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Qifei Li, Mingjie Tang, Anhong Zhou
People are taking up antioxidants in their daily diet and being exposed to a potential diesel exhaust particles (DEP)-containing environment. Thus it is important to study in vitro cellular responses when cells are exposed to DEP with or without antioxidant treatment. The investigation of DEP and resveratrol (RES) on cellular biophysical and biochemical changes is needed to better understand the mechanisms of DEP and RES in mammalian cells. A combination of two non-invasive techniques (atomic force microscopy, AFM, and Raman spectroscopy, RM) and multimodal tools were applied to evaluate the biophysical, biochemical alterations and cytokine, membrane potential and cell cycle of cells with or without RES pretreatment to different times of DEP exposure...
December 9, 2016: Journal of Applied Toxicology: JAT
Alessandro Erba, Dominique Caglioti, Claudio Marcelo Zicovich-Wilson, Roberto Dovesi
Two alternative approaches for the quantum-mechanical calculation of the nuclear-relaxation term of elastic and piezoelectric tensors of crystalline materials are illustrated and their computational aspects discussed: (i) a numerical approach based on the geometry optimization of atomic positions at strained lattice configurations and (ii) a quasi-analytical approach based on the evaluation of the force- and displacement-response internal-strain tensors as combined with the interatomic force-constant matrix...
December 9, 2016: Journal of Computational Chemistry
Michele Menotta, Sara Biagiotti, Giulia Bartolini, Bianchi Marzia, Sara Orazi, Aldo Germani, Luciana Chessa, Mauro Magnani
Ataxia telangiectasia is a rare genetic disease and no therapy is currently available. Glucocorticoid analogues have been shown to improve the neurological symptoms of treated patients. In the present study ataxia telangiectasia and wild type cells were used as a cellular model and treated with dexamethasone. The cells were subsequently investigated for membrane and whole cell mechanical properties by atomic force microscopy. In addition, cytoskeleton protein dynamics and nuclear shapes were assayed by fluorescence microscopy, while western blots were used to assess actin and tubulin content...
December 8, 2016: Cell Biochemistry and Biophysics
Muthukumaran Rajagopalan, Sangeetha Balasubramanian, Ilya Ioshikhes, Amutha Ramaswamy
Post translational modifications have a profound role in the regulation of several biological processes such as transcription, replication, and DNA repair. Acetylation and phosphorylation form a major class of post translational modifications involved in nucleosomal regulation by modifying its structure. The effect of post translational modifications on nucleosome structure could be better explored when the molecular trajectories explaining the time dependent structural evolution over a period of time is examined at the atomic level...
December 8, 2016: European Biophysics Journal: EBJ
Ying Huang, Chunying Rong, Ruiqin Zhang, Shubin Liu
Wave function theory (WFT) and density functional theory (DFT)-the two most popular solutions to electronic structure problems of atoms and molecules-share the same origin, dealing with the same subject yet using distinct methodologies. For example, molecular orbitals are artifacts in WFT, whereas in DFT, electron density plays the dominant role. One question that needs to be addressed when using these approaches to appreciate properties related to molecular structure and reactivity is if there is any link between the two...
January 2017: Journal of Molecular Modeling
Arata Nagasaka, Tomoyasu Shinoda, Takumi Kawaue, Makoto Suzuki, Kazuaki Nagayama, Takeo Matsumoto, Naoto Ueno, Ayano Kawaguchi, Takaki Miyata
Cell-producing events in developing tissues are mechanically dynamic throughout the cell cycle. In many epithelial systems, cells are apicobasally tall, with nuclei and somata that adopt different apicobasal positions because nuclei and somata move in a cell cycle-dependent manner. This movement is apical during G2 phase and basal during G1 phase, whereas mitosis occurs at the apical surface. These movements are collectively referred to as interkinetic nuclear migration, and such epithelia are called "pseudostratified...
2016: Frontiers in Cell and Developmental Biology
Sushil Kumar, Charles T Hash, Nepolean Thirunavukkarasu, Govind Singh, Vengaldas Rajaram, Abhishek Rathore, Senthilvel Senapathy, Mahesh D Mahendrakar, Rattan S Yadav, Rakesh K Srivastava
Pearl millet is a multipurpose grain/fodder crop of the semi-arid tropics, feeding many of the world's poorest and most undernourished people. Genetic variation among adapted pearl millet inbreds and hybrids suggests it will be possible to improve grain micronutrient concentrations by selective breeding. Using 305 loci, a linkage map was constructed to map QTLs for grain iron [Fe] and zinc [Zn] using replicated samples of 106 pearl millet RILs (F6) derived from ICMB 841-P3 × 863B-P2. The grains of the RIL population were evaluated for Fe and Zn content using atomic absorption spectrophotometer...
2016: Frontiers in Plant Science
José P Faria, James J Davis, Janaka N Edirisinghe, Ronald C Taylor, Pamela Weisenhorn, Robert D Olson, Rick L Stevens, Miguel Rocha, Isabel Rocha, Aaron A Best, Matthew DeJongh, Nathan L Tintle, Bruce Parrello, Ross Overbeek, Christopher S Henry
Understanding gene function and regulation is essential for the interpretation, prediction, and ultimate design of cell responses to changes in the environment. An important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. These gene sets, Atomic Regulons (ARs), represent fundamental units of function within a cell and could be used to associate genes of unknown function with cellular processes and to enable rational genetic engineering of cellular systems...
2016: Frontiers in Microbiology
Aida Razi, Robert A Britton, Joaquin Ortega
Cryo-electron microscopy (cryo-EM) had played a central role in the study of ribosome structure and the process of translation in bacteria since the development of this technique in the mid 1980s. Until recently cryo-EM structures were limited to ∼10 Å in the best cases. However, the recent advent of direct electron detectors has greatly improved the resolution of cryo-EM structures to the point where atomic resolution is now achievable. This improved resolution will allow cryo-EM to make groundbreaking contributions in essential aspects of ribosome biology, including the assembly process...
December 8, 2016: Nucleic Acids Research
Manasi A Pethe, Aliza B Rubenstein, Sagar D Khare
Characterizing the substrate specificity of protease enzymes is critical for illuminating the molecular basis of their diverse and complex roles in a wide array of biological processes. Rapid and accurate prediction of their extended substrate specificity would also aid in the design of custom proteases capable of selectively and controllably cleaving biotechnologically or therapeutically relevant targets. However, current in silico approaches for protease specificity prediction, rely on, and are therefore limited by, machine learning of sequence patterns in known experimental data...
December 5, 2016: Journal of Molecular Biology
Meilin Zhu, Xiancai Zeng, Yanxue Jiang, Xiaoting Fan, Sihong Chao, Hongbin Cao, Wensheng Zhang
Arsenic species and a possible source of methylated arsenic in a Panax Notoginseng (PN) medicinal plant were explored to further understand the change of inorganic arsenic to the less toxic methylated form to minimize the health risks associated with its medicinal use. Arsenic speciation in PN from major planting areas was determined using high-performance liquid chromatography coupled with hydride generator-atomic fluorescence (HPLC-HG-AFS). Pot experiments were performed to explore the source of methylated arsenic in PN, and the arsenite methyltransferase (arsM) gene abundance was determined using quantitative reverse transcription PCR (q-RTPCR)...
December 5, 2016: Chemosphere
Beatrice Ellen Tyrrell, Andrew Cameron Sayce, Kelly Lyn Warfield, Joanna Louise Miller, Nicole Zitzmann
Influenza virus causes three to five million severe respiratory infections per year in seasonal epidemics, and sporadic pandemics, three of which occurred in the twentieth century and are a continuing global threat. Currently licensed antivirals exclusively target the viral neuraminidase or M2 ion channel, and emerging drug resistance necessitates the development of novel therapeutics. It is believed that a host-targeted strategy may combat the development of antiviral drug resistance. To this end, a class of molecules known as iminosugars, hydroxylated carbohydrate mimics with the endocyclic oxygen atom replaced by a nitrogen atom, are being investigated for their broad-spectrum antiviral potential...
December 8, 2016: Critical Reviews in Microbiology
Behzad Lotfi, Aliakbar Tarlani, Peyman Akbari-Moghaddam, Maryam Mirza-Aghayan, Ali Ahmadi Peyghan, Jacques Muzart, Reza Zadmard
A new derivative of dipodal 1,3-calix[4]arene-based chemosensor (R), which was containing several binding sites have been synthesized and characterized by NMR, IR and LC-MS spectroscopic methods. The selectivity of Rhas been investigated in aqueous methanol, resulting in fluorescence shift and selective recognition of Ag(+) among 20 various alkali, alkaline earth and transition metal ions. Microstructural features of R and its complex with Ag(+)have been investigated by Atomic Force Microscopy (AFM). AFM images can clearly differentiate R from its complex of Ag(+)...
December 1, 2016: Biosensors & Bioelectronics
Arezoo Tahan
DFT/B3LYP calculations were employed to study the effects of tautomerism and explicit/implicit water molecules on Nuclear Quadrupole Resonance (NQR) and Nuclear Magnetic Resonance (NMR) tensors of nitrogen nuclei in tetrazole-5-thione structure. The obtained results revealed that nuclear quadrupole coupling constant (χ) and isotropic chemical shielding (σiso ) values of nitrogen nuclei in tetrazole ring of five possible tautomeric forms of tetrazole-5-thione, i.e. two thione forms called tautomers A and E and three thiol forms called tautomers B, C, and D, were functions of resonance energy(E2 ) values of nitrogen lone pairs...
December 8, 2016: Magnetic Resonance in Chemistry: MRC
Ingmar Bürstel, Elisabeth Siebert, Stefan Frielingsdorf, Ingo Zebger, Bärbel Friedrich, Oliver Lenz
Hydrogenases are nature's key catalysts involved in both microbial consumption and production of molecular hydrogen. H2 exhibits a strongly bonded, almost inert electron pair and requires transition metals for activation. Consequently, all hydrogenases are metalloenzymes that contain at least one iron atom in the catalytic center. For appropriate interaction with H2, the iron moiety demands for a sophisticated coordination environment that cannot be provided just by standard amino acids. This dilemma has been overcome by the introduction of unprecedented chemistry-that is, by ligating the iron with carbon monoxide (CO) and cyanide (or equivalent) groups...
December 5, 2016: Proceedings of the National Academy of Sciences of the United States of America
Ya Feng, Defa Liu, Baojie Feng, Xu Liu, Lin Zhao, Zhuojin Xie, Yan Liu, Aiji Liang, Cheng Hu, Yong Hu, Shaolong He, Guodong Liu, Jun Zhang, Chuangtian Chen, Zuyan Xu, Lan Chen, Kehui Wu, Yu-Tzu Liu, Hsin Lin, Zhi-Quan Huang, Chia-Hsiu Hsu, Feng-Chuan Chuang, Arun Bansil, X J Zhou
Silicene, analogous to graphene, is a one-atom-thick 2D crystal of silicon, which is expected to share many of the remarkable properties of graphene. The buckled honeycomb structure of silicene, along with enhanced spin-orbit coupling, endows silicene with considerable advantages over graphene in that the spin-split states in silicene are tunable with external fields. Although the low-energy Dirac cone states lie at the heart of all novel quantum phenomena in a pristine sheet of silicene, a hotly debated question is whether these key states can survive when silicene is grown or supported on a substrate...
December 7, 2016: Proceedings of the National Academy of Sciences of the United States of America
Stefan Zeller, Maksim Kunitski, Jörg Voigtsberger, Anton Kalinin, Alexander Schottelius, Carl Schober, Markus Waitz, Hendrik Sann, Alexander Hartung, Tobias Bauer, Martin Pitzer, Florian Trinter, Christoph Goihl, Christian Janke, Martin Richter, Gregor Kastirke, Miriam Weller, Achim Czasch, Markus Kitzler, Markus Braune, Robert E Grisenti, Wieland Schöllkopf, Lothar Ph H Schmidt, Markus S Schöffler, Joshua B Williams, Till Jahnke, Reinhard Dörner
Quantum tunneling is a ubiquitous phenomenon in nature and crucial for many technological applications. It allows quantum particles to reach regions in space which are energetically not accessible according to classical mechanics. In this "tunneling region," the particle density is known to decay exponentially. This behavior is universal across all energy scales from nuclear physics to chemistry and solid state systems. Although typically only a small fraction of a particle wavefunction extends into the tunneling region, we present here an extreme quantum system: a gigantic molecule consisting of two helium atoms, with an 80% probability that its two nuclei will be found in this classical forbidden region...
December 6, 2016: Proceedings of the National Academy of Sciences of the United States of America
Saied M Soliman, Assem Barakat
Intermolecular interactions play a vital role in crystal structures. Therefore, we conducted a topological study, using Hirshfeld surfaces and atom in molecules (AIM) analysis, to decompose and analyze, respectively, the different intermolecular interactions in six hydrazone-diacetyl platinum(II) complexes. Using AIM and natural bond orbital (NBO) analyses, we determined the type, nature, and strength of the interactions. All the studied complexes contain C-H⋯O interactions, and the presence of bond critical points along the intermolecular paths underlines their significance...
December 6, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Sergey V Popov, Pavel A Markov, Olga A Patova, Fedor V Vityazev, Larisa A Bakutova, Mikhail F Borisenkov, Ekaterina A Martinson, Boris A Ananchenko, Eugene A Durnev, Andrey A Burkov, Sergey G Litvinets, Vladimir A Belyi, Elena A Ipatova
Pectin hydrogel particles (PHPs) were prepared by ionotropic gelation of low methylesterified pectin of Tanacetum vulgare L. with calcium ions. Wet PHPs prepared from TVF exhibited a smaller diameter and the lower weight as well as exhibited the best textural properties in terms of hardness and elasticity compared to the PHPs prepared from commercial low methylesterified pectin (CU701) used for comparison. Upon air drying, PHPs prepared from CU701 became small and dense microspheres whereas the dry PHPs prepared from TVF exhibited a drop-like shape...
December 8, 2016: Journal of Biomaterials Science. Polymer Edition
Dan-Ping Gong, Tai-Bao Gao, Deng-Ke Cao, Michael D Ward
Cyclometalated Ir(iii) complexes [Ir(dfppy)2(qbiH)](PF6) (1), [Ir(dfppy)2(qbim)](PF6)·H2O (2), [Ir(dfppy)2(qbio)](PF6) (3) and [Ir(dfppy)2(qbi)] (4) have been designed and prepared, in which the N^N ligands qbiH, qbim and qbio incorporate different substituent groups R on their imidazole units (H atom, CH3 group and n-C8H17 group, respectively) in order to explore the influence of the substituent groups R and the protonation/deprotonation state of imidazole units in these Ir(iii) complexes on their structures and luminescence behaviors...
December 8, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
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