, based on previous information as well as on kinetic parameters determined here for recombinant versions of five of the cycle enzymes (malonyl-CoA/succinyl-CoA reductase, 3-hydroxypropionyl-CoA synthetase, 3-hydroxypropionyl-CoA dehydratase, acryloyl-CoA reductase, and succinic semialdehyde reductase)...
October 19, 2016: Metabolic Engineering
M J de Veth, V M Artegoitia, S R Campagna, H Lapierre, F Harte, C L Girard
The metabolites of choline have a central role in many mammalian biological processes, and choline supplementation to the periparturient dairy cow improves hepatic lipid metabolism. However, variability in responses to choline supplementation has highlighted a lack of understanding of choline absorption in the lactating dairy cow. Our objective was to determine net choline absorption by measuring net portal fluxes of choline and choline metabolites in cows receiving either dietary supplements of rumen-protected choline (RPC) or abomasal delivery of choline (ADC)...
October 19, 2016: Journal of Dairy Science
Ana M Denis-Bacelar, Sarah J Chittenden, David P Dearnaley, Antigoni Divoli, Joe M O'Sullivan, V Ralph McCready, Bernadette Johnson, Yong Du, Glenn D Flux
PURPOSE: To investigate the role of patient-specific dosimetry as a predictive marker of survival and as a potential tool for individualised molecular radiotherapy treatment planning of bone metastases from castration-resistant prostate cancer, and to assess whether higher administered levels of activity are associated with a survival benefit. METHODS: Clinical data from 57 patients who received 2.5-5.1 GBq of (186)Re-HEDP as part of NIH-funded phase I/II clinical trials were analysed...
October 21, 2016: European Journal of Nuclear Medicine and Molecular Imaging
Sayed-Rzgar Hosseini, Andreas Wagner
BACKGROUND: Biological systems are rife with examples of pre-adaptations or exaptations. They range from the molecular scale - lens crystallins, which originated from metabolic enzymes - to the macroscopic scale, such as feathers used in flying, which originally served thermal insulation or waterproofing. An important class of exaptations are novel and useful traits with non-adaptive origins. Whether such origins could be frequent cannot be answered with individual examples, because it is a question about a biological system's potential for exaptation...
October 21, 2016: BMC Systems Biology
H Abdalla, A Abramowski, F Aharonian, F Ait Benkhali, A G Akhperjanian, T Andersson, E O Angüner, M Arrieta, P Aubert, M Backes, A Balzer, M Barnard, Y Becherini, J Becker Tjus, D Berge, S Bernhard, K Bernlöhr, E Birsin, R Blackwell, M Böttcher, C Boisson, J Bolmont, P Bordas, J Bregeon, F Brun, P Brun, M Bryan, T Bulik, M Capasso, J Carr, S Casanova, N Chakraborty, R Chalme-Calvet, R C G Chaves, A Chen, J Chevalier, M Chrétien, S Colafrancesco, G Cologna, B Condon, J Conrad, C Couturier, Y Cui, I D Davids, B Degrange, C Deil, J Devin, P deWilt, A Djannati-Ataï, W Domainko, A Donath, L O'C Drury, G Dubus, K Dutson, J Dyks, M Dyrda, T Edwards, K Egberts, P Eger, J-P Ernenwein, S Eschbach, C Farnier, S Fegan, M V Fernandes, A Fiasson, G Fontaine, A Förster, S Funk, M Füßling, S Gabici, M Gajdus, Y A Gallant, T Garrigoux, G Giavitto, B Giebels, J F Glicenstein, D Gottschall, A Goyal, M-H Grondin, M Grudzińska, D Hadasch, J Hahn, J Hawkes, G Heinzelmann, G Henri, G Hermann, O Hervet, A Hillert, J A Hinton, W Hofmann, C Hoischen, M Holler, D Horns, A Ivascenko, A Jacholkowska, M Jamrozy, M Janiak, D Jankowsky, F Jankowsky, M Jingo, T Jogler, L Jouvin, I Jung-Richardt, M A Kastendieck, K Katarzyński, U Katz, D Kerszberg, B Khélifi, M Kieffer, J King, S Klepser, D Klochkov, W Kluźniak, D Kolitzus, Nu Komin, K Kosack, S Krakau, M Kraus, F Krayzel, P P Krüger, H Laffon, G Lamanna, J Lau, J-P Lees, J Lefaucheur, V Lefranc, A Lemière, M Lemoine-Goumard, J-P Lenain, E Leser, R Liu, T Lohse, M Lorentz, I Lypova, V Marandon, A Marcowith, C Mariaud, R Marx, G Maurin, N Maxted, M Mayer, P J Meintjes, M Meyer, A M W Mitchell, R Moderski, M Mohamed, K Morå, E Moulin, T Murach, M de Naurois, F Niederwanger, J Niemiec, L Oakes, P O'Brien, H Odaka, S Ohm, M Ostrowski, S Öttl, I Oya, M Padovani, M Panter, R D Parsons, M Paz Arribas, N W Pekeur, G Pelletier, C Perennes, P-O Petrucci, B Peyaud, S Pita, H Poon, D Prokhorov, H Prokoph, G Pühlhofer, M Punch, A Quirrenbach, S Raab, A Reimer, O Reimer, M Renaud, R de Los Reyes, F Rieger, C Romoli, S Rosier-Lees, G Rowell, B Rudak, C B Rulten, V Sahakian, D Salek, D A Sanchez, A Santangelo, M Sasaki, R Schlickeiser, F Schüssler, A Schulz, U Schwanke, S Schwemmer, M Settimo, A S Seyffert, N Shafi, I Shilon, R Simoni, H Sol, F Spanier, G Spengler, F Spies, Ł Stawarz, R Steenkamp, C Stegmann, F Stinzing, K Stycz, I Sushch, J-P Tavernet, T Tavernier, A M Taylor, R Terrier, L Tibaldo, M Tluczykont, C Trichard, R Tuffs, J van der Walt, C van Eldik, B van Soelen, G Vasileiadis, J Veh, C Venter, A Viana, P Vincent, J Vink, F Voisin, H J Völk, T Vuillaume, Z Wadiasingh, S J Wagner, P Wagner, R M Wagner, R White, A Wierzcholska, P Willmann, A Wörnlein, D Wouters, R Yang, V Zabalza, D Zaborov, M Zacharias, A A Zdziarski, A Zech, F Zefi, A Ziegler, N Żywucka
: A search for dark matter linelike signals iss performed in the vicinity of the Galactic Center by the H.E.S.S. experiment on observational data taken in 2014. An unbinned likelihood analysis iss developed to improve the sensitivity to linelike signals. The upgraded analysis along with newer data extend the energy coverage of the previous measurement down to 100 GeV. The 18 h of data collected with the H.E.S.S. array allow one to rule out at 95% C.L. the presence of a 130 GeV line (at l=-1...
October 7, 2016: Physical Review Letters
Bhavisha Bakrania, Joey P Granger, Romain Harmancey
The mammalian heart is a major consumer of ATP and requires a constant supply of energy substrates for contraction. Not surprisingly, alterations of myocardial metabolism have been linked to the development of contractile dysfunction and heart failure. Therefore, unraveling the link between metabolism and contraction should shed light on some of the mechanisms governing cardiac adaptation or maladaptation in disease states. The isolated working rat heart preparation can be used to follow, simultaneously and in real time, cardiac contractile function and flux of energy providing substrates into oxidative metabolic pathways...
September 28, 2016: Journal of Visualized Experiments: JoVE
Joan Yw Liu, Cheryl Reeves, Beate Diehl, Antonietta Coppola, Aliya Al-Hajri, Chandrashekar Hoskote, Salim Al Mughairy, Mohamed Tachrount, Michael Groves, Zuzanna Michalak, Kevin Mills, Andrew W McEvoy, Anna Miserocchi, Sanjay M Sisodiya, Maria Thom
OBJECTIVE: This study reports on a novel brain pathology in young patients with Frontal Lobe Epilepsy that is distinct from Focal Cortical Dysplasia. METHODS: Surgical specimens from twenty young adults with frontal lobe epilepsy (mean age, 30 years) were investigated with histological/immunohistochemical markers for cortical laminar architecture, mammalian target of rapamycin pathway activation and inhibition, cellular autophagy, and synaptic vesicle-mediated trafficking as well as proteomics analysis...
October 20, 2016: Annals of Neurology
Teresa Delgado-Goni, Maria Falck Miniotis, Slawomir Wantuch, Harold G Parkes, Richard Marais, Paul Workman, Martin O Leach, Mounia Beloueche-Babari
Understanding the impact of BRAF signaling inhibition in human melanoma on key disease mechanisms is important for developing biomarkers of therapeutic response and combination strategies to improve long term disease control. This work investigates the downstream metabolic consequences of BRAF inhibition with vemurafenib, the molecular and biochemical processes that underpin them, their significance for antineoplastic activity and potential as non-invasive imaging response biomarkers.(1)H NMR spectroscopy showed that vemurafenib decreases the glycolytic activity of BRAF mutant (WM266...
October 7, 2016: Molecular Cancer Therapeutics
Sebastian Sippel, Holger Lange, Miguel D Mahecha, Michael Hauhs, Paul Bodesheim, Thomas Kaminski, Fabian Gans, Osvaldo A Rosso
Data analysis and model-data comparisons in the environmental sciences require diagnostic measures that quantify time series dynamics and structure, and are robust to noise in observational data. This paper investigates the temporal dynamics of environmental time series using measures quantifying their information content and complexity. The measures are used to classify natural processes on one hand, and to compare models with observations on the other. The present analysis focuses on the global carbon cycle as an area of research in which model-data integration and comparisons are key to improving our understanding of natural phenomena...
2016: PloS One
Xiangbin Song, Zifa Li, Fei Liu, Zhenyong Wang, Lin Wang
Previous study has demonstrated that puerarin (PU) exerts nephroprotective effect against Pb-induced cytotoxicity in primary rat proximal tubular (rPT) cells. Autophagy can protect cells from various cytotoxic stimuli, but its role in the process of PU against Pb-induced nephrotoxicity is still unknown. This study aims to investigate whether PU can alleviate Pb-induced renal damage by recovering autophagy. Data showed that Pb inhibited the autophagic flux, as evidenced by the accumulation of LC3-II and p62 as well as the confocal microscopy analysis of GFP-LC3 puncta and punctate spots of monodansylcadaverine staining, whereas coadministration of PU could restore Pb-induced autophagy inhibition...
October 20, 2016: Journal of Biochemical and Molecular Toxicology
Amit Ghosh, David Ando, Jennifer Gin, Weerawat Runguphan, Charles Denby, George Wang, Edward E K Baidoo, Chris Shymansky, Jay D Keasling, Héctor García Martín
Efficient redirection of microbial metabolism into the abundant production of desired bioproducts remains non-trivial. Here, we used flux-based modeling approaches to improve yields of fatty acids in Saccharomyces cerevisiae. We combined (13)C labeling data with comprehensive genome-scale models to shed light onto microbial metabolism and improve metabolic engineering efforts. We concentrated on studying the balance of acetyl-CoA, a precursor metabolite for the biosynthesis of fatty acids. A genome-wide acetyl-CoA balance study showed ATP citrate lyase from Yarrowia lipolytica as a robust source of cytoplasmic acetyl-CoA and malate synthase as a desirable target for downregulation in terms of acetyl-CoA consumption...
2016: Frontiers in Bioengineering and Biotechnology
Hu Ningjing, Huang Peng, Zhang Hui, Wang Xiaojing, Zhu Aimei, Liu Jihua, Shi Xuefa
Geochemical sources, spatio-temporal distribution, and associated environmental risk of Cd in the Bohai Sea were investigated using data from 405 surface sediment samples and two sediment cores. Local point Cd sources, TOC content, and currents are the main controlling factors of Cd distribution. The contribution of Cd from river discharge surpasses that from atmospheric deposition. Sediment-quality guidelines, enrichment factors, and chemical fraction analysis were used to assess metal toxicity in the collected sediments...
October 18, 2016: Environmental Science and Pollution Research International
Bernardo Duarte, Maria Teresa Cabrita, Carla Gameiro, Ana Rita Matos, Rita Godinho, João Carlos Marques, Isabel 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
Jeong Wook Lee, Jongho Yi, Tae Yong Kim, Sol Choi, Jung Ho Ahn, Hyohak Song, Moon-Hee Lee, Sang Yup Lee
Succinic acid (SA) is a four carbon dicarboxylic acid of great industrial interest that can be produced by microbial fermentation. Here we report development of a high-yield homo-SA producing Mannheimia succiniciproducens strain by metabolic engineering. The PALFK strain (ldhA(-), pta(-), ackA(-), fruA(-)) was developed based on optimization of carbon flux towards SA production while minimizing byproducts formation through the integrated application of in silico genome-scale metabolic flux analysis, omics analyses, and reconstruction of central carbon metabolism...
October 13, 2016: Metabolic Engineering
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)
Yo Sasaki, Takashi Nakagawa, Xianrong Mao, Aaron DiAntonio, Jeffrey Milbrandt
Overexpression of the NAD(+) biosynthetic enzyme NMNAT1 leads to preservation of injured axons. While increased NAD(+) or decreased NMN levels are thought to be critical to this process, the mechanism(s) of this axon protection remain obscure. Using steady-state and flux analysis of NAD(+) metabolites in healthy and injured mouse dorsal root ganglion axons, we find that rather than altering NAD(+) synthesis, NMNAT1 instead blocks the injury-induced, SARM1-dependent NAD(+) consumption that is central to axon degeneration...
October 13, 2016: ELife
Titus S van Erp, Mahmoud Moqadam, Enrico Riccardi, Anders Lervik
We introduce an approach to analyze collective variables regarding their predictive power for a reaction. The method is based on already available path sampling data produced by for instance transition interface sampling or forward flux sampling which are path sampling methods used for efficient computation of reaction rates. By a search in collective variable space a measure of predic- tiveness can be optimized and, in addition, the number of collective variables can be reduced using projection operations which keep this measure invariant...
October 12, 2016: Journal of Chemical Theory and Computation
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