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https://www.readbyqxmd.com/read/28342406/phase-change-heat-transfer-during-cryosurgery-of-lung-cancer-using-hyperbolic-heat-conduction-model
#1
Ajay Kumar, Sushil Kumar, V K Katiyar, Shirley Telles
The paper reports a numerical study of phase change heat transfer process in lung cancer undergoing cryosurgery. A two dimensional hyperbolic bio-heat model with non-ideal property of tissue, blood perfusion and metabolism is used to analyze the problem. The governing equations are solved by finite difference method based on enthalpy formulation. Effects of relaxation time of heat flux in hyperbolic model on freezing process have been examined. A comparative investigation of two different models (hyperbolic and parabolic bio-heat models) is also presented...
March 16, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28338935/impact-of-the-ion-transportome-of-chloroplasts-on-the-optimization-of-photosynthesis
#2
Ildikò Szabò, Cornelia Spetea
Ions play fundamental roles in all living cells, and their gradients are often essential to fuel transport, regulate enzyme activities, and transduce energy within cells. Regulation of their homeostasis is essential for cell metabolism. Recent results indicate that modulation of ion fluxes might also represent a useful strategy to regulate one of the most important physiological processes taking place in chloroplasts, photosynthesis. Photosynthesis is highly regulated, due to its unique role as a cellular engine for growth in the light...
March 13, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338755/red-blotch-disease-alters-grape-berry-development-and-metabolism-by-interfering-with-the-transcriptional-and-hormonal-regulation-of-ripening
#3
Barbara Blanco-Ulate, Helene Hopfer, Rosa Figueroa-Balderas, Zirou Ye, Rosa M Rivero, Alfonso Albacete, Francisco Pérez-Alfocea, Renata Koyama, Michael M Anderson, Rhonda J Smith, Susan E Ebeler, Dario Cantu
Grapevine red blotch-associated virus (GRBaV) is a major threat to the wine industry in the USA. GRBaV infections (aka red blotch disease) compromise crop yield and berry chemical composition, affecting the flavor and aroma properties of must and wine. In this study, we combined genome-wide transcriptional profiling with targeted metabolite analyses and biochemical assays to characterize the impact of the disease on red-skinned berry ripening and metabolism. Using naturally infected berries collected from two vineyards, we were able to identify consistent berry responses to GRBaV across different environmental and cultural conditions...
January 27, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338129/prediction-of-metabolic-fluxes-from-gene-expression-data-with-huber-penalty-convex-optimization-function
#4
Shao-Wu Zhang, Wang-Long Gou, Yan Li
As one of the critical parameters of a metabolic pathway, the metabolic flux in a metabolic network serves as an essential role in physiology and pathology. Constraint-based metabolic models are the widely used frameworks for predicting metabolic fluxes in genome-scale metabolic networks. Integrating the transcriptomic data into the constraint-based metabolic models can effectively predict context-specific fluxes across different conditions. However, these methods always need user-defined thresholds to identify the expression levels of metabolic genes or restrain the rate of biomass production, and the predictive results are sensitive to the thresholds...
March 24, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28336394/ts1cje-down-syndrome-model-mice-exhibit-environmental-stimuli-triggered-locomotor-hyperactivity-and-sociability-concurrent-with-increased-flux-through-central-dopamine-and-serotonin-metabolism
#5
Atsushi Shimohata, Keiichi Ishihara, Satoko Hattori, Hiroyuki Miyamoto, Hiromasa Morishita, Guy Ornthanalai, Matthieu Raveau, Abdul Shukkur Ebrahim, Kenji Amano, Kazuyuki Yamada, Haruhiko Sago, Satoshi Akiba, Nobuko Mataga, Niall P Murphy, Tsuyoshi Miyakawa, Kazuhiro Yamakawa
Ts1Cje mice have a segmental trisomy of chromosome 16 that is orthologous to human chromosome 21 and display Down syndrome-like cognitive impairments. Despite the occurrence of affective and emotional impairments in patients with Down syndrome, these parameters are poorly documented in Down syndrome mouse models, including Ts1Cje mice. Here, we conducted comprehensive behavioral analyses, including anxiety-, sociability-, and depression-related tasks, and biochemical analyses of monoamines and their metabolites in Ts1Cje mice...
March 20, 2017: Experimental Neurology
https://www.readbyqxmd.com/read/28335680/ampk-knockdown-in-placental-labyrinthine-progenitor-cells-results-in-restriction-of-critical-energy-resources-and-terminal-differentiation-failure
#6
Christopher A Waker, Renee E Albers, Richard L Pye, Savannah R Doliboa, Christopher N Wyatt, Thomas L Brown, Debra Ann Mayes
Placental abnormalities can cause Pregnancy-Associated Disorders including preeclampsia, intrauterine growth restriction, and placental insufficiency that result in complications for both the mother and fetus. Trophoblast cells within the labyrinthine layer of the placenta facilitate the exchange of nutrients, gases, and waste between mother and fetus; therefore, the development of this cell layer is critical for fetal development. As trophoblast cells differentiate, it is assumed their metabolism changes with their energy requirements...
March 23, 2017: Stem Cells and Development
https://www.readbyqxmd.com/read/28335577/gc-ms-metabolomic-analysis-to-reveal-the-metabolites-and-biological-pathways-involved-in-the-developmental-stages-and-tissue-response-of-panax-ginseng
#7
Jia Liu, Yang Liu, Yu Wang, Ann Abozeid, Yuan-Gang Zu, Xiao-Ning Zhang, Zhong-Hua Tang
Ginsenosides, the major compounds present in ginseng, are known to have numerous physiological and pharmacological effects. The physiological processes, enzymes and genes involved in ginsenoside synthesis in P. ginseng have been well characterized. However, relatively little information is known about the dynamic metabolic changes that occur during ginsenoside accumulation in ginseng. To explore this topic, we isolated metabolites from different tissues at different growth stages, and identified and characterized them by using gas chromatography coupled with mass spectrometry (GC-MS)...
March 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28334697/constraint-based-stoichiometric-modelling-from-single-organisms-to-microbial-communities
#8
REVIEW
Willi Gottstein, Brett G Olivier, Frank J Bruggeman, Bas Teusink
Microbial communities are ubiquitously found in Nature and have direct implications for the environment, human health and biotechnology. The species composition and overall function of microbial communities are largely shaped by metabolic interactions such as competition for resources and cross-feeding. Although considerable scientific progress has been made towards mapping and modelling species-level metabolism, elucidating the metabolic exchanges between microorganisms and steering the community dynamics remain an enormous scientific challenge...
November 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28334215/systematic-inference-of-functional-phosphorylation-events-in-yeast-metabolism
#9
Yu Chen, Yonghong Wang, Jens Nielsen
Motivation: Protein phosphorylation is a post-translational modification that affects proteins by changing their structure and conformation in a rapid and reversible way, and it is an important mechanism for metabolic regulation in cells. Phosphoproteomics enables high-throughput identification of phosphorylation events on metabolic enzymes, but identifying functional phosphorylation events still requires more detailed biochemical characterization. Therefore, development of computational methods for investigating unknown functions of a large number of phosphorylation events identified by phosphoproteomics has received increased attention...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334199/stepwise-inference-of-likely-dynamic-flux-distributions-from-metabolic-time-series-data
#10
Mojdeh Faraji, Eberhard O Voit
Motivation: Most metabolic pathways contain more reactions than metabolites and therefore have a wide stoichiometric matrix that corresponds to infinitely many possible flux distributions that are perfectly compatible with the dynamics of the metabolites in a given dataset. This under-determinedness poses a challenge for the quantitative characterization of flux distributions from time series data and thus for the design of adequate, predictive models. Here we propose a method that reduces the degrees of freedom in a stepwise manner and leads to a dynamic flux distribution that is, in a statistical sense, likely to be close to the true distribution...
March 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333921/bioenergetics-based-modeling-of-plasmodium-falciparum-metabolism-reveals-its-essential-genes-nutritional-requirements-and-thermodynamic-bottlenecks
#11
Anush Chiappino-Pepe, Stepan Tymoshenko, Meriç Ataman, Dominique Soldati-Favre, Vassily Hatzimanikatis
Novel antimalarial therapies are urgently needed for the fight against drug-resistant parasites. The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex. Computational methods can handle this complexity and allow integrative analyses of cell metabolism. In this study, we present a genome-scale metabolic model (iPfa) of the deadliest malaria parasite, Plasmodium falciparum, and its thermodynamics-based flux analysis (TFA). Using previous absolute concentration data of the intraerythrocytic parasite, we applied TFA to iPfa and predicted up to 63 essential genes and 26 essential pairs of genes...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28333226/exploring-the-human-microbiome-from-multiple-perspectives-factors-altering-its-composition-and-function
#12
David Rojo, Celia Méndez-García, Beata Anna Raczkowska, Rafael Bargiela, Andrés Moya, Manuel Ferrer, Coral Barbas
Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors...
February 25, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28332598/metabolic-flux-redirection-and-transcriptomic-reprogramming-in-the-albino-tea-cultivar-yu-jin-xiang-with-an-emphasis-on-catechin-production
#13
Guo-Feng Liu, Zhuo-Xiao Han, Lin Feng, Li-Ping Gao, Ming-Jun Gao, Margaret Y Gruber, Zhao-Liang Zhang, Tao Xia, Xiao-Chun Wan, Shu Wei
In this study, shade-induced conversion from a young pale/yellow leaf phenotype to a green leaf phenotype was studied using metabolic and transcriptomic profiling and the albino cultivar 'Yu-Jin-Xiang' ('YJX') of Camellia sinensis for a better understanding of mechanisms underlying the phenotype shift and the altered catechin and theanine production. Shaded leaf greening resulted from an increase in leaf chlorophyll and carotenoid abundance and chloroplast development. A total of 1,196 differentially expressed genes (DEGs) were identified between the 'YJX' pale and shaded green leaves, and these DEGs affected 'chloroplast organization' and 'response to high light' besides many other biological processes and pathways...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28330953/your-mitochondria-are-what-you-eat-a-high-fat-or-a-high-sucrose-diet-eliminates-metabolic-flexibility-in-isolated-mitochondria-from-rat-skeletal-muscle
#14
Wenche Jørgensen, Kasper A Rud, Ole H Mortensen, Lis Frandsen, Niels Grunnet, Bjørn Quistorff
Extreme diets consisting of either high fat (HF) or high sucrose (HS) may lead to insulin resistance in skeletal muscle, often associated with mitochondrial dysfunction. However, it is not known if these diets alter normal interactions of pyruvate and fatty acid oxidation at the level of the mitochondria. Here, we report that rat muscle mitochondria does show the normal Randle-type fat-carbohydrate interaction seen in vivo. The mechanism behind this metabolic flexibility at the level of the isolated mitochondria is a regulation of the flux-ratio: pyruvate dehydrogenase (PDH)/β-oxidation to suit the actual substrate availability, with the PDH flux as the major point of regulation...
March 2017: Physiological Reports
https://www.readbyqxmd.com/read/28329733/comparison-of-transcriptional-expression-patterns-of-carotenoid-metabolism-in-cabernet-sauvignon-grapes-from-two-regions-with-distinct-climate
#15
Wei-Kai Chen, Ke-Ji Yu, Bin Liu, Yi-Bin Lan, Run-Ze Sun, Qiang Li, Fei He, Qiu-Hong Pan, Chang-Qing Duan, Jun Wang
The downstream flux of carotenoid metabolism in grape berries includes the biosynthesis of norisoprenoids, a group of important aroma compounds, and the production of ABA, a well-known plant hormone. This study focused on the transcriptional profiling comparison of genes participating in the biosynthesis of carotenoids, norisoprenoids, and ABA in Vitis vinifera 'Cabernet Sauvignon' grapes at pea size, veraison, and ripening stages. The grapes were obtained from Changli (CL, eastern China) and Gaotai (GT, western China) regions and analyzed using RNA-sequencing technology...
March 9, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28325918/robust-analysis-of-fluxes-in-genome-scale-metabolic-pathways
#16
Michael MacGillivray, Amy Ko, Emily Gruber, Miranda Sawyer, Eivind Almaas, Allen Holder
Constraint-based optimization, such as flux balance analysis (FBA), has become a standard systems-biology computational method to study cellular metabolisms that are assumed to be in a steady state of optimal growth. The methods are based on optimization while assuming (i) equilibrium of a linear system of ordinary differential equations, and (ii) deterministic data. However, the steady-state assumption is biologically imperfect, and several key stoichiometric coefficients are experimentally inferred from situations of inherent variation...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325659/construction-of-a-novel-d-lactate-producing-pathway-from-dihydroxyacetone-phosphate-of-the-calvin-cycle-in-cyanobacterium-synechococcus-elongatus-pcc%C3%A2-7942
#17
Yasutaka Hirokawa, Ryota Goto, Yoshitaka Umetani, Taizo Hanai
Using engineered cyanobacteria to produce various chemicals from carbon dioxide is a promising technology for a sustainable future. Lactate is a valuable commodity that can be used for the biodegradable plastic, polylactic acid. Typically, lactate production using engineered cyanobacteria was via the conversion of pyruvate in glycolysis by lactate dehydrogenase. In cyanobacteria, the metabolic flux in the Calvin cycle is higher than that in glycolysis under photoautotrophic conditions. The construction of a novel lactate producing pathway that uses metabolites from the Calvin cycle could potentially increase lactate productivity in cyanobacteria...
March 18, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28324488/flow-cytometer-monitoring-of-bnip3-and-bnip3l-nix-dependent-mitophagy
#18
Matilda Šprung, Ivan Dikic, Ivana Novak
Mitochondria are organelles with numerous vital roles in cellular metabolism. Impaired or damaged mitochondria are degraded in autophagolysosomes in a process known as mitophagy. Given the fundamental role of mitophagy in maintenance of cellular homeostasis, methods and techniques with which to study this process are constantly evolving and emerging. So far, mitophagy flux was mostly monitored using fluorescently labeled LC3 protein on autophagosomal membrane and any of the labeled outer mitochondrial membrane proteins...
March 22, 2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28323016/identifying-the-shared-metabolic-objectives-of-glycerol-bioconversion-in-klebsiella-pneumoniae-under-different-culture-conditions
#19
Gongxian Xu, Caixia Li
This paper addresses the problem of identifying the shared metabolic objectives of glycerol bioconversion in Klebsiella pneumoniae for production of 1,3-propanediol (1,3-PD) under different culture conditions. To achieve this goal, we propose a multi-level programming model. This model includes three optimization problems, where the constraint region of the first level problem is implicitly determined by the other two optimization problems. The optimized objectives of the first and second level problems are to minimize the set of fluxes that are of major importance to glycerol metabolism and the difference between the observed fluxes and those computed by the model, respectively...
March 18, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28321334/the-interpretation-of-cholesterol-balance-derived-synthesis-data-and-surrogate-noncholesterol-plasma-markers-for-cholesterol-synthesis-under-lipid-lowering-therapies
#20
REVIEW
Frans Stellaard, Dieter Lütjohann
The cholesterol balance procedure allows the calculation of cholesterol synthesis based on the assumption that loss of endogenous cholesterol via fecal excretion and bile acid synthesis is compensated by de novo synthesis. Under ezetimibe therapy hepatic cholesterol is diminished which can be compensated by hepatic de novo synthesis and hepatic extraction of plasma cholesterol. The plasma lathosterol concentration corrected for total cholesterol concentration (R_Lath) as a marker of de novo cholesterol synthesis is increased during ezetimibe treatment but unchanged under treatment with ezetimibe and simvastatin...
2017: Cholesterol
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