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Flux analysis

Cheng Jin, Jianjiang Feng, Lei Wang, Heng Yu, Jiang Liu, Jiwen Lu, Jie Zhou
In this paper, we present an approach for left atrial appendage (LAA) multi-phase fast segmentation and quantitative assisted diagnosis of atrial fibrillation (AF) based on 4D-CT data. We take full advantage of the temporal dimension information to segment the living, flailed LAA based on a parametric max-flow method and graph-cut approach to build 3-D model of each phase. To assist the diagnosis of AF, we calculate the volumes of 3-D models, and then generate a "volume-phase" curve to calculate the important dynamic metrics: ejection fraction, filling flux, and emptying flux of the LAA's blood by volume...
March 9, 2018: Computers in Biology and Medicine
Juan García de la Concepción, Martín Ávalos, Pedro Cintas, José Luis Jiménez
Computational strategies have gained increasing impact in the de novo design of large molecular sets targeted to a desired application. Here, we show that DFT-assisted theoretical analyses of cycloadditions involving mesoionic dipoles and strained cycloalkynes unveil a series of unexplored mesomeric betaines as vastly superior candidates for orthogonal applications. Thus, isosydnones, thiosydnones, and a six-membered homolog in particular, 6-oxo-1,3-oxazinium-4-olate, do exhibit enhanced reactivity with respect to sydnones, the archetypal mesoionic ring employed so far in orthogonal chemistry...
March 13, 2018: Chemistry: a European Journal
Kevin W George, Mitchell Thompson, Joonhoon Kim, Edward E K Baidoo, George Wang, Veronica Teixeira Benites, Christopher J Petzold, Leanne Jade G Chan, Suzan Yilmaz, Petri Turhanen, Paul D Adams, Jay D Keasling, Taek Soon Lee
Isopentenyl pyrophosphate (IPP) toxicity presents a challenge in engineered microbial systems since its formation is unavoidable in terpene biosynthesis. In this work, we develop an experimental platform to study IPP toxicity in isoprenol-producing Escherichia coli. We first characterize the physiological response to IPP accumulation, demonstrating that elevated IPP levels are linked to growth inhibition, reduced cell viability, and plasmid instability. We show that IPP toxicity selects for pathway "breakage", using proteomics to identify a reduction in phosphomevalonate kinase (PMK) as a probable recovery mechanism...
March 9, 2018: Metabolic Engineering
Wenyou Hu, Huifeng Wang, Lurui Dong, Biao Huang, Ole K Borggaard, Hans Christian Bruun Hansen, Yue He, Peter E Holm
Intensive human activities, in particular agricultural and industrial production have led to heavy metal accumulation in the peri-urban agricultural soils of China threatening soil environmental quality and agricultural product security. A combination of spatial analysis (SA), Pb isotope ratio analysis (IRA), input fluxes analysis (IFA), and positive matrix factorization (PMF) model was successfully used to assess the status and sources of heavy metals in typical peri-urban agricultural soils from a rapidly developing region of China...
March 9, 2018: Environmental Pollution
Darragh Mullins, Derek Coburn, Louise Hannon, Edward Jones, Eoghan Clifford, Martin Glavin
Wastewater treatment facilities are continually challenged to meet both environmental regulations and reduce running costs (particularly energy and staffing costs). Improving the efficiency of operational monitoring at wastewater treatment plants (WWTPs) requires the development and implementation of appropriate performance metrics; particularly those that are easily measured, strongly correlate to WWTP performance, and can be easily automated, with a minimal amount of maintenance or intervention by human operators...
March 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Saratram Gopalakrishnan, Himadri B Pakrasi, Costas D Maranas
Completeness and accuracy of metabolic mapping models impacts the reliability of flux estimation in photoautotrophic systems. In this study, metabolic fluxes under photoautotrophic growth conditions in the widely-used cyanobacterium Synechocystis PCC 6803 are quantified by re-analyzing an existing dataset using genome-scale isotopic instationary13 C-Metabolic Flux Analysis (INST-MFA). The reconstructed carbon mapping model imSyn617 and implemented algorithmic updates afforded an approximately 48% reduction in computation time...
March 8, 2018: Metabolic Engineering
Erzsebet Polyak, Julian Ostrovsky, Min Peng, Stephen D Dingley, Mai Tsukikawa, Young Joon Kwon, Shana E McCormack, Michael Bennett, Rui Xiao, Christoph Seiler, Zhe Zhang, Marni J Falk
Oxidative stress is a known contributing factor in mitochondrial respiratory chain (RC) disease pathogenesis. Yet, no efficient means exists to objectively evaluate the comparative therapeutic efficacy or toxicity of different antioxidant compounds empirically used in human RC disease. We postulated that pre-clinical comparative analysis of diverse antioxidant drugs having suggested utility in primary RC disease using animal and cellular models of RC dysfunction may improve understanding of their integrated effects and physiologic mechanisms, and enable prioritization of lead antioxidant molecules to pursue in human clinical trials...
February 23, 2018: Molecular Genetics and Metabolism
Weilu Lin, Zejian Wang, Mingzhi Huang, Yingping Zhuang, Siliang Zhang
The isotopically non-stationary 13C labelling experiments, as an emerging experimental technique, can estimate the intracellular fluxes of the cell culture under an isotopic transient period. However, to the best of our knowledge, the issue of the structural identifiability analysis of non-stationary isotope experiments is not well addressed in the literature. In this work, the local structural identifiability analysis for non-stationary cumomer balance equations is conducted based on the Taylor series approach...
March 8, 2018: Mathematical Biosciences
Jiangpei Han, Liangsheng Shi, Yakun Wang, Zhuowei Chen, Laosheng Wu
Anaerobic batch experiments were conducted to study the regulatory role of endogenous iron in greenhouse gas emissions under intensive nitrogen fertilization in subtropical soils of China. Fe2+ , Fe3+ , and NO3 - -N dynamics and N2 O, CH4 , and CO2 emissions, as well as the relationships between N fertilizer, endogenous iron, and greenhouse gas emissions were investigated. The emissions of N2 O increased to different extents from all the test soils by N1 (260 mg N kg-1 ) application compared with N0. After 24 days of anaerobic incubation, the cumulative emissions of N2 O from red soils in De'an (DR) were significantly higher than that from paddy soils in De'an (DP) and Qujialing (QP) under N1...
March 10, 2018: Environmental Science and Pollution Research International
Shenglin Weng, Yiping Li, Jin Wei, Wei Du, Xiaomeng Gao, Wencai Wang, Jianwei Wang, Kumud Acharya, Liancong Luo
The identification of coherent structures is very important in investigating the sediment transport mechanism and controlling the eutrophication in shallow lakes. This study analyzed the turbulence characteristics and the sensitivity of quadrant analysis to threshold level. Simultaneous in situ measurements of velocities and suspended sediment concentration (SSC) were conducted in Lake Taihu with acoustic Doppler velocimeter (ADV) and optical backscatter sensor (OBS) instruments. The results show that the increase in hole size makes the difference between dominant and non-dominant events more distinct...
March 10, 2018: Environmental Science and Pollution Research International
Howard Ramirez-Malule, Stefan Junne, Mariano Nicolás Cruz-Bournazou, Peter Neubauer, Rigoberto Ríos-Estepa
Clavulanic acid (CA) is produced by Streptomyces clavuligerus (S. clavuligerus) as a secondary metabolite. Knowledge about the carbon flux distribution along the various routes that supply CA precursors would certainly provide insights about metabolic performance. In order to evaluate metabolic patterns and the possible accumulation of tricarboxylic acid (TCA) cycle intermediates during CA biosynthesis, batch and subsequent continuous cultures with steadily declining feed rates were performed with glycerol as the main substrate...
March 9, 2018: Applied Microbiology and Biotechnology
Yi Ern Cheah, Jamey D Young
Typically,13 C flux analysis relies on assumptions of both metabolic and isotopic steady state. If metabolism is steady but isotope labeling is not allowed to fully equilibrate, isotopically nonstationary metabolic flux analysis (INST-MFA) can be used to estimate fluxes. This requires solution of differential equations that describe the time-dependent labeling of network metabolites, while iteratively adjusting the flux and pool size parameters to match the transient labeling measurements. INST-MFA holds a number of unique advantages over approaches that rely solely upon steady-state isotope enrichments...
March 6, 2018: Current Opinion in Biotechnology
Brett G Olivier, Frank T Bergmann
Constraint-based modeling is a well established modeling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size and complexity such steady-state flux models are, typically, analyzed using constraint-based optimization techniques, for example, flux balance analysis (FBA). The Flux balance constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modeling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing...
March 9, 2018: Journal of Integrative Bioinformatics
Xiaomei Liu, Qing Zhang, Weixiao Wang, Dongjiao Zuo, Jing Wang, Feng Zhou, Liping Niu, Xiangyang Li, Suping Qin, Yanbo Kou, Fanyun Kong, Wei Pan, Yugang Wang, Dianshuai Gao, Hong Sun, Jessica M Meves, Kuiyang Zheng, Renxian Tang
BACKGROUND/AIMS: Multiple sclerosis (MS) is an autoimmune disease in the central nervous system associated with demyelination and axonal injury. Astrocyte activation is involved in the pathogenesis of MS and experimental autoimmune encephalomyelitis (EAE), an animal model of MS. This study was designed to find potential lncRNAs in EAE mice and activated astrocytes. METHODS: we performed microarray analysis of lncRNAs from the brain tissues of EAE mice and primary mouse astrocytes treated with IL-9(50 ng/ml)...
March 2, 2018: Cellular Physiology and Biochemistry
Fan Yang, Johnson Efome, Dipak Rana, Takeshi Matsuura, Christopher Lan
Among other applications, metal-organic frameworks (MOFs) are slowly gaining grounds as fillers for desalination composite membranes. In this study, superhydrophobic poly (vinylidene fluoride) (PVDF) nanofibrous membranes were fabricated with MOF (Iron-BTC) loading of up to 5 wt.% via electro-spinning on a nonwoven substrate. To improve attachment of nanofibers unto the substrate, a substrate pre-treatment method called 'solvent basing' was employed. Iron content in the nanofiber, measured by dispersive X-ray spectroscopy (EDS), increased proportionally with the increase of MOF concentration in the spinning dope, indicating a uniform distribution of MOF in the nanofiber...
March 8, 2018: ACS Applied Materials & Interfaces
Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Jorge M Arevalillo, Mariana Díaz-Almirón, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Hilario Navarro, Rosa Aras-López, Irene Dapía, Rocío López-Vacas, Paolo Nanni, Sara Llorente-Armijo, Pedro Arias, Alberto M Borobia, Paloma Maín, Jaime Feliú, Enrique Espinosa, Juan Ángel Fresno Vara
Metabolic reprogramming is a hallmark of cancer. It has been described that breast cancer subtypes present metabolism differences and this fact enables the possibility of using metabolic inhibitors as targeted drugs in specific scenarios. In this study, breast cancer cell lines were treated with metformin and rapamycin, showing a heterogeneous response to treatment and leading to cell cycle disruption. The genetic causes and molecular effects of this differential response were characterized by means of SNP genotyping and mass spectrometry-based proteomics...
February 9, 2018: Oncotarget
Achim Dickmanns, Christopher P Zschiedrich, Johannes Arens, Iwan Parfentev, Jan Gundlach, Romina Hofele, Piotr Neumann, Henning Urlaub, Boris Görke, Ralf Ficner, Jorg Stulke
Utilization of energy-rich carbon sources such as glucose is fundamental to the evolutionary success of bacteria. Glucose can be catabolized via glycolysis for feeding the intermediary metabolism. The methylglyoxal synthase MgsA produces methylglyoxal from the glycolytic intermediate dihydroxyacetone phosphate. Methylglyoxal is toxic, requiring stringent regulation of MgsA activity. In the Gram-positive bacterium Bacillus subtilis , an interaction with the phosphoprotein Crh controls MgsA activity. In the absence of preferred carbon sources, Crh is present in the nonphosphorylated state and binds to and thereby inhibits MgsA...
March 7, 2018: Journal of Biological Chemistry
Sarah J Mitchell, Michel Bernier, Miguel A Aon, Sonia Cortassa, Eun Young Kim, Evandro F Fang, Hector H Palacios, Ahmed Ali, Ignacio Navas-Enamorado, Andrea Di Francesco, Tamzin A Kaiser, Tyler B Waltz, Ning Zhang, James L Ellis, Peter J Elliott, David W Frederick, Vilhelm A Bohr, Mark S Schmidt, Charles Brenner, David A Sinclair, Anthony A Sauve, Joseph A Baur, Rafael de Cabo
The role in longevity and healthspan of nicotinamide (NAM), the physiological precursor of NAD+ , is elusive. Here, we report that chronic NAM supplementation improves healthspan measures in mice without extending lifespan. Untargeted metabolite profiling of the liver and metabolic flux analysis of liver-derived cells revealed NAM-mediated improvement in glucose homeostasis in mice on a high-fat diet (HFD) that was associated with reduced hepatic steatosis and inflammation concomitant with increased glycogen deposition and flux through the pentose phosphate and glycolytic pathways...
March 6, 2018: Cell Metabolism
Jingjing Dai, Yong Liang, Honglin Li, Wubi Zhou, Bing Wang, Aijia Gong, Rongbo Zhang
The role of vitamin D in the regulation of lung immune defense and inflammatory response has attracted more and more attention. Vitamin D deficiency is closely related to respiratory tract infections. However, few studies have elucidated the mechanism of vitamin D deficiency on host pulmonary resistance to Aspergillus fumigatus ( A. fumigatus ). In this paper, the role of autophagy and Treg regulation in the treatment of rat models of A. fumigatus infection with vitamin D was investigated. We intratracheally injected the A...
2018: American Journal of Translational Research
Zhi Li, Yu Wang, Linling Wang, Zeyang Zhou
BACKGROUND: Microsporidia are a group of eukaryotic intracellular parasites that infect almost all vertebrates and invertebrates. However, there is little information available of how microsporidia obtain nutrients and energy from host cells. The purpose of this study was to investigate the energy and material requirements of Nosema bombycis for the invasion procedure through analyzing the global variation of the gene expression, protein abundance, fatty acids level and ATP flux induced by the microsporidia N...
March 6, 2018: Parasites & Vectors
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