keyword
MENU ▼
Read by QxMD icon Read
search

Flux analysis

keyword
https://www.readbyqxmd.com/read/28098205/reliable-and-efficient-solution-of-genome-scale-models-of-metabolism-and-macromolecular-expression
#1
Ding Ma, Laurence Yang, Ronan M T Fleming, Ines Thiele, Bernhard O Palsson, Michael A Saunders
Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many orders of magnitude. Data values also have greatly varying magnitudes. Standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME models have 70,000 constraints and variables and will grow larger)...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28095693/solvation-dynamics-in-liquid-water-iii-energy-fluxes-and-structural-changes
#2
Rossend Rey, James T Hynes
In previous installments it has been shown how a detailed analysis of energy fluxes induced by electronic excitation of a solute can provide a quantitative understanding of the dominant molecular energy flow channels characterizing solvation---and in particular, hydration--- relaxation dynamics. Here this work and power approach is complemented with a detailed characterization of the changes induced by such energy fluxes. We first examine the water solvent's spatial and orientational distributions and the assorted energy fluxes in the various hydration shells of the solute to provide a molecular picture of the relaxation...
January 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28093899/crucial-role-of-donor-density-in-the-performance-of-oxynitride-perovskite-latio2n-for-photocatalytic-water-oxidation-reaction
#3
Feng-Qiang Xiong, Lipeng Wan, Yue Li, Tiju Thomas, Francis Joseph DiSalvo, Minghui Yang
LaTiO2N photocatalysts were prepared via thermal ammonalysis of flux-synthesized La2Ti2O7 and La2TiO5, and were investigated for water oxidation. Though LaTiO2N derived from La2TiO5 appears defect-free in UV-Vis-NIR and electron paramagnetic resonance spectroscopies, its performance is much lower than conventional La2Ti2O7-derived LaTiO2N with defects. It is shown by Mott-Schottky analysis that La2TiO5-derived LaTiO2N has significantly lower donor density; this can result in insufficient build-in electric field for the separation of photogenerated electrons and holes...
January 17, 2017: ChemSusChem
https://www.readbyqxmd.com/read/28093405/distributedfba-jl-high-level-high-performance-flux-balance-analysis-in-julia
#4
Laurent Heirendt, Ines Thiele, Ronan M T Fleming
MOTIVATION: Flux balance analysis, and its variants, are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. RESULTS: DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes...
January 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28092823/ph-lactate-and-hypoxia-reciprocity-in-regulating-high-affinity-monocarboxylate-transporter-expression-in-glioblastoma
#5
James P Caruso, Brandon J Koch, Philip D Benson, Elsa Varughese, Michael D Monterey, Amy E Lee, Ajal M Dave, Sam Kiousis, Andrew E Sloan, Saroj P Mathupala
Highly malignant brain tumors harbor the aberrant propensity for aerobic glycolysis, the excessive conversion of glucose to lactic acid even in the presence of ample tissue oxygen. Lactic acid is rapidly effluxed to the tumor microenvironment via a group of plasma-membrane transporters denoted monocarboxylate transporters (MCTs) to prevent "self-poisoning." One isoform, MCT2, has the highest affinity for lactate and thus should have the ability to respond to microenvironment conditions such as hypoxia, lactate, and pH to help maintain high glycolytic flux in the tumor...
January 13, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28088694/metabolic-network-modeling-with-model-organisms
#6
REVIEW
L Safak Yilmaz, Albertha Jm Walhout
Flux balance analysis (FBA) with genome-scale metabolic network models (GSMNM) allows systems level predictions of metabolism in a variety of organisms. Different types of predictions with different accuracy levels can be made depending on the applied experimental constraints ranging from measurement of exchange fluxes to the integration of gene expression data. Metabolic network modeling with model organisms has pioneered method development in this field. In addition, model organism GSMNMs are useful for basic understanding of metabolism, and in the case of animal models, for the study of metabolic human diseases...
January 12, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28088059/infrared-analysis-of-clay-bricks-incorporated-with-spent-shea-waste-from-the-shea-butter-industry
#7
A N Adazabra, G Viruthagiri, N Shanmugam
The peculiar challenge of effective disposing abundant spent shea waste and the excellent compositional variation tolerance of clay material offered an impetus to examine the incorporation of spent shea waste into clay material as an eco-friendly disposal route in making clay bricks. For this purpose, the chemical constituent, mineralogical compositions and thermal behavior of both clay material and spent shea waste were initially characterized from which modelled brick specimens incorporating 5-20 wt% of the waste into the clay material were prepared...
January 11, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28087530/pgas-a-low-ph-induced-promoter-as-a-dynamic-gene-expression-control-tool-for-the-metabolic-engineering-of-aspergillus-niger
#8
Xian Yin, Hyun-Dong Shin, Jianghua Li, Guocheng Du, Long Liu, Jian Chen
: The dynamic control of gene expression is important for adjusting fluxes in order to obtain desired products and achieve appropriate cell growth, particularly when the synthesis of a desired product drains metabolites required for cell growth. For dynamic gene expression, a promoter responsive to a particular environmental stressor is vital. Here, we report a low pH-inducible promoter, Pgas, which promotes minimal gene expression at pH values of greater than 5.0, but functioned efficiently at low pH values, such as pH 2...
January 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28087332/exo-mfa-a-13c-metabolic-flux-analysis-to-dissect-tumor-microenvironment-secreted-exosome-contributions-towards-cancer-cell-metabolism
#9
Abhinav Achreja, Hongyun Zhao, Lifeng Yang, Tae Hyun Yun, Juan Marini, Deepak Nagrath
Dissecting the pleiotropic roles of tumor micro-environment (TME) on cancer progression has been brought to the foreground of research on cancer pathology. Extracellular vesicles such as exosomes, transport proteins, lipids, and nucleic acids, to mediate intercellular communication between TME components and have emerged as candidates for anti-cancer therapy. We previously reported that cancer-associated fibroblast (CAF) derived exosomes (CDEs) contain metabolites in their cargo that are utilized by cancer cells for central carbon metabolism and promote cancer growth...
January 10, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28081159/osmoregulation-in-the-halophilic-bacterium-halomonas-elongata-a-case-study-for-integrative-systems-biology
#10
Viktoria Kindzierski, Silvia Raschke, Nicole Knabe, Frank Siedler, Beatrix Scheffer, Katharina Pflüger-Grau, Friedhelm Pfeiffer, Dieter Oesterhelt, Alberto Marin-Sanguino, Hans-Jörg Kunte
Halophilic bacteria use a variety of osmoregulatory methods, such as the accumulation of one or more compatible solutes. The wide diversity of compounds that can act as compatible solute complicates the task of understanding the different strategies that halophilic bacteria use to cope with salt. This is specially challenging when attempting to go beyond the pathway that produces a certain compatible solute towards an understanding of how the metabolic network as a whole addresses the problem. Metabolic reconstruction based on genomic data together with Flux Balance Analysis (FBA) is a promising tool to gain insight into this problem...
2017: PloS One
https://www.readbyqxmd.com/read/28079117/high-field-transport-properties-of-a-p-doped-bafe2as2-film-on-technical-substrate
#11
Kazumasa Iida, Hikaru Sato, Chiara Tarantini, Jens Hänisch, Jan Jaroszynski, Hidenori Hiramatsu, Bernhard Holzapfel, Hideo Hosono
High temperature (high-Tc) superconductors like cuprates have superior critical current properties in magnetic fields over other superconductors. However, superconducting wires for high-field-magnet applications are still dominated by low-Tc Nb3Sn due probably to cost and processing issues. The recent discovery of a second class of high-Tc materials, Fe-based superconductors, may provide another option for high-field-magnet wires. In particular, AEFe2As2 (AE: Alkali earth elements, AE-122) is one of the best candidates for high-field-magnet applications because of its high upper critical field, Hc2, moderate Hc2 anisotropy, and intermediate Tc...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078675/overexpression-of-a-diacylglycerol-acyltransferase-gene-in-phaeodactylum-tricornutum-directs-carbon-towards-lipid-biosynthesis
#12
Jorge Dinamarca, Orly Levitan, G K Kumaraswamy, Desmond S Lun, Paul Falkowski
Under nutrient deplete conditions, diatoms accumulate between 15 to 25% of their dry weight as lipids, primarily as triacylglycerols (TAGs). As in most eukaryotes, these organisms produce TAGs via the acyl-CoA dependent Kennedy pathway. The last step in this pathway is catalyzed by diacylglycerol acyltransferase (DGAT) that acylates diacylglycerol (DAG) to produce TAG. To test our hypothesis that DGAT plays a major role in controlling the flux of carbon towards lipids, we overexpressed a specific type II DGAT gene, DGAT2D, in the model diatom Phaeodactylum tricornutum...
January 12, 2017: Journal of Phycology
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
#13
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/28075474/isomahanine-induces-endoplasmic-reticulum-stress-and-simultaneously-triggers-p38%C3%A2-mapk-mediated-apoptosis-and-autophagy-in-multidrug-resistant-human-oral-squamous-cell-carcinoma-cells
#14
Tanyarath Utaipan, Anan Athipornchai, Apichart Suksamrarn, Surasak Chunsrivirot, Warangkana Chunglok
Advanced oral squamous cell carcinoma (OSCC) is typically aggressive and closely correlated with disease recurrence and poor survival. Multidrug resistance (MDR) is the most critical problem leading to therapeutic failure. Investigation of novel anticancer candidates targeting multidrug-resistant OSCC cells may provide a basis for developing effective strategies for OSCC treatment. In the present study, we investigated the cytotoxic mechanism of a carbazole alkaloid, namely isomahanine, in a multidrug‑resistant OSCC cell line CLS-354/DX...
February 2017: Oncology Reports
https://www.readbyqxmd.com/read/28074840/observational-evidence-for-cloud-cover-enhancement-over-western-european-forests
#15
Adriaan J Teuling, Christopher M Taylor, Jan Fokke Meirink, Lieke A Melsen, Diego G Miralles, Chiel C van Heerwaarden, Robert Vautard, Annemiek I Stegehuis, Gert-Jan Nabuurs, Jordi Vilà-Guerau de Arellano
Forests impact regional hydrology and climate directly by regulating water and heat fluxes. Indirect effects through cloud formation and precipitation can be important in facilitating continental-scale moisture recycling but are poorly understood at regional scales. In particular, the impact of temperate forest on clouds is largely unknown. Here we provide observational evidence for a strong increase in cloud cover over large forest regions in western Europe based on analysis of 10 years of 15 min resolution data from geostationary satellites...
January 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/28073473/how-rising-co2-and-global-warming-may-stimulate-harmful-cyanobacterial-blooms
#16
REVIEW
Petra M Visser, Jolanda M H Verspagen, Giovanni Sandrini, Lucas J Stal, Hans C P Matthijs, Timothy W Davis, Hans W Paerl, Jef Huisman
Climate change is likely to stimulate the development of harmful cyanobacterial blooms in eutrophic waters, with negative consequences for water quality of many lakes, reservoirs and brackish ecosystems across the globe. In addition to effects of temperature and eutrophication, recent research has shed new light on the possible implications of rising atmospheric CO2 concentrations. Depletion of dissolved CO2 by dense cyanobacterial blooms creates a concentration gradient across the air-water interface. A steeper gradient at elevated atmospheric CO2 concentrations will lead to a greater influx of CO2, which can be intercepted by surface-dwelling blooms, thus intensifying cyanobacterial blooms in eutrophic waters...
April 2016: Harmful Algae
https://www.readbyqxmd.com/read/28070562/biological-and-chemical-adaptation-to-endogenous-hydrogen-peroxide-production-in-streptococcus-pneumoniae-d39
#17
John P Lisher, Ho-Ching Tiffany Tsui, Smirla Ramos-Montañez, Kristy L Hentchel, Julia E Martin, Jonathan C Trinidad, Malcolm E Winkler, David P Giedroc
The catalase-negative, facultative anaerobe Streptococcus pneumoniae D39 is naturally resistant to hydrogen peroxide (H2O2) produced endogenously by pyruvate oxidase (SpxB). Here, we investigate the adaptive response to endogenously produced H2O2. We show that lactate oxidase, which converts lactate to pyruvate, positively impacts pyruvate flux through SpxB and that ΔlctO mutants produce significantly lower H2O2. In addition, both the SpxB pathway and a candidate pyruvate dehydrogenase complex (PDHC) pathway contribute to acetyl coenzyme A (acetyl-CoA) production during aerobic growth, and the pyruvate format lyase (PFL) pathway is the major acetyl-CoA pathway during anaerobic growth...
January 2017: MSphere
https://www.readbyqxmd.com/read/28067287/smartphone-based-low-light-detection-for-bioluminescence-application
#18
Huisung Kim, Youngkee Jung, Iyll-Joon Doh, Roxana Andrea Lozano-Mahecha, Bruce Applegate, Euiwon Bae
We report a smartphone-based device and associated imaging-processing algorithm to maximize the sensitivity of standard smartphone cameras, that can detect the presence of single-digit pW of radiant flux intensity. The proposed hardware and software, called bioluminescent-based analyte quantitation by smartphone (BAQS), provides an opportunity for onsite analysis and quantitation of luminescent signals from biological and non-biological sensing elements which emit photons in response to an analyte. A simple cradle that houses the smartphone, sample tube, and collection lens supports the measuring platform, while noise reduction by ensemble averaging simultaneously lowers the background and enhances the signal from emitted photons...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28065897/trfba-an-algorithm-to-integrate-genome-scale-metabolic-and-transcriptional-regulatory-networks-with-incorporation-of-expression-data
#19
Ehsan Motamedian, Maryam Mohammadi, Seyed Abbas Shojaosadati, Mona Heydari
MOTIVATION: Integration of different biological networks and data-types has been a major challenge in systems biology. The present study introduces the transcriptional regulated flux balance analysis (TRFBA) algorithm that integrates transcriptional regulatory and metabolic models using a set of expression data for various perturbations. RESULTS: TRFBA considers the expression levels of genes as a new continuous variable and introduces two new linear constraints...
January 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28065673/spectral-analysis-of-reflex-cutaneous-vasodilatation-during-passive-heat-stress
#20
Matthew M Mallette, Gary J Hodges, Gregory W McGarr, David A Gabriel, Stephen S Cheung
Previous work has demonstrated that spectral analysis is a useful tool to non-invasively ascertain the mechanisms of control of the cutaneous circulation. The majority of work using spectral analysis has focused on local control mechanisms, with none examining reflex control. Skin blood flow was analysed using spectral analysis on the dorsal aspect of the forearm of 7 males and 7 females during passive heat stress, with mean forearm and local temperature at the site of measurement maintained at thermoneutral (33°C) to minimize the effect of local control mechanisms...
January 5, 2017: Microvascular Research
keyword
keyword
65002
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"