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Tuan Anh Ho, Yifeng Wang, Louise J Criscenti
Kerogen plays a central role in hydrocarbon generation in an oil/gas reservoir. In a subsurface environment, kerogen is constantly subjected to stress confinement or relaxation. The interplay between mechanical deformation and gas adsorption of the materials could be an important process for shale gas production but unfortunately is poorly understood. Using a hybrid Monte Carlo/molecular dynamics simulation, we show here that a strong chemo-mechanical coupling may exist between gas adsorption and mechanical strain of a kerogen matrix...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Neeladri Sekhar Roy, Subrata Debnath, Abhijit Chakraborty, Prasenjit Chakraborty, Indrani Bera, Raka Ghosh, Nanda Ghoshal, Saikat Chakrabarti, Siddhartha Roy
Localized separation of strands of duplex DNA is a necessary step in many DNA-dependent processes, including transcription and replication. Little is known about how these strand separations occur. The strand-separated E.coli RNA polymerase-promoter open-complex structure showed four bases of the non-template strand, the master base -11A, -7, -6 and +2, in a flipped state and inserted into protein pockets. To explore whether any property of these bases in the duplex state pre-disposes them to flipping, NMR studies were performed on a wild-type promoter in the duplex state...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Konda Reddy Karnati, Yixuan Wang
Two widely used anticancer drugs, doxorubicin (DOX) and paclitaxel (PTX), possess distinct physical properties and chemotherapy specificity. In order to investigate their interaction mechanism with single-walled carbon nanotubes (SWCNTs), co-loading and releasing from the SWCNTs, all-atom molecular dynamics (MD) simulations were firstly carried out for different SWCNT systems, followed by binding free energy calculation with MM-PBSA. The results indicate that the co-loading of DOX and PTX onto the pristine SWCNT is exothermic and spontaneous...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Jeannine Steinmeyer, Heidi-Kristin Walter, Mathilde A Bichelberger, Violetta Schneider, Tomáš Kubař, Franziska Rönicke, Bettina Olshausen, Karin Nienhaus, Gerd Ulrich Nienhaus, Ute Schepers, Marcus Elstner, Hans-Achim Wagenknecht
Two fluorescent dyes covalently attached in diagonal interstrand orientation to siRNA undergo energy transfer and thereby enable a dual color fluorescence readout (red/green) for hybridization. Three different structural variations were carried out and compared by their optical properties, including (i) the base surrogate approach with an acyclic linker as a substitute of the 2-deoxyriboside between the phosphodiester bridges, (ii) the 2'-modification of conventional ribofuranosides and (iii) the arabino-configured 2'-modification...
March 22, 2018: Organic & Biomolecular Chemistry
Lingci Zhao, Irina P Suarez, Diego F Gauto, Rodolfo M Rasia, Jin Wang
The intrinsically disordered protein domain DCL1-A is the first report of a complete double stranded RNA binding domain folding upon binding. DCL1-A recognizes the dsRNA by acquiring a well-folded structure after engagement with its interaction partner. Despite the structural characterization of the interaction complex underlying the recognition of dsRNA has been established, the dynamics of disorder-to-order transitions in the binding process remains elusive. Here we have developed a coarse-grained structure-based model with consideration of electrostatic interactions to explore the mechanism of the coupled folding and binding...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Madhusudhanan Gogul Ramnath, Ramaraj Thirugnanasampandan, Nagarajan NagaSundaram, Gunasekaran Bhuvaneswari
BACKGROUND: Genus Isodon (Lamiaceae) is a prolific source for bioactive terpenoids. Nowadays, people move towards natural products because of undesirable effects of chemotherapeutic drugs. OBJECTIVE: In silico and in vitro approach were attempted to screen bioactive terpenoids isolated from Isodon wightii with acetylcholinesterase and histone deacetylase3 receptors, Methods: Terpenoids such as abietic acid, oleanolic acid, α-amyrin acetate, β-amyrin acetate were docked with AchE and HDAC3 receptors using AutoDock Vina (version 1...
March 20, 2018: Current Computer-aided Drug Design
Junjian Chen, Meng Gao, Lin Wang, Shiwu Li, Jingcai He, Anjun Qin, Li Ren, Yingjun Wang, Ben Zhong Tang
Multi-drug resistant bacterial infection has become one of the most serious threats to human health. Antimicrobial peptides (AMPs) have been identified as potential alternatives to antibiotics owing to their excellent bactericidal activity. However, the complicated bactericidal mechanism of AMPs is still poorly understood. Fluorescence imaging has many advantages in terms of dynamic monitoring, easy operation, and high sensitivity. In this study, we developed an aggregation-induced emission (AIE)-active probe AMP-2HBT by decorating of the antimicrobial peptide HHC36 (KRWWKWWRR) with an AIEgen of 2-(2-hydroxyphenyl)benzothiazole (HBT)...
March 22, 2018: ACS Applied Materials & Interfaces
Teresa S Henriques, Madalena D Costa, Pooja Mathur, Priyam Mathur, Roger B Davis, Murray A Mittleman, Kamal R Khabbaz, Ary L Goldberger, Balachundhar Subramaniam
Complexity measures are intended to assess the cardiovascular system's capacity to respond to stressors. We sought to determine if decreased BP complexity is associated with increased estimated risk as obtained from two standard instruments: the Society of Thoracic Surgeons' (STS) Risk of Mortality and Morbidity Index and the European System for Cardiac Operative Risk Evaluation Score (EuroSCORE II). In this observational cohort study, preoperative systolic, diastolic, mean (MAP) and pulse pressure (PP) time series were derived in 147 patients undergoing cardiac surgery...
March 21, 2018: Journal of Clinical Monitoring and Computing
Alessandro Mauro, Nicola Massarotti, Mohamed Salahudeen, Mario R Romano, Vito Romano, Perumal Nithiarasu
The present work describes the application of the generalised porous medium model to study heat and fluid flow in healthy and glaucomatous eyes of different subject specimens, considering the presence of ocular cavities and porous tissues. The 2D computational model, implemented into the open-source software OpenFOAM, has been verified against benchmark data for mixed convection in domains partially filled with a porous medium. The verified model has been employed to simulate the thermo-fluid dynamic phenomena occurring in the anterior section of four patient-specific human eyes, considering the presence of anterior chamber (AC), trabecular meshwork (TM), Schlemm's canal (SC), and collector channels (CC)...
March 22, 2018: Medical & Biological Engineering & Computing
João R Bezerra-Neto, Natalia G Sousa, Luis P M Dos Santos, Adriana N Correia, Pedro de Lima-Neto
The effect of water on the physicochemical properties of an ethylene glycol and choline chloride mixture containing Cu2+ ions was investigated by electrochemical techniques and molecular dynamics simulation. The experiments and computational calculations were carried out by increasing the water content from 0 up to 10% (v/v). The cyclic voltammetry and chronopotentiometry techniques showed that the diffusion coefficient of Cu2+ ions increased and that the peak potentials for both the Cu2+/Cu+ and Cu+/Cu redox couples shifted towards more positive potentials with the increase in the water content in the solution...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Markus Boeckle, Georgine Szipl, Thomas Bugnyar
Background: Acoustic parameters of animal signals have been shown to correlate with various phenotypic characteristics of the sender. These acoustic characteristics can be learned and categorized and thus are a basis for perceivers' recognition abilities. One of the most demanding capacities is individual recognition, achievable only after repeated interactions with the same individual. Still, class-level recognition might be potentially important to perceivers who have not previously encountered callers but can classify unknown individuals according to the already learned categories...
2018: Frontiers in Zoology
Michael Bitterlich, Philipp Franken, Jan Graefe
Arbuscular mycorrhizal fungi (AMF) proliferate in soils and are known to affect soil structure. Although their contribution to structure is extensively investigated, the consequences of those processes for soil water extractability and transport has, so far, gained surprisingly little attention. Therefore we asked, whether AMF can affect water retention and unsaturated hydraulic conductivity under exclusion of root ingrowth, in order to minimize plant driven effects. We carried out experiments with tomato inoculated with Rhizoglomus irregulare in a soil substrate with sand and vermiculite that created variation in colonization by mixed pots with wild type (WT) plants and mycorrhiza resistant (RMC) mutants...
2018: Frontiers in Plant Science
Oliver Edenharter, Stephan Schneuwly, Juan A Navarro
Friedreich's ataxia (FRDA) is the most important recessive ataxia in the Caucasian population. It is caused by a deficit of the mitochondrial protein frataxin. Despite its pivotal effect on biosynthesis of iron-sulfur clusters and mitochondrial energy production, little is known about the influence of frataxin depletion on homeostasis of the cellular mitochondrial network. We have carried out a forward genetic screen to analyze genetic interactions between genes controlling mitochondrial homeostasis and Drosophila frataxin...
2018: Frontiers in Molecular Neuroscience
Linard Filli, Tabea Sutter, Christopher S Easthope, Tim Killeen, Christian Meyer, Katja Reuter, Lilla Lörincz, Marc Bolliger, Michael Weller, Armin Curt, Dominik Straumann, Michael Linnebank, Björn Zörner
Gait dysfunction is a common and relevant symptom in multiple sclerosis (MS). This study aimed to profile gait pathology in gait-impaired patients with MS using comprehensive 3D gait analysis and clinical walking tests. Thirty-seven patients with MS walked on the treadmill at their individual, sustainable speed while 20 healthy control subjects walked at all the different patient's paces, allowing for comparisons independent of walking velocity. Kinematic analysis revealed pronounced restrictions in knee and ankle joint excursion, increased gait variability and asymmetry along with impaired dynamic stability in patients...
March 21, 2018: Scientific Reports
Chuansong Quan, Weifeng Shi, Yang Yang, Yongchun Yang, Xiaoqing Liu, Wen Xu, Hong Li, Juan Li, Qianli Wang, Zhou Tong, Gary Wong, Cheng Zhang, Sufang Ma, Zhenghai Ma, Guanghua Fu, Zewu Zhang, Yu Huang, Houhui Song, Liuqing Yang, William J Liu, Yingxia Liu, Wenjun Liu, George F Gao, Yuhai Bi
H7N9 virus has caused five infection waves since it emerged in 2013. The highest number of human cases was seen in Wave Five; however, the underlying reasons have not been thoroughly elucidated. In this study, the geographical distribution, phylogeny and genetic evolution of 240 H7N9 viruses in Wave Five, including 35 new isolates from patients and poultry in nine provinces, were comprehensively analyzed together with strains from first four waves. Geographical distribution analysis displayed the newly-emerging highly pathogenic (HP) and low pathogenic (LP) H7N9 viruses were co-circulating, causing human and poultry infections across China...
March 21, 2018: Journal of Virology
Jonathan M Waters, Tania M King, Ceridwen I Fraser, Dave Craw
The subtropical front (STF) generally represents a substantial oceanographic barrier to dispersal between cold-sub-Antarctic and warm-temperate water masses. Recent studies have suggested that storm events can drastically influence marine dispersal and patterns. Here we analyse biological and geological dispersal driven by two major, contrasting storm events in southern New Zealand, 2017. We integrate biological and physical data to show that a severe southerly system in July 2017 disrupted this barrier by promoting movement of substantial numbers of southern sub-Antarctic Durvillaea kelp rafts across the STF, to make landfall in mainland NZ...
March 2018: Journal of the Royal Society, Interface
D Himmelhan, O Rawashdeh, H H A Oelschläger
This study characterizes the early postnatal development of the visual neocortex in C3H/HeNRj mice. These mice are homozygous for the Pde6brd1 mutation, which causes retinal degeneration starting from postnatal day 7 (P7). To monitor the development of the visual cortex between P3 and P28 we used eight antigens known to be expressed at different developmental stages (Nestin, tau3, β3- Tubulin, Calbindin, Doublecortin, MAP2, Parvalbumin and NeuN). Using semiquantitative analysis we traced the expression and localization of different developmental markers throughout the layers of the visual cortex...
March 18, 2018: Mechanisms of Development
Roelof B Toonen, Klaas J Wardenaar, Elisabeth H Bos, Sonja L van Ockenburg, Peter de Jonge
BACKGROUND: Many biological variables sampled from human subjects show a diurnal pattern, which poses special demands on the techniques used to analyze such data. Furthermore, most biological variables belong to nonlinear dynamical systems, which may make linear statistical techniques less suitable to analyze their dynamics. The current study investigates the usefulness of two analysis techniques based on nonlinear lagged vector embeddings: sequentially weighted global linear maps (SMAP), and bundle embeddings...
March 21, 2018: BMC Medical Research Methodology
Neha Maurya, Mehraj Ud Din Parray, Jitendra Kumar Maurya, Amit Kumar, Rajan Patel
The binding nature of amphiphilic drugs viz. promethazine hydrochloride (PMT) and adiphenine hydrochloride (ADP), with human hemoglobin (Hb) was unraveled by fluorescence, absorbance, time resolved fluorescence, fluorescence resonance energy transfer (FRET) and circular dichroism (CD) spectral techniques in combination with molecular docking and molecular dynamic simulation methods. The steady state fluorescence spectra indicated that both PMT and ADP quenches the fluorescence of Hb through static quenching mechanism which was further confirmed by time resolved fluorescence spectra...
March 11, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Agnieszka Drozd, Dominika Wojewska, Manuel David Peris-Díaz, Piotr Jakimowicz, Artur Krężel
Metallothioneins (MTs), small cysteine-rich proteins, present in four major isoforms, are key proteins involved in zinc and copper homeostasis in mammals. To date, only one X-ray crystal structure of a MT has been solved. It demonstrates seven bivalent metal ions bound in two structurally independent domains with M4S11 (α) and M3S9 (β) clusters. Recent discoveries indicate that Zn(ii) ions are bound with MT2 with the range from nano- to picomolar affinity, which determines its cellular zinc buffering properties that are demonstrated by the presence of partially Zn(ii)-depleted MT2 species...
March 21, 2018: Metallomics: Integrated Biometal Science
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