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https://www.readbyqxmd.com/read/28102930/modulation-of-the-thermodynamic-signatures-of-an-rna-thermometer-by-osmolytes-and-salts
#1
Mimi Gao, Loana Arns, Roland Winter
Folding of ribonucleic acids (RNAs) is driven by several factors, such as base pairing and stacking, chain entropy, and ion-mediated electrostatics, which have been studied in great detail. However, the power of background molecules in the cellular milieu is often neglected. Herein, we study the effect of common osmolytes on the folding equilibrium of a hairpin-structured RNA and, using pressure perturbation, provide novel thermodynamic and volumetric insights into the modulation mechanism. The presence of TMAO causes an increased thermal stability and a more positive volume change for the helix-to-coil transition, whereas urea destabilizes the hairpin and leads to an increased expansibility of the unfolded state...
January 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28102398/low-temperature-heat-capacity-standard-entropy-standard-enthalpy-and-magnetic-property-a-new-1d-cu-ii-coordination-polymer-incorporating-tetrazole-1-acetic-acid-and-p-nitrobenzoic-acid
#2
Qi Yang, Jing Ge, Xin Liu, Quan Shi, Hongshan Ke, Qing Wei, Gang Xie, Sanping Chen, Shengli Gao
A new 1D Cu(II) coordination polymer, formulated as {[Cu(TZA)(PNA)]·H2O}n (1) (HTZA = tetrazole-1-acetic acid, HPNA = p-nitrobenzoic acid), was synthesized and structurally characterized. Thermogravimetric analysis demonstrated that the main frame of 1 exhibited good thermostability up to 473 K. The non-isothermal kinetics for the first exothermic process of 1 were studied by Kissinger and Ozawa methods. The magnetic study revealed that 1 possessed antiferromagnetic exchange interactions between Cu(II) ions through the carboxyl-bridge...
January 19, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28102365/viral-phylogenomics-using-an-alignment-free-method-a-three-step-approach-to-determine-optimal-length-of-k-mer
#3
Qian Zhang, Se-Ran Jun, Michael Leuze, David Ussery, Intawat Nookaew
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28101950/molecular-binding-of-toxic-phenothiazinium-derivatives-azures-to-bovine-serum-albumin-a-comparative-spectroscopic-calorimetric-and-in-silico-study
#4
Somnath Das, Md Maidul Islam, Gopal Chandra Jana, Anirudha Patra, Pradeep K Jha, Maidul Hossain
In this paper, the comparative binding behavior of antimalarial drug azure A, azure B and azure C with bovine serum albumin (BSA) has been studied. The interaction has been confirmed by multispectroscopic (UV, fluorescence, Fourier transform infrared (FT-IR), and circular dichroism) and molecular docking techniques. The experimental results show that azure B has the highest BSA binding affinity followed by azure A and azure C. The experimental evidence of binding showed a static quenching mechanism in the interaction azures with BSA...
January 19, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28100048/unanticipated-stickiness-of-%C3%AE-pinene
#5
Hilary M Chase, Junming Ho, Mary Alice Upshur, Regan J Thomson, Victor S Batista, Franz M Geiger
Hilary M. Chase1#, Junming Ho2#, Mary Alice Upshur1, Regan J. Thomson1, Victor S. Batista3, Franz M. Geiger1* 1Department of Chemistry, Northwestern University, Evanston, IL. 60208, United States; 2 Agency for Science, Technology and Research, Institute of High Performance Computing, 1 Fusionopolis Way #16-16 Connexis North, Singapore 138632; 3Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT. 06520, United States # These authors contributed equally to this work. *corresponding author: geigerf@chem...
January 19, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28097060/why-choose-random-forest-to-predict-rare-species-distribution-with-few-samples-in-large-undersampled-areas-three-asian-crane-species-models-provide-supporting-evidence
#6
Chunrong Mi, Falk Huettmann, Yumin Guo, Xuesong Han, Lijia Wen
Species distribution models (SDMs) have become an essential tool in ecology, biogeography, evolution and, more recently, in conservation biology. How to generalize species distributions in large undersampled areas, especially with few samples, is a fundamental issue of SDMs. In order to explore this issue, we used the best available presence records for the Hooded Crane (Grus monacha, n = 33), White-naped Crane (Grus vipio, n = 40), and Black-necked Crane (Grus nigricollis, n = 75) in China as three case studies, employing four powerful and commonly used machine learning algorithms to map the breeding distributions of the three species: TreeNet (Stochastic Gradient Boosting, Boosted Regression Tree Model), Random Forest, CART (Classification and Regression Tree) and Maxent (Maximum Entropy Models)...
2017: PeerJ
https://www.readbyqxmd.com/read/28095421/approximate-inference-for-time-varying-interactions-and-macroscopic-dynamics-of-neural-populations
#7
Christian Donner, Klaus Obermayer, Hideaki Shimazaki
The models in statistical physics such as an Ising model offer a convenient way to characterize stationary activity of neural populations. Such stationary activity of neurons may be expected for recordings from in vitro slices or anesthetized animals. However, modeling activity of cortical circuitries of awake animals has been more challenging because both spike-rates and interactions can change according to sensory stimulation, behavior, or an internal state of the brain. Previous approaches modeling the dynamics of neural interactions suffer from computational cost; therefore, its application was limited to only a dozen neurons...
January 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28095404/entropy-transfer-between-residue-pairs-and-allostery-in-proteins-quantifying-allosteric-communication-in-ubiquitin
#8
Aysima Hacisuleyman, Burak Erman
It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others...
January 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28095075/a-pilot-study-using-entropy-as-a-non-invasive-assessment-of-running
#9
Andrew M Murray, Joong Hyun Ryu, John Sproule, Anthony P Turner, Phil Graham-Smith, Marco Cardinale
PURPOSE: Running performance is influenced by the interaction of biomechanical and physiological factors. Miniaturised accelerometers worn by the athlete can be used to quantify mechanical aspects of running and be used as a non-invasive tool to assess training status and progression. The aim of this study was to define and validate a method to assess running regularity and allow the estimation of an individual's V̇O2 and/or blood lactate [La]b based on data collected with accelerometers and heart rate (HR)...
January 17, 2017: International Journal of Sports Physiology and Performance
https://www.readbyqxmd.com/read/28095013/the-tipping-point-of-perceived-change-asymmetric-thresholds-in-diagnosing-improvement-versus-decline
#10
Ed O'Brien, Nadav Klein
Change often emerges from a series of small doses. For example, a person may conclude that a happy relationship has eroded not from 1 obvious fight but from smaller unhappy signs that at some point "add up." Everyday fluctuations therefore create ambiguity about when they reflect substantive shifts versus mere noise. Ten studies reveal an asymmetry in this first point when people conclude "official" change: people demand less evidence to diagnose lasting decline than lasting improvement, despite similar evidential quality...
February 2017: Journal of Personality and Social Psychology
https://www.readbyqxmd.com/read/28094527/binding-and-inhibitory-effect-of-dyes-amaranth-and-tartrazine-on-amyloid-fibrillation-in-lysozyme
#11
Anirban Basu, Gopinatha Suresh Kumar
Interaction of two food colorant dyes, amaranth and tartrazine, with lysozyme was studied employing multiple biophysical techniques. The dyes exhibited hypochromic changes in the presence of lysozyme. The intrinsic fluorescence of lysozyme was quenched by both dyes; amaranth was a more efficient quencher than tartrazine. The equilibrium constant of amaranth was higher than that of tartarzine. From FRET analysis, the binding distances for amaranth and tartrazine were calculated to be 4.51 and 3.93 nms, respectively...
January 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28094513/native-state-volume-fluctuations-in-proteins-as-a-mechanism-for-dynamic-allostery
#12
Anthony B Law, Paul J Sapienza, Jun Zhang, Xiaobing Zuo, Chad M Petit
Allostery enables tight regulation of protein function in the cellular environment. While existing models of allostery are firmly rooted in the current structure-function paradigm, the mechanistic basis for allostery in the absence of structural change remains unclear. In this study, we show that a typical globular protein is able to undergo significant changes in volume under native conditions while exhibiting no additional changes in protein structure. These native state volume fluctuations were found to correlate with changes in internal motions that were previously recognized as a source of allosteric entropy...
January 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28092636/an-analysis-of-intrinsic-variations-of-low-frequency-shear-wave-speed-in-a-stochastic-tissue-model-the-first-application-for-staging-liver-fibrosis
#13
Yu Wang, Min Wang, Jingfeng Jiang
Shear wave elastography is increasingly being used to non-invasively stage liver fibrosis by measuring shear wave speed (SWS). This study quantitatively investigates intrinsic variations among SWS measurements obtained from heterogeneous media such as fibrotic livers. More specifically, it aims to demonstrate that intrinsic variations in SWS measurements, in general, follow a non-Gaussian distribution and are related to the heterogeneous nature of the medium being measured. Using the principle of maximum entropy (ME), our primary objective is to derive a probability density function (PDF) of the SWS distribution in conjunction with a lossless stochastic tissue model...
February 7, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28092039/calorimetric-measurement-of-sh2-domain-ligand-affinities
#14
Marissa A McKercher, Deborah S Wuttke
Isothermal titration calorimetry (ITC) has emerged as a leading approach in the characterization of protein/ligand interactions. This technique measures the heat change of a system upon binding of a ligand to a biomolecule, and thereby requires no immobilization, intrinsic fluorescence, or labeling of any kind of either species. If properly designed, a single experiment can not only measure the binding affinity, but also determine additional binding and thermodynamic parameters, including the enthalpy, entropy, and the stoichiometry of the interaction...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092010/allocation-and-simulation-study-of-carbon-emission-quotas-among-china-s-provinces-in-2020
#15
Xing Zhou, Xueling Guan, Ming Zhang, Yao Zhou, Meihua Zhou
China will form its carbon market in 2017 to focus on the allocation of regional carbon emission quota in order to cope with global warming. The rationality of the regional allocation has become an important consideration for the government in ensuring stable growth in different regions that are experiencing disparity in resource endowment and economic status. Based on constructing the quota allocation indicator system for carbon emission, the emission quota for each province in different scenarios and schemes in 2020 is simulated by the multifactor hybrid weighted Shannon entropy allocation model...
January 16, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28091551/reversible-martensitic-transformation-under-low-magnetic-fields-in-magnetic-shape-memory-alloys
#16
N M Bruno, S Wang, I Karaman, Y I Chumlyakov
Magnetic field-induced, reversible martensitic transformations in NiCoMnIn meta-magnetic shape memory alloys were studied under constant and varying mechanical loads to understand the role of coupled magneto-mechanical loading on the transformation characteristics and the magnetic field levels required for reversible phase transformations. The samples with two distinct microstructures were tested along the [001] austenite crystallographic direction using a custom designed magneto-thermo-mechanical characterization device while carefully controlling their thermodynamic states through isothermal constant stress and stress-varying magnetic field ramping...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28090612/quantum-chemical-study-and-isothermal-titration-calorimetry-of-%C3%AE-cyclodextrin-complexes-with-mianserin-in-aqueous-solution
#17
Anna Ignaczak, Bartłomiej Pałecz, Sylwia Belica-Pacha
β-Cyclodextrin (β-CD) is studied as a carrier of the drug mianserin (MIA). β-CD with MIA adducts with 1 : 1 and 2 : 1 stoichiometry are investigated in vacuo and in water using quantum chemical methods: PM6 and B3LYP/6-31G(d,p). An effect of the dispersion correction GD2 and the basis set superposition error on the complexation energies is also evaluated. Additionally, the interaction between MIA hydrochloride and β-CD in aqueous solution at 298.15 K is examined experimentally by isothermal titration calorimetry...
January 16, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28089620/the-use-of-information-theory-for-the-evaluation-of-biomarkers-of-aging-and-physiological-age
#18
David Blokh, Ilia Stambler
The present work explores the application of information theoretical measures, such as entropy and normalized mutual information, for research of biomarkers of aging. The use of information theory affords unique methodological advantages for the study of aging processes, as it allows evaluating non-linear relations between biological parameters, providing the precise quantitative strength of those relations, both for individual and multiple parameters, showing cumulative or synergistic effect. Here we illustrate those capabilities utilizing a dataset on heart disease, including diagnostic parameters routinely available to physicians...
January 12, 2017: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/28088157/stochastic-thermodynamics-of-a-chemical-nanomachine-the-channeling-enzyme-tryptophan-synthase
#19
Dimitri Loutchko, Maximilian Eisbach, Alexander S Mikhailov
The enzyme tryptophan synthase is characterized by a complex pattern of allosteric interactions that regulate the catalytic activity of its two subunits and opening or closing of their ligand gates. As a single macromolecule, it implements 13 different reaction steps, with an intermediate product directly channeled from one subunit to another. Based on experimental data, a stochastic model for the operation of tryptophan synthase has been earlier constructed [D. Loutchko, D. Gonze, and A. S. Mikhailov, J. Phys...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088014/reduced-complexity-of-force-and-muscle-activity-during-low-level-isometric-contractions-of-the-ankle-in-diabetic-individuals
#20
E Y Suda, P Madeleine, R P Hirata, A Samani, T T Kawamura, I C N Sacco
BACKGROUND: This study evaluated the structure and amount of variability of surface electromyography (sEMG) patterns and ankle force data during low-level isometric contractions in diabetic subjects with different degrees of neuropathy. METHODS: We assessed 10 control subjects and 38 diabetic patients, classified as absent, mild, moderate, or severe neuropathy, by a fuzzy system based on clinical variables. Multichannel sEMG (64-electrode matrix) of tibialis anterior and gastrocnemius medialis muscles were acquired during isometric contractions at 10%, 20%, and 30% of the maximum voluntary contraction, and force levels during dorsi- and plantarflexion were recorded...
January 4, 2017: Clinical Biomechanics
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