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Kathia Sandoval, Yan Ding, Piero Gardinali
Comprehensive characterization of exposure media used in toxicology studies is still an area of significant divergence when evaluating potential oil spill impacts. When preparing exposure media used for toxicology testing, small variations in simple parameters such as mixing energy, oil type and loading can significantly affect the concentration of the oil components to which test organisms are exposed. The key goal of this study was compare and contrast the physical and chemical compositions of oil water mixtures prepared using fresh and weathered Macondo-related oils under different conditions of mixing and in the presence/absence of chemical dispersants...
October 23, 2016: Science of the Total Environment
Manoel Antonio Dos Santos, Maria Laura de Paula Lopes Pereira-Martins
The tasks of caregiving for children with disabilities involve contextual life stressors. The study aimed to investigate the coping strategies used by parents of children with intellectual disabilities (ID). The search included articles published between 2001 and 2015 on the PubMed, LILACS and PsycINFO databases, using the following key words: intellectual disability, coping, parents, caregivers, family. Thirteen articles were selected, the majority of which adopt a cross-sectional, comparative and quantitative approach...
October 2016: Ciência & Saúde Coletiva
Erica H Craig, Jennifer R Adams, Lisette P Waits, Mark R Fuller, Diana M Whittington
Understanding the genetics of a population is a critical component of developing conservation strategies. We used archived tissue samples from golden eagles (Aquila chrysaetos canadensis) in three geographic regions of western North America to conduct a preliminary study of the genetics of the North American subspecies, and to provide data for United States Fish and Wildlife Service (USFWS) decision-making for golden eagle management. We used a combination of mitochondrial DNA (mtDNA) D-loop sequences and 16 nuclear DNA (nDNA) microsatellite loci to investigate the extent of gene flow among our sampling areas in Idaho, California and Alaska and to determine if we could distinguish birds from the different geographic regions based on their genetic profiles...
2016: PloS One
James S Pryke, Francois Roets, Michael J Samways
Southern Africa's grassland biodiversity is threatened by habitat transformation such as commercial forestry. Ecological networks (ENs) have been instigated to alleviate the pressure of habitat transformation on local biodiversity. ENs are large scale webs of corridors and patches of natural vegetation criss-crossing production landscapes that can simulate conditions in protected areas (PAs). Many ENs have lost many native large mammal species, which have been replaced by domestic livestock to retain natural grazing dynamics, which could have an impact on the long-term value of ENs for insects...
2016: PloS One
Alireza Mashaghi, Sergey Bezrukavnikov, David P Minde, Anne S Wentink, Roman Kityk, Beate Zachmann-Brand, Matthias P Mayer, Günter Kramer, Bernd Bukau, Sander J Tans
The Hsp70 system is a central hub of chaperone activity in all domains of life. Hsp70 performs a plethora of tasks, including folding assistance, protection against aggregation, protein trafficking, and enzyme activity regulation, and interacts with non-folded chains, as well as near-native, misfolded, and aggregated proteins. Hsp70 is thought to achieve its many physiological roles by binding peptide segments that extend from these different protein conformers within a groove that can be covered by an ATP-driven helical lid...
October 26, 2016: Nature
GuiYun Hang, WenLi Yu, Tao Wang, Zhen Li
In order to determine the adsorption mechanism of water on the crystal surfaces of the explosive JOB-9003 and the effect of this adsorption on the sensitivity and detonation performance of this explosive, a model of the crystal of JOB-9003 was created in the software package Materials Studio (MS). The adsorption process was simulated, and molecular dynamics simulation was performed with the COMPASS force field in the NPT ensemble to calculate the sensitivity and detonation performance of the explosive. The results show that the maximum trigger bond length decreases whereas the interaction energy of the trigger bond and the cohesive energy density increase after adsorption, indicating that the sensitivity of JOB-9003 decreases...
November 2016: Journal of Molecular Modeling
Priya Antony, Bincy Baby, Ranjit Vijayan
Phosphatidylinositols and their phosphorylated derivatives, phosphoinositides, play a central role in regulating diverse cellular functions. These phospholipids have been shown to interact with the hydrophobic TH domain of the tumor necrosis factor (TNF)-α-induced protein 8 (TIPE) family of proteins. However, the precise mechanism of interaction of these lipids is unclear. Here we report the binding mode and interactions of these phospholipids in the TH domain, as elucidated using molecular docking and simulations...
November 2016: Journal of Molecular Modeling
Wang Heping, Geng Xingguo, Li Xiaoguang, Zang Duyang
This paper presents an exploration of the separation behavior and pattern formation in a shear binary fluid with dynamic temperature after slow cooling via coupled lattice Boltzmann method. The phase separation procedure can be divided into three different stages: spinodal decomposition, domain growth, and domain stretch. The effect of thermal diffusion was observed to be more significant than that of shear convection in the spinodal decomposition stage, while the opposite was observed in the domain growth stage...
October 2016: European Physical Journal. E, Soft Matter
Ruchi Malik, Bhanwar Singh Choudhary, Shubham Srivastava, Pakhuri Mehta, Manish Sharma
Alzheimer's disease (AD), a progressive neurodegenerative disorder is the most common cause of dementia among elderly people. To date, the successful therapeutic strategy to treat AD is maintaining the levels of acetylcholine via inhibiting acetylcholinesterase (AChE). The present study involves identification of newer AChE inhibitors by dual approach of e-pharmacophore and structure based virtual screening of Asinex library. Robustness of docking protocol was validated by enrichment calculation with ROC value 0...
October 26, 2016: Journal of Biomolecular Structure & Dynamics
Austin M Faught, Michael Trager, Fang-Fang Yin, John Kirkpatrick, Justus Adamson
PURPOSE: The recent development of multifocal stereotactic radiosurgery (SRS) using a single isocenter volumetric modulated arc theory (VMAT) technique warrants a re-examination of the quality assurance (QA) tolerances for routine mechanical QA recommended by the American Association of Physicists in Medicine Task Group Report Number 142. Multifocal SRS can result in targets with small volumes being at a large off-axis distance from the treatment isocenter. Consequently, angular errors in the collimator, patient support assembly (PSA), or gantry could have an increased impact on target coverage...
October 2016: Medical Physics
Marta Tarkanovskaja, Kuno Kooser, Helena Levola, Ergo Nõmmiste, Edwin Kukk
Photofragmentation of small gas-phase acetamide clusters (CH3CONH2)n (n ≤ 10) produced by a supersonic expansion source has been studied using time-of-flight ion mass spectroscopy combined with tunable vacuum-ultraviolet (VUV) synchrotron radiation. Fragmentation channels of acetamide clusters under VUV photoionization resulting in protonated and ammoniated clusters formation were identified with the discussion about the preceding intramolecular rearrangements. Acetamide-2,2,2-d3 clusters were also studied in an experiment with a gas discharge lamp as a VUV light source; comparison with the main experiment gave insights into the mechanism of formation of protonated acetamide clusters, indicating that proton transfer from amino group plays a dominant role in that process...
September 28, 2016: Journal of Chemical Physics
Irina V Fedorova, Michael A Krestyaninov, Lyubov P Safonova
Car-Parrinello molecular dynamics simulations of phosphoric acid (H3PO4)-N,N-dimethylformamide (DMF) mixtures over the whole composition range have been carried out. It has been found that the neutral molecules are the dominant species in this system. The concentration dependences of the average number of H-bonds per proton acceptor atom in P=O and C=O groups as well as per proton donor atom in DMFH(+) ions towards phosphate species have been discussed. The H-bonding between components in all investigated mixtures of H3PO4 and DMF is possible...
September 28, 2016: Journal of Chemical Physics
Alexander W Peterson, Michael Halter, Anne L Plant, John T Elliott
Surface plasmon resonance (SPR) imaging allows real-time label-free imaging based on index of refraction and changes in index of refraction at an interface. Optical parameter analysis is achieved by application of the Fresnel model to SPR data typically taken by an instrument in a prism based figuration. We carry out SPR imaging on a microscope by launching light into a sample and collecting reflected light through a high numerical aperture microscope objective. The SPR microscope enables spatial resolution that approaches the diffraction limit and has a dynamic range that allows detection of subnanometer to submicrometer changes in thickness of biological material at a surface...
September 2016: Review of Scientific Instruments
H Pathak, J C Palmer, D Schlesinger, K T Wikfeldt, J A Sellberg, L G M Pettersson, A Nilsson
The thermodynamic response functions of water exhibit an anomalous increase upon cooling that becomes strongly amplified in the deeply supercooled regime due to structural fluctuations between disordered and tetrahedral local structures. Here, we compare structural data from recent x-ray laser scattering measurements of water at 1 bar and temperatures down to 227 K with structural properties computed for several different water models using molecular dynamics simulations. Based on this comparison, we critically evaluate four different thermodynamic scenarios that have been invoked to explain the unusual behavior of water...
October 7, 2016: Journal of Chemical Physics
Giorgio Cinacchi, Alberto Maria Pintus, Alessandro Tani
The mechanism of diffusion of helical particles in the new screw-like nematic phase is studied by molecular dynamics numerical simulation. Several dynamical indicators are reported that evidence and microscopically characterise the special translo-rotational motion by which helical particles move in this chiral liquid-crystalline phase. Besides mean square displacements and diffusion coefficients resolved parallel and perpendicular to the nematic director, a suitable translo-rotational van Hove self-correlation function and a sequence of translational and rotational velocity, self- and distinct-, time correlation functions are calculated...
October 7, 2016: Journal of Chemical Physics
Maria A Trachsel, Timo Wiedmer, Susan Blaser, Hans-Martin Frey, Quansong Li, Sergi Ruiz-Barragan, Lluís Blancafort, Samuel Leutwyler
We have investigated the S0 → S1 UV vibronic spectrum and time-resolved S1 state dynamics of jet-cooled amino-keto 1-methylcytosine (1MCyt) using two-color resonant two-photon ionization, UV/UV holeburning and depletion spectroscopies, as well as nanosecond and picosecond time-resolved pump/delayed ionization measurements. The experimental study is complemented with spin-component-scaled second-order coupled-cluster and multistate complete active space second order perturbation ab initio calculations. Above the weak electronic origin of 1MCyt at 31 852 cm(-1) about 20 intense vibronic bands are observed...
October 7, 2016: Journal of Chemical Physics
Wynton C McClary, John Paul Sumida, Michele Scian, Lorela Paco, William M Atkins
Cytochrome P4503A4 (CYP3A4) is a peripheral membrane protein that plays a major role in enzymatic detoxication of many drugs and toxins. CYP3A4 has an integral membrane N-terminal helix and a localized patch comprised of the G'- and F'-helix regions that are embedded in the membrane, but the effects of membrane composition on CYP3A4 function are unknown. Here, circular dichroism and differential scanning calorimetry were used to compare the stability of CYP3A4 in lipid bilayer nanodiscs with varying ratios of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC): 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)...
October 26, 2016: Biochemistry
Anirban Sharma, Pradip Kr Ghorai
Confinement effect on structural and dynamical properties of 1, 3 - dimethylimidazolium bromide ([MMIM][Br]) ionic liquid (IL) have been investigated by molecular dynamics simulation. We use zeolite faujasite (NaY) as hydrophilic confinement and dealuminated faujasite (DAY) as hydrophobic confinement. Presence of extra framework cation [Na+] in NaY makes the host hydrophilic, whereas DAY with no extra framework cation is hydrophobic. Though both NaY and DAY have almost similar structures, IL shows markedly different structural and dynamical properties in these confinements and in bulk...
October 26, 2016: Journal of Physical Chemistry. B
Jordana K Thibado, Ashley N Martfeld, Denise V Greathouse, Roger E Koeppe
An essential component of mammalian cells, cholesterol exerts significant influence on the physical properties of the cell membrane and in turn its constituents, including membrane proteins. Although sparse, polar amino-acid residues are highly conserved in membrane proteins and play pivotal roles in determining specific structural and functional properties. To gain greater understanding of particular polar residues in the membrane environment, we have examined two specific "guest" Arg residues within a well-defined and deuterium-labeled "host" framework provided by the transmembrane helical peptide GWALP23 (acetyl-GGALWLALALALALALALWLAGA-amide)...
October 26, 2016: Biochemistry
Xurui Zhang, Plamen Tchoukov, Rogerio Manica, Louxiang Wang, Qingxia Liu, Zhenghe Xu
Interactions involving deformable surfaces reveal a number of distinguishing physicochemical characteristics that do not exist in interactions between rigid solid surfaces. A unique fully custom-designed instrument, referred to as integrated thin liquid film force apparatus (ITLFFA), was developed to study the interactions between one deformable and one solid surface in liquid. Incorporating a bimorph force sensor with interferometry, this device allows for the simultaneous measurement of the time-dependent interaction force and the corresponding spatiotemporal film thickness of the intervening liquid film...
October 26, 2016: Soft Matter
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