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https://www.readbyqxmd.com/read/29166724/-beneficial-effects-of-schisandrin-b-on-the-cardiac-structure-and-function-in-a-mice-model-of-myocardial-infarction
#1
P S Chen, J Liu, H Y Meng, P Wu, Z J Yang
Objective: To investigate whether Schisandrin B (Sch B) could improve cardiac structure and function in myocardial infarction (MI) mice and related mechanisms. Methods: Male C57BL/6J mice were randomized into sham (n=8), MI+ Sch B (n=24, 80 mg·kg(-1)·d(-1) per gavage) or MI+ vehicle (n=24, equal volume). After treatment for 3 weeks, cardiac function was detected by echocardiography measurement.Infarction size was measured by Evans blue and TTC staining.HE and Masson trichrome staining were used to observe the myocardial inflammation, structure and fibrosis...
November 24, 2017: Zhonghua Xin Xue Guan Bing za Zhi
https://www.readbyqxmd.com/read/29166573/interaction-of-hsp90-with-phospholipid-model-membranes
#2
Muhan Zhang, Daoying Wang, Pengpeng Li, Chong Sun, Rong Xu, Zhiming Geng, Weimin Xu, Zhaoqi Dai
Heat shock protein 90 (Hsp90) is an essential molecular chaperone with versatile functions in cell homeostatic control under both normal and stress conditions. Hsp90 has been found to be expressed on the cell surface, but the mechanism of Hsp90 association to the membrane remains obscure. In this study, the direct interaction of Hsp90 and phospholipid vesicles was characterized, and the role of Hsp90 on membrane physical state was explored. Using surface plasmon resonance (SPR), we observed a strong interaction between Hsp90 and different compositions of lipid...
November 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29166154/predator-persistence-through-variability-of-resource-productivity-in-tritrophic-systems
#3
Floor H Soudijn, André M de Roos
The trophic structure of species communities depends on the energy transfer between trophic levels. Primary productivity varies strongly through time, challenging the persistence of species at higher trophic levels. Yet resource variability has mostly been studied in systems with only one or two trophic levels. We test the effect of variability in resource productivity in a tritrophic model system including a resource, a size-structured consumer, and a size-specific predator. The model complies with fundamental principles of mass conservation and the body-size dependence of individual-level energetics and predator-prey interactions...
December 2017: American Naturalist
https://www.readbyqxmd.com/read/29166114/communication-recovering-the-flat-plane-condition-in-electronic-structure-theory-at-semi-local-dft-cost
#4
Akash Bajaj, Jon Paul Janet, Heather J Kulik
The flat-plane condition is the union of two exact constraints in electronic structure theory: (i) energetic piecewise linearity with fractional electron removal or addition and (ii) invariant energetics with change in electron spin in a half filled orbital. Semi-local density functional theory (DFT) fails to recover the flat plane, exhibiting convex fractional charge errors (FCE) and concave fractional spin errors (FSE) that are related to delocalization and static correlation errors. We previously showed that DFT+U eliminates FCE but now demonstrate that, like other widely employed corrections (i...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166094/structure-and-electronic-states-of-a-graphene-double-vacancy-with-an-embedded-si-dopant
#5
Reed Nieman, Adélia J A Aquino, Trevor P Hardcastle, Jani Kotakoski, Toma Susi, Hans Lischka
Silicon represents a common intrinsic impurity in graphene, bonding to either three or four carbon neighbors, respectively, in a single or double carbon vacancy. We investigate the effect of the latter defect (Si-C4) on the structural and electronic properties of graphene using density functional theory. Calculations based both on molecular models and with periodic boundary conditions have been performed. The two-carbon vacancy was constructed from pyrene (pyrene-2C) which was then expanded to circumpyrene-2C...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166074/low-lying-vibronic-level-structure-of-the-ground-state-of-the-methoxy-radical-slow-electron-velocity-map-imaging-sevi-spectra-and-k%C3%A3-ppel-domcke-cederbaum-kdc-vibronic-hamiltonian-calculations
#6
Marissa L Weichman, Lan Cheng, Jongjin B Kim, John F Stanton, Daniel M Neumark
A joint experimental and theoretical study is reported on the low-lying vibronic level structure of the ground state of the methoxy radical using slow photoelectron velocity-map imaging spectroscopy of cryogenically cooled, mass-selected anions (cryo-SEVI) and Köppel-Domcke-Cederbaum (KDC) vibronic Hamiltonian calculations. The KDC vibronic model Hamiltonian in the present study was parametrized using high-level quantum chemistry, allowing the assignment of the cryo-SEVI spectra for vibronic levels of CH3O up to 2000 cm(-1) and of CD3O up to 1500 cm(-1) above the vibrational origin, using calculated vibronic wave functions...
June 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166061/modeling-hydroxylated-nanosilica-testing-the-performance-of-reaxff-and-ffsioh-force-fields
#7
Antoni Macià Escatllar, Piero Ugliengo, Stefan T Bromley
We analyze the performance of the FFSiOH force field and two parameterisations of the ReaxFF force field for modeling hydroxylated nanoscale silica (SiO2). Such nanosystems are fundamental in numerous aspects of geochemistry and astrochemistry and also play a key role during the hydrothermal synthesis of technologically important nanoporous silicas (e.g., catalysts, absorbents, and coatings). We consider four aspects: structure, relative energies, vibrational spectra, and hydroxylation energies, and compare the results with those from density functional calculations employing a newly defined dataset (HND: Hydroxylated Nanosilica Dataset)...
June 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166051/a-time-correlation-function-approach-to-nuclear-dynamical-effects-in-x-ray-spectroscopy
#8
Sven Karsten, Sergey I Bokarev, Saadullah G Aziz, Sergei D Ivanov, Oliver Kühn
Modern X-ray spectroscopy has proven itself as a robust tool for probing the electronic structure of atoms in complex environments. Despite working on energy scales that are much larger than those corresponding to nuclear motions, taking nuclear dynamics and the associated nuclear correlations into account may be of importance for X-ray spectroscopy. Recently, we have developed an efficient protocol to account for nuclear dynamics in X-ray absorption and resonant inelastic X-ray scattering spectra [Karsten et al...
June 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29165654/infusions-of-nerve-growth-factor-into-the-developing-frontal-cortex-leads-to-deficits-in-behavioral-flexibility-and-increased-perseverance
#9
Sagar J Desai, Brian L Allman, Nagalingam Rajakumar
In the pursuit of further establishing a neurodevelopmental animal model to investigate the mechanisms underlying impaired executive function, a core and severely debilitating symptom of schizophrenia, we sought to characterize the deficits in behavioral flexibility in adult rats following neonatal infusions of nerve growth factor (NGF) into the medial part of the developing frontal cortex. Our previous studies using this neonatal frontal cortical lesion model have shown that it leads to adult-onset positive and negative symptom-like features, and several neuropathological abnormalities of schizophrenia...
November 17, 2017: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/29165648/structure-modeling-of-rna-using-sparse-nmr-constraints
#10
Benfeard Williams, Bo Zhao, Arpit Tandon, Feng Ding, Kevin M Weeks, Qi Zhang, Nikolay V Dokholyan
RNAs fold into distinct molecular conformations that are often essential for their functions. Accurate structure modeling of complex RNA motifs, including ubiquitous non-canonical base pairs and pseudoknots, remains a challenge. Here, we present an NMR-guided all-atom discrete molecular dynamics (DMD) platform, iFoldNMR, for rapid and accurate structure modeling of complex RNAs. We show that sparse distance constraints from imino resonances, which can be readily obtained from routine NMR experiments and easier to compile than laborious assignments of non-solvent-exchangeable protons, are sufficient to direct a DMD search for low-energy RNA conformers...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165610/gramene-2018-unifying-comparative-genomics-and-pathway-resources-for-plant-research
#11
Marcela K Tello-Ruiz, Sushma Naithani, Joshua C Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J Geniza, Yinping Jiao, Young Koung Lee, Bo Wang, Joseph Mulvaney, Kapeel Chougule, Justin Elser, Noor Al-Bader, Sunita Kumari, James Thomason, Vivek Kumar, Daniel M Bolser, Guy Naamati, Electra Tapanari, Nuno Fonseca, Laura Huerta, Haider Iqbal, Maria Keays, Alfonso Munoz-Pomer Fuentes, Amy Tang, Antonio Fabregat, Peter D'Eustachio, Joel Weiser, Lincoln D Stein, Robert Petryszak, Irene Papatheodorou, Paul J Kersey, Patti Lockhart, Crispin Taylor, Pankaj Jaiswal, Doreen Ware
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165498/tomographic-magnetic-particle-imaging-of-cancer-targeted-nanoparticles
#12
Hamed Arami, Eric Teeman, Alyssa Troksa, Haydin Bradshaw, Katayoun Saatchi, Asahi Tomitaka, Sanjiv Sam Gambhir, Urs O Häfeli, Denny Liggitt, Kannan M Krishnan
Magnetic Particle Imaging (MPI) is an emerging, whole body biomedical imaging technique, with sub-millimeter spatial resolution and high sensitivity to a biocompatible contrast agent consisting of an iron oxide nanoparticle core and a biofunctionalized shell. Successful application of MPI for imaging of cancer depends on the nanoparticles (NPs) accumulating at tumors at sufficient levels relative to other sites. NPs' physiochemical properties such as size, crystallographic structure and uniformity, surface coating, stability, blood circulation time and magnetization determine the efficacy of their tumor accumulation and MPI signal generation...
November 22, 2017: Nanoscale
https://www.readbyqxmd.com/read/29165477/barley-beta-glucans-varying-in-molecular-mass-and-oligomer-structure-affect-cecal-fermentation-and-microbial-composition-but-not-blood-lipid-profiles-in-hypercholesterolemic-rats
#13
Mette S Mikkelsen, Morten G Jensen, Tina S Nielsen
There is an unmet need for appealing and functional barley β-glucan (BG) food matrices that can provide sufficient and active BG doses to consumers. We investigated how molecular mass and oligomer structure important for BG food and health properties affected plasma lipids and gut parameters in hypercholesterolemic rats. Following 3 weeks on a high-cholestrol diet, rats were given a high-cholesterol diet supplemented with either cellulose (control) or purified barley BGs with low (100 or 150 kDa; glucagel or lowBG, respectively) or medium (530 kDa; mediumBG) molecular masses varying in cellotriosyl/cellotetraosyl oligomer ratio for 4 weeks...
November 22, 2017: Food & Function
https://www.readbyqxmd.com/read/29165235/synthesis-of-n-acetyl-d-quinovosamine-in-rhizobium-etli-ce3-is-completed-after-its-4-keto-precursor-is-linked-to-a-carrier-lipid
#14
Tiezheng Li, K Dale Noel
Bacterial O-antigens are synthesized on lipid carriers before being transferred to lipopolysaccharide core structures. Rhizobium etli CE3 lipopolysaccharide is a model for understanding O-antigen biological function. CE3 O-antigen structure and genetics are known. However, proposed enzymology for CE3 O-antigen synthesis has been examined very little in vitro, and even the sugar added to begin the synthesis is uncertain. A model based on mutagenesis studies predicts that 2-acetamido-2,6-dideoxy-d-glucose (QuiNAc) is the first O-antigen sugar and that genes wreV, wreQ and wreU direct QuiNAc synthesis and O-antigen initiation...
November 22, 2017: Microbiology
https://www.readbyqxmd.com/read/29164920/cardiac-structure-and-function-predicts-functional-decline-in-the-oldest-old
#15
David Leibowitz, Jeremy M Jacobs, Irit Lande-Stessman, Dan Gilon, Jochanan Stessman
Background This study examined the association between cardiac structure and function and the deterioration in activities of daily living (ADLs) in an age-homogenous, community-dwelling population of patients born in 1920-1921 over a five-year follow-up period. Design Longitudinal cohort study. Methods Patients were recruited from the Jerusalem Longitudinal Cohort Study, which has followed an age-homogenous cohort of Jerusalem residents born in 1920-1921. Patients underwent home echocardiography and were followed up for five years...
January 1, 2017: European Journal of Preventive Cardiology
https://www.readbyqxmd.com/read/29164898/ionic-solution-what-goes-right-and-wrong-with-continuum-solvation-modeling
#16
Changhao Wang, Pengyu Ren, Ray Luo
Solvent-mediated electrostatic interactions were well recognized to be important in the structure and function of molecular systems. Ionic interaction is an important component in electrostatic interactions, especially in highly charged molecules, such as nucleic acids. Here we focus on the quality of the widely used PBSA continuum models in modeling ionic interactions by comparing with both explicit solvent simulations and experiment. In this work, the molality-dependent chemical potentials for sodium chloride (NaCl) electrolyte were first simulated in the SPC/E explicit solvent...
November 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29164857/modeling-insight-into-battery-electrolyte-electrochemical-stability-and-interfacial-structure
#17
Oleg Borodin, Xiaoming Ren, Jenel Vatamanu, Arthur von Wald Cresce, Jaroslaw Knap, Kang Xu
Electroactive interfaces distinguish electrochemistry from chemistry and enable electrochemical energy devices like batteries, fuel cells, and electric double layer capacitors. In batteries, electrolytes should be either thermodynamically stable at the electrode interfaces or kinetically stable by forming an electronically insulating but ionically conducting interphase. In addition to a traditional optimization of electrolytes by adding cosolvents and sacrificial additives to preferentially reduce or oxidize at the electrode surfaces, knowledge of the local electrolyte composition and structure within the double layer as a function of voltage constitutes the basis of manipulating an interphase and expanding the operating windows of electrochemical devices...
November 22, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29164646/b-factor-profile-prediction-for-rna-flexibility-using-support-vector-machines
#18
Ivantha Guruge, Ghazaleh Taherzadeh, Jian Zhan, Yaoqi Zhou, Yuedong Yang
Determining the flexibility of structured biomolecules is important for understanding their biological functions. One quantitative measurement of flexibility is the atomic Debye-Waller factor or temperature B-factor. Most existing studies are limited to temperature B-factors of proteins and their prediction. Only one method attempted to predict temperature B-factors of ribosomal RNA. Here, we developed and compared machine-learning techniques in prediction of temperature B-factors of RNAs. The best model based on Support Vector Machines yields Pearson's correction coefficient at 0...
November 21, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29164638/the-piwi-interacting-rna-molecular-pathway-insights-from-cultured-silkworm-germline-cells
#19
Kazuhiro Sakakibara, Mikiko C Siomi
The PIWI-interacting RNA (piRNA) pathway, one of the major eukaryotic small RNA silencing pathways, is a genome surveillance system that silences selfish genes in animal gonads. piRNAs guide PIWI protein to target genes through Watson-Crick RNA-RNA base-parings. Loss of piRNA function causes genome instability, inducing failure in gametogenesis and infertility. Studies using fruit flies and mice as key experimental models have resulted in tremendous progress in understanding the mechanism underlying the piRNA pathway...
November 22, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29164389/early-life-stress-induces-motor-coordination-dysfunction-in-adult-mice
#20
Michifumi Kokubo, Syutaro Toya, Izuki Amano, Yusuke Takatsuru
Although child abuse has become a serious social problem in most countries, the neural mechanisms by which it induces adulthood mental disorders is not yet fully understood. Mice exposed to early-life stresses, such as maternal deprivation (MD) during lactation, are a good model for studying the effects of neglect of humans in early life. Early-life stress induces structural/functional changes of neurons in the hippocampus, prefrontal cortex, and amygdala, and causes mental disorders in adulthood. In this study, we found motor coordination dysfunction in male MD mice...
November 21, 2017: Journal of Physiological Sciences: JPS
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