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https://www.readbyqxmd.com/read/28453682/distributedfba-jl-high-level-high-performance-flux-balance-analysis-in-julia
#1
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...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28448924/sediment-transfer-at-different-spatial-and-temporal-scales-in-the-sichuan-hilly-basin-china-synthesizing-data-from-multiple-approaches-and-preliminary-interpretation-in-the-context-of-climatic-and-anthropogenic-drivers
#2
Valentin Golosov, Adrian L Collins, Qiang Tang, Xinbao Zhang, Ping Zhou, Xiubin He, Anbang Wen
Quantifying sediment production and transfer at different spatial and temporal scales in a changing environment is critical in understanding the potential effects of climatic and anthropogenic drivers. Accordingly, estimates of soil erosion and sediment production at hillslope field, first-order small catchment (<0.25km(2)) and river basin scales in the Sichuan Hilly Basin of Southwestern China, generated using a variety of techniques, including fallout radionuclide tracing, runoff plot observations, core chronology dating and conventional sediment flux monitoring, were synthesized and interpreted in the context of potential climatic and human controls...
April 24, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28448918/erosion-of-the-alberta-badlands-produces-highly-variable-and-elevated-heavy-metal-concentrations-in-the-red-deer-river-alberta
#3
Jason G Kerr, Colin A Cooke
Erosion is important in the transport of heavy metals from terrestrial to fluvial environments. In this study, we investigated riverine heavy metal (Cd, Cu, Hg and Pb) dynamics in the Red Deer River (RDR) watershed at sites upstream (n=2) and downstream (n=7) of the Alberta badlands, an area of naturally high erosion. At sites draining the badlands, total water column Cd, Cu, Hg and Pb concentrations frequently exceeded guidelines for the protection of freshwater biota. Furthermore, peak concentrations of total Cd (9...
April 24, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28448436/role-of-archaeal-hera-protein-in-the-biology-of-the-bacterium-thermus-thermophilus
#4
Alba Blesa, Nieves G Quintans, Ignacio Baquedano, Carlos P Mata, José R Castón, José Berenguer
Intense gene flux between prokaryotes result in high percentage of archaeal genes in the genome of the thermophilic bacteria Thermus spp. Among these archaeal genes a homolog to the Sulfolobus spp. HerA protein appears in all of the Thermus spp. strains so far sequenced (HepA). The role of HepA in Thermus thermophilus HB27 has been analyzed using deletion mutants, and its structure resolved at low resolution by electron microscopy. Recombinant HepA shows DNA-dependent ATPase activity and its structure revealed a double ring, conically-shaped hexamer with an upper diameter of 150 Å and a bottom module of 95 Å...
April 27, 2017: Genes
https://www.readbyqxmd.com/read/28447632/a-universal-model-for-solar-eruptions
#5
Peter F Wyper, Spiro K Antiochos, C Richard DeVore
Magnetically driven eruptions on the Sun, from stellar-scale coronal mass ejections to small-scale coronal X-ray and extreme-ultraviolet jets, have frequently been observed to involve the ejection of the highly stressed magnetic flux of a filament. Theoretically, these two phenomena have been thought to arise through very different mechanisms: coronal mass ejections from an ideal (non-dissipative) process, whereby the energy release does not require a change in the magnetic topology, as in the kink or torus instability; and coronal jets from a resistive process involving magnetic reconnection...
April 26, 2017: Nature
https://www.readbyqxmd.com/read/28446901/anaerobic-methanotrophic-archaea-of-the-anme-2d-cluster-are-active-in-a-low-sulfate-iron-rich-freshwater-sediment
#6
Hannah S Weber, Kirsten S Habicht, Bo Thamdrup
ANaerobic MEthanotrophic (ANME) archaea remove the greenhouse gas methane from anoxic environments and diminish its flux to the atmosphere. High methane removal efficiencies are well documented in marine environments, whereas anaerobic oxidation of methane (AOM) was only recently indicated as an important methane sink in freshwater systems. Freshwater AOM-mediating microorganisms lack taxonomic identification and only little is known about metabolic adaptions to prevailing biogeochemical conditions. One of the first study sites providing information about AOM activity in freshwater sediment is Lake Ørn, a low-sulfate, iron-rich Danish lake...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28446789/imaging-of-underground-cavities-with-cosmic-ray-muons-from-observations-at-mt-echia-naples
#7
G Saracino, L Amato, F Ambrosino, G Antonucci, L Bonechi, L Cimmino, L Consiglio, R D ' Alessandro, E De Luzio, G Minin, P Noli, L Scognamiglio, P Strolin, A Varriale
Muography is an imaging technique based on the measurement of absorption profiles for muons as they pass through rocks and earth. Muons are produced in the interactions of high-energy cosmic rays in the Earth's atmosphere. The technique is conceptually similar to usual X-ray radiography, but with extended capabilities of investigating over much larger thicknesses of matter thanks to the penetrating power of high-energy muons. Over the centuries a complex system of cavities has been excavated in the yellow tuff of Mt...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446744/levetiracetam-pharmacokinetics-in-a-patient-with-intracranial-hemorrhage-undergoing-continuous-veno-venous-hemofiltration
#8
Edward T Van Matre, Scott W Mueller, Douglas N Fish, Robert MacLaren, Luis F Cava, Robert T Neumann, Tyree H Kiser
BACKGROUND Levetiracetam is an antiepileptic drug frequently used in critically ill patients. Levetiracetam is primarily eliminated as a parent compound via glomerular filtration and requires dose adjustment in renal insufficiency, but the literature on patients receiving continuous veno-venous hemofiltration (CVVH) is scant. CASE REPORT We report the levetiracetam pharmacokinetic profile of a patient being treated with levetiracetam 1000 mg intravenously every 12 h who required continuous veno-venous hemofiltration (CVVH)...
April 27, 2017: American Journal of Case Reports
https://www.readbyqxmd.com/read/28446262/dietary-supplementation-of-branched-chain-amino-acids-increases-muscle-net-amino-acid-fluxes-through-elevating-their-substrate-availability-and-intramuscular-catabolism-in-young-pigs
#9
Liufeng Zheng, Fangrui Zuo, Shengjun Zhao, Pingli He, Hongkui Wei, Quanhang Xiang, Jiaman Pang, Jian Peng
Branched-chain amino acids (BCAA) have been clearly demonstrated to have anabolic effects on muscle protein synthesis. However, little is known about their roles in the regulation of net AA fluxes across skeletal muscle in vivo. This study was aimed to investigate the effect and related mechanisms of dietary supplementation of BCAA on muscle net amino acid (AA) fluxes using the hindlimb flux model. In all fourteen 4-week-old barrows were fed reduced-protein diets with or without supplemental BCAA for 28 d. Pigs were implanted with carotid arterial, femoral arterial and venous catheters, and fed once hourly with intraarterial infusion of p-amino hippurate...
April 27, 2017: British Journal of Nutrition
https://www.readbyqxmd.com/read/28446125/soluble-transferrin-receptor-as-a-marker-of-erythropoiesis-in-patients-undergoing-high-flux-hemodialysis
#10
Pei Yin, Jijun Li, Yan Song
Anemia is a common complication in chronic kidney disease (CKD) patients receiving hemodialysis. The effect of high-flux dialysis (HFD) on anemia remains unclear. This prospective study aimed to evaluate the effect of HFD on anemia, and the potential of soluble transferrin receptor (sTfR) as a marker of iron status and erythropoiesis in CKD patients on hemodialysis. Forty patients, who switched from conventional low-flux dialysis to HFD for 12 months, were enrolled in this study. The levels of sTfR, hemoglobin, iron, and nutritional markers, as well as the dose of recombinant human erythropoietin (rhEPO) and use of chalybeate were determined at 0, 2, 6, and 12 months after starting HFD...
April 27, 2017: Bosnian Journal of Basic Medical Sciences
https://www.readbyqxmd.com/read/28446019/a-novel-fusion-bead-procedure-for-nuclear-forensics-employing-synthetic-enstatite-to-dissolve-uraniferous-and-other-challenging-materials-prior-to-la-icp-ms
#11
David G Reading, Ian W Croudace, Phillip Edward Warwick
There is an increasing demand for rapid and effective analytical tools to support nuclear forensic investigations of seized or suspect materials. Some methods are simply adapted from other scientific disciplines and can effectively be used to rapidly prepare complex materials for subsequent analysis. A novel sample fusion method is developed, tested and validated to produce homogeneous, flux-free glass beads of geochemical reference materials (GRMs), uranium ores, and uranium ore concentrates (UOC) prior to the analysis of 14 rare earth elements (REE) via LA-ICP-MS...
April 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28444733/hybridization-increases-mitochondrial-production-of-reactive-oxygen-species-in-sunfish
#12
Sherry N N Du, Fariborz Khajali, Neal J Dawson, Graham R Scott
Mitochondrial dysfunction and oxidative stress have been suggested to be possible mechanisms underlying hybrid breakdown, as a result of mito-nuclear incompatibilities in respiratory complexes of the electron transport system. However, it remains unclear whether hybridization increases the production of reactive oxygen species (ROS) by mitochondria. We used high-resolution respirometry and fluorometry on isolated liver mitochondria to examine mitochondrial physiology and ROS emission in naturally occurring hybrids of pumpkinseed (Lepomis gibbosus) and bluegill (L...
April 26, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28443619/programming-mrna-decay-to-modulate-synthetic-circuit-resource-allocation
#13
Ophelia S Venturelli, Mika Tei, Stefan Bauer, Leanne Jade G Chan, Christopher J Petzold, Adam P Arkin
Synthetic circuits embedded in host cells compete with cellular processes for limited intracellular resources. Here we show how funnelling of cellular resources, after global transcriptome degradation by the sequence-dependent endoribonuclease MazF, to a synthetic circuit can increase production. Target genes are protected from MazF activity by recoding the gene sequence to eliminate recognition sites, while preserving the amino acid sequence. The expression of a protected fluorescent reporter and flux of a high-value metabolite are significantly enhanced using this genome-scale control strategy...
April 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28441870/protein-nanocellulose-interactions-in-paper-filters-for-advanced-separation-applications
#14
Simon Johan Gustafsson, Levon Manukyan, Albert Mihranyan
Protein-based pharmaceutics are widely explored for healthcare applications, and six out of ten best selling drugs today are biologicals. The goal of this work was to evaluate the protein nanocellulose interactions in paper filter for advanced separation applications such as virus removal filtration and bioprocessing. The protein recovery was measured for bovine serum albumin (BSA), γ-Globulin and Lysozyme using biuret total protein reagent and polyacrylamide gel electrophoresis (SDS-PAGE), and the throughput was characterized in terms of flux values from fixed volume filtrations at various protein concentrations and under worst-case experimental conditions...
April 26, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28441141/crystal-growth-and-stoichiometry-dependent-properties-of-the-ferromagnetic-weyl-semimetal-zrco2-x-sn
#15
Satya K Kushwaha, Karoline Stolze, Zhijun Wang, Max Hirschberger, Jingjing Lin, B Andrei Bernevig, N Phuan Ong, Robert J Cava
We report the growth of high quality bulk crystals, through crystallization from molten Sn flux, of the predicted ferromagnetic Weyl metal ZrCo2-x Sn with the L21 Heusler phase structure. The concentration of Co vacancies in the single crystals is found to be dependent on the initial concentration of Co in the flux. The saturation magnetization increases approximately linearly with decreasing Co deficiency and the ferromagnetic transition temperature changes significantly. p-type carrier conduction and an anomalous Hall effect are observed...
April 25, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28439687/colloid-characterization-and-in-situ-release-in-shallow-groundwater-under-different-hydrogeology-conditions
#16
Jingjing Zhou, Dan Liu, Wenjing Zhang, Xuequn Chen, Ying Huan, Xipeng Yu
Changes to groundwater hydrodynamics and chemistry can lead to colloid release that can have a major impact on the groundwater environment. To analyze the effects of colloid release caused by artificial groundwater recharge, field and laboratory tests on colloid characterization and colloid release were conducted. The field tests were carried out at an artificial recharge test site in Shandong Province. In the field investigation, one recharge water sample and five groundwater samples were collected and filtered through three levels of ultrafiltration membranes, with pore sizes of 0...
April 24, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28437863/sirt3-acts-as-a-negative-regulator-of-autophagy-dictating-hepatocyte-susceptibility-to-lipotoxicity
#17
Songtao Li, Xiaobing Dou, Hua Ning, Qing Song, Wei Wei, Ximei Zhang, Chen Shen, Jiaxin Li, Changhao Sun, Zhenyuan Song
Lipotoxicity induced by saturated fatty acids (SFAs) plays a central role in the pathogenesis of non-alcoholic fatty liver disease (NAFLD); however, the exact mechanism(s) remain to be fully elucidated. SIRT3 is an NAD(+) -dependent deacetylase primarily located inside mitochondria. In this study, we demonstrated that a SFAs-rich high-fat diet (HFD) was more detrimental to the liver than an isocaloric unsaturated FAs-rich HFD. Unexpectedly, SIRT3 expression/activity were significantly elevated in the livers of mice exposed to the SFAs-rich HFD...
April 24, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28437526/prominin-1-is-a-novel-regulator-of-autophagy-in-the-human-retinal-pigment-epithelium
#18
Sujoy Bhattacharya, Jinggang Yin, Christina S Winborn, Qiuhua Zhang, Junming Yue, Edward Chaum
Purpose: Prominin-1 (Prom1) is a transmembrane glycoprotein, which is expressed in stem cell lineages, and has recently been implicated in cancer stem cell survival. Mutations in the Prom1 gene have been shown to disrupt photoreceptor disk morphogenesis and cause an autosomal dominant form of Stargardt-like macular dystrophy (STGD4). Despite the apparent structural role of Prom1 in photoreceptors, its role in other cells of the retina is unknown. The purpose of this study is to investigate the role of Prom1 in the highly metabolically active cells of the retinal pigment epithelium (RPE)...
April 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28436089/a-novel-dense-granule-protein-gra41-regulates-timing-of-egress-and-calcium-sensitivity-in-toxoplasma-gondii
#19
Kaice A LaFavers, Karla M Márquez-Nogueras, Isabelle Coppens, Silvia N J Moreno, Gustavo Arrizabalaga
Toxoplasma gondii is an obligate intracellular apicomplexan parasite with high seroprevalence in humans. Repeated lytic cycles of invasion, replication and egress drive both the propagation and the virulence of this parasite. Key steps in this cycle, including invasion and egress, depend on tightly regulated calcium fluxes and, while many of the calcium-dependent effectors have been identified, the factors that detect and regulate the calcium fluxes are mostly unknown. To address this knowledge gap, we used a forward genetic approach to isolate mutants resistant to extracellular exposure to the calcium ionophore A23187...
April 24, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/28436004/engineering-of-an-h2-o2-auto-scavenging-in-vivo-cascade-for-pinoresinol-production
#20
Yongkun Lv, Xiaozhong Cheng, Guocheng Du, Jingwen Zhou, Jian Chen
Pinoresinol is a natural lignan with a high market value that has potential pharmacological and food supplement applications. Pinoresinol is currently isolated from plants, which suffers from low efficiency and yield. To produce pinoresinol from inexpensive and industrially available eugenol, an in vivo enzymatic cascade composed of vanillyl alcohol oxidase and peroxidase was designed, which scavenges H2 O2 automatically and eliminates protein purification and cofactor addition. Two peroxidases were screened and identified from Escherichia coli BL21 (DE3), and tested in the enzymatic cascade...
April 24, 2017: Biotechnology and Bioengineering
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