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https://www.readbyqxmd.com/read/28107632/structural-changes-in-acetophenone-fluid-films-as-a-function-of-nano-scale-thickness
#1
Samantha L Nania, Scott K Shaw
We report experimental observations of a developing fluid-solid interface by examining acetophenone films of varying thicknesses, supported on solid silver substrates. A dynamic wetting technique provides experimental control of fluid film thickness as a function of rotational velocity. Ellipsometry and infrared reflection absorption spectroscopy data are analyzed to provide absolute film thickness and details of the changing chemical environment for varying film thickness. This data is compared to theoretical models that predict fluid film thicknesses based on physical-chemical properties of the acetophenone/silver pair...
January 20, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28107609/carbon-nanodot-solar-cells-from-renewable-precursors
#2
Maria-Magdalena Titirici, Adam Marinovic, Steve Dunn, Lim Swee Kiat, Joe Briscoe
It has recently been shown that waste biomass can be converted into a wide range of functional materials, including those with desirable optical and electronic properties, offering the opportunity to find new uses for these renewable resources. Photovoltaics is one area where finding the combination of abundant, low-cost and non-toxic materials with the necessary functionality can be challenging. In this paper we compare the performance of carbon nanodots derived from a wide range of biomaterials obtained from different biomass sources as sensitizers for TiO2-based nanostructured solar cells; polysaccharides (chitosan and chitin), monosaccharide (D-glucose), amino acids (L-arginine and L-cysteine) and raw lobster shells are all used to produce carbon nanodots via hydrothermal carbonisation...
January 20, 2017: ChemSusChem
https://www.readbyqxmd.com/read/28107510/effect-of-the-crystal-environment-on-side-chain-conformational-dynamics-in-cyanovirin-n-investigated-through-crystal-and-solution-molecular-dynamics-simulations
#3
Logan S Ahlstrom, Ivan I Vorontsov, Jun Shi, Osamu Miyashita
Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure...
2017: PloS One
https://www.readbyqxmd.com/read/28107498/delineating-substrate-diversity-of-disparate-short-chain-dehydrogenase-reductase-from-debaryomyces-hansenii
#4
Arindam Ghatak, Nagakumar Bharatham, Anirudh P Shanbhag, Santanu Datta, Janani Venkatraman
Short-chain dehydrogenase reductases (SDRs) have been utilized for catalyzing the reduction of many aromatic/aliphatic prochiral ketones to their respective alcohols. However, there is a paucity of data that elucidates their innate biological role and diverse substrate space. In this study, we executed an in-depth biochemical characterization and substrate space mapping (with 278 prochiral ketones) of an unannotated SDR (DHK) from Debaryomyces hansenii and compared it with structurally and functionally characterized SDR Synechococcus elongatus...
2017: PloS One
https://www.readbyqxmd.com/read/28107009/nmr-and-computation-reveal-a-pressure-sensitive-folded-conformation-of-trp-cage
#5
Soichiro Kitazawa, Martin J Fossat, Scott A McCallum, Angel E Garcia, Catherine Ann Royer
Beyond defining the structure and stability of folded states of proteins, primary amino acid sequences determine all of the features of their conformational landscapes. Characterizing how sequence modulates the population of protein excited states or folding pathways requires atomic level detailed structural and energetic information. Such insight is essential for improving protein design strategies, as well as for interpreting protein evolution. Here, high pressure NMR and molecular dynamics simulations were combined to probe the conformational landscape of a small model protein, the tryptophan cage variant, Tc5b...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28106997/time-and-nanoparticle-concentration-affect-the-extractability-of-cu-from-cuo-np-amended-soil
#6
Xiaoyu Gao, Eleanor Spielman-Sun, Sónia Morais Rodrigues, Elizabeth A Casman, Gregory V Lowry
We assess the effect of CuO nanoparticle (NP) concentration and soil aging time on the extractability of Cu from a standard sandy soil (Lufa 2.1). The soil was dosed with CuO NP or Cu(NO3)2 at 10 mg Cu kg-1 soil (mg/kg) or 100 mg/kg total copper, then extracted using either 0.01M CaCl2 or 0.005M DTPA (pH 7.6) extraction fluids at selected times over 31 days. For 100 mg/kg CuO NP, the amount of DTPA-extractable Cu in soil increased from 3 wt% immediately after mixing to 38 wt% after 31 days. In contrast, the extractability of Cu(NO3)2 was highest initially, decreasing with time...
January 20, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28106947/3d-bioprinting-and-its-in-vivo-applications
#7
REVIEW
Nhayoung Hong, Gi-Hoon Yang, JaeHwan Lee, GeunHyung Kim
The purpose of 3D bioprinting technology is to design and create functional 3D tissues or organs in situ for in vivo applications. 3D cell-printing, or additive biomanufacturing, allows the selection of biomaterials and cells (bioink), and the fabrication of cell-laden structures in high resolution. 3D cell-printed structures have also been used for applications such as research models, drug delivery and discovery, and toxicology. Recently, numerous attempts have been made to fabricate tissues and organs by using various 3D printing techniques...
January 20, 2017: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
https://www.readbyqxmd.com/read/28106879/bacterial-community-segmentation-facilitates-the-prediction-of-ecosystem-function-along-the-coast-of-the-western-antarctic-peninsula
#8
Jeff S Bowman, Linda A Amaral-Zettler, Jeremy J Rich, Catherine M Luria, Hugh W Ducklow
Bacterial community structure can be combined with observations of ecophysiological data to build predictive models of microbial ecosystem function. These models are useful for understanding how function might change in response to a changing environment. Here we use five spring-summer seasons of bacterial community structure and flow cytometry data from a productive coastal site along the western Antarctic Peninsula to construct models of bacterial production (BP), an ecosystem function that heterotrophic bacteria provide...
January 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/28106517/traditional-invasive-and-synchrotron-based-non-invasive-assessments-of-3d-printed-hybrid-cartilage-constructs
#9
Adeola Deborah Olubamiji, Ning Zhu, Tuanjie Chang, Chijioke Nwankwo, Zohreh Izadifar, Ali Honaramooz, Daniel Chen, B Frank Eames
Three-dimensional (3D)-printed constructs made of polycaprolactone (PCL) and chondrocyte-impregnated alginate hydrogel (hybrid cartilage constructs) mimic the biphasic nature of articular cartilage, offering promise for cartilage tissue engineering (CTE) applications. However, the regulatory pathway for medical device development requires validation of such constructs through in vitro bench tests and in vivo preclinical examinations premarket approval. Furthermore, non-invasive imaging techniques are required for effective evaluation of the progress of these cartilage constructs, especially when implanted in animal models or human subjects...
January 20, 2017: Tissue Engineering. Part C, Methods
https://www.readbyqxmd.com/read/28106419/probing-the-nodal-structure-of-landau-level-wave-functions-in-real-space
#10
J R Bindel, J Ulrich, M Liebmann, M Morgenstern
The inversion layer of p-InSb(110) obtained by Cs adsorption of 1.8% of a monolayer is used to probe the Landau level wave functions within smooth potential valleys by scanning tunneling spectroscopy at 14 T. The nodal structure becomes apparent as a double peak structure of each spin polarized first Landau level, while the zeroth Landau level exhibits a single peak per spin level only. The real space data show single rings of the valley-confined drift states for the zeroth Landau level and double rings for the first Landau level...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106402/molecular-orbital-rule-for-quantum-interference-in-weakly-coupled-dimers-%C3%A2-low-energy-giant-conductance-switching-induced-by-orbital-level-crossing
#11
Daijiro Nozaki, Andreas Lücke, Wolf Gero Schmidt
Destructive Quantum interference (QI) in molecular junctions has attracted much attention in recent years. It can tune the conductance of molecular devices dramatically, which implies numerous potential applications in thermoelectric and switching applications. There are several schemes that address and rationalize QI in single molecular devices. Dimers play a particular role in this respect, since the QI signal may disappear, depending on the dislocation of monomers. In this Letter, we derive a simple rule that governs the occurrence of QI in weakly coupled dimer stacks of both alternant and non-alternant polyaromatic hydrocarbons (PAHs) and extends the Tada-Yoshizawa scheme...
January 20, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28106310/mechanism-of-type-iii-protein-secretion-regulation-of-flha-conformation-by-a-functionally-critical-charged-residue-cluster
#12
Marc Erhardt, Paige Wheatley, Eun A Kim, Takanori Hirano, Yang Zhang, Mayukh K Sarkar, Kelly T Hughes, David F Blair
The bacterial flagellum contains a specialized secretion apparatus in its base that pumps certain protein subunits through the growing structure to their sites of installation beyond the membrane. A related apparatus functions in the injectisomes of gram-negative pathogens to export virulence factors into host cells. This mode of protein export is termed type-III secretion (T3S). Details of the T3S mechanism are unclear. It is energized by the proton gradient; here, a mutational approach was used to identify proton-binding groups that might function in transport...
January 20, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28105941/the-loss-of-photosynthetic-pathways-in-the-plastid-and-nuclear-genomes-of-the-non-photosynthetic-mycoheterotrophic-eudicot-monotropa-hypopitys
#13
Nikolai V Ravin, Eugeny V Gruzdev, Alexey V Beletsky, Alexander M Mazur, Egor B Prokhortchouk, Mikhail A Filyushin, Elena Z Kochieva, Vitaly V Kadnikov, Andrey V Mardanov, Konstantin G Skryabin
BACKGROUND: Chloroplasts of most plants are responsible for photosynthesis and contain a conserved set of about 110 genes that encode components of housekeeping gene expression machinery and photosynthesis-related functions. Heterotrophic plants obtaining nutrients from other organisms and their plastid genomes represent model systems in which to study the effects of relaxed selective pressure on photosynthetic function. The most evident is a reduction in the size and gene content of the plastome, which correlates with the loss of genes encoding photosynthetic machinery which become unnecessary...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28105917/proclat-a-new-bioinformatics-tool-for-in-silico-protein-reclassification-case-study-of-drab-a-protein-coded-from-the-dratgb-operon-in-azospirillum-brasilense
#14
Elisa Terumi Rubel, Roberto Tadeu Raittz, Nilson Antonio da Rocha Coimbra, Michelly Alves Coutinho Gehlen, Fábio de Oliveira Pedrosa
BACKGROUND: Azopirillum brasilense is a plant-growth promoting nitrogen-fixing bacteria that is used as bio-fertilizer in agriculture. Since nitrogen fixation has a high-energy demand, the reduction of N2 to NH4(+) by nitrogenase occurs only under limiting conditions of NH4(+) and O2. Moreover, the synthesis and activity of nitrogenase is highly regulated to prevent energy waste. In A. brasilense nitrogenase activity is regulated by the products of draG and draT. The product of the draB gene, located downstream in the draTGB operon, may be involved in the regulation of nitrogenase activity by an, as yet, unknown mechanism...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105914/homology-modeling-and-molecular-dynamics-provide-structural-insights-into-tospovirus-nucleoprotein
#15
Rayane Nunes Lima, Muhammad Faheem, João Alexandre Ribeiro Gonçalves Barbosa, Marcelo Depólo Polêto, Hugo Verli, Fernando Lucas Melo, Renato Oliveira Resende
BACKGROUND: Tospovirus is a plant-infecting genus within the family Bunyaviridae, which also includes four animal-infecting genera: Hantavirus, Nairovirus, Phlebovirus and Orthobunyavirus. Compared to these members, the structures of Tospovirus proteins still are poorly understood. Despite multiple studies have attempted to identify candidate N protein regions involved in RNA binding and protein multimerization for tospovirus using yeast two-hybrid systems (Y2HS) and site-directed mutagenesis, the tospovirus ribonucleocapsids (RNPs) remains largely uncharacterized at the molecular level and the lack of structural information prevents detailed insight into these interactions...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105461/the-hepatic-lymphatic-vascular-system-structure-function-markers-and-lymphangiogenesis
#16
REVIEW
Masatake Tanaka, Yasuko Iwakiri
The lymphatic vascular system has been minimally explored in the liver despite its essential functions including maintenance of tissue fluid homeostasis. The discovery of specific markers for lymphatic endothelial cells has advanced the study of lymphatics by methods including imaging, cell isolation, and transgenic animal models and has resulted in rapid progress in lymphatic vascular research during the last decade. These studies have yielded concrete evidence that lymphatic vessel dysfunction plays an important role in the pathogenesis of many diseases...
November 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28104999/development-of-a-scale-assessing-beliefs-about-thirdhand-smoke-baths
#17
Regine Haardörfer, Carla J Berg, Cam Escoffery, Łucja T Bundy, Melbourne Hovell, Michelle C Kegler
BACKGROUND: Similarly to secondhand smoke (SHS), thirdhand smoke (THS) beliefs may be correlated with smoking behaviors and smokefree policies in the home. Thus, there is a need to develop and validate measures to assess beliefs about THS. METHODS: A list of 19 items related to THS were generated by an expert panel and tested in a pilot study. Based on results from an exploratory factor analysis, two factors emerged: THS persistence in the environment and THS impact on health...
2017: Tobacco Induced Diseases
https://www.readbyqxmd.com/read/28104926/the-bending-stress-distribution-in-bilayered-and-graded-zirconia-based-dental-ceramics
#18
Douglas Fabris, Júlio C M Souza, Filipe S Silva, Márcio Fredel, Joana Mesquita-Guimarães, Yu Zhang, Bruno Henriques
The purpose of this study was to evaluate the biaxial flexural stresses in classic bilayered and in graded zirconia-feldspathic porcelain composites. A finite element method and an analytical model were used to simulate the piston-on-ring test and to predict the biaxial stress distributions across the thickness of the bilayer and graded zirconia-feldspathic porcelain discs. An axisymmetric model and a flexure formula of Hsueh et al. were used in the FEM and analytical analysis, respectively. Four porcelain thicknesses were tested in the bilayered discs...
July 2016: Ceramics International
https://www.readbyqxmd.com/read/28104813/structural-modeling-defines-transmembrane-residues-in-adam17-that-are-crucial-for-rhbdf2-adam17-dependent-proteolysis
#19
Xue Li, Thorsten Maretzky, Jose Manuel Perez-Aguilar, Sébastien Monette, Gisela Weskamp, Sylvain Le Gall, Bruce Beutler, Harel Weinstein, Carl P Blobel
A disintegrin and metalloproteinase 17 (ADAM17) controls the release of the pro-inflammatory cytokine tumor necrosis factor α (TNFα) and is crucial for protecting the skin and intestinal barrier by proteolytic activation of Epidermal growth factor receptor (EGFR)-ligands. The seven-membrane spanning inactive Rhomboid2 (iRhom2; Rhbdf2) is required for ADAM17-dependent TNFα shedding and crosstalk with the EGFR, and a point mutation (sinecure, sin) in the first transmembrane domain (TMD) of Rhbdf2 (Rhbdf2(sin)) blocks TNFα shedding, yet little is known about the underlying mechanism...
January 19, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28104810/the-foxp2-forkhead-domain-binds-to-a-variety-of-dna-sequences-with-different-rates-and-affinities
#20
Helen Webb, Olga Steeb, Ashleigh Blane, Lia Rotherham, Shaun Aron, Phillip Machanick, Heini Dirr, Sylvia Fanucchi
FOXP2 is a member of the P subfamily of FOX transcription factors, the DNA binding domain of which is the winged helix forkhead domain. In this work we show that the FOXP2 forkhead domain is able to bind to various DNA sequences, including a novel sequence identified in this work, with different affinities and rates as detected using surface plasmon resonance. Combining the experimental work with molecular docking, we show that high affinity sequences remain bound to the protein for longer, form a greater number of interactions with the protein and induce a greater structural change in the protein than low affinity sequences...
January 18, 2017: Journal of Biochemistry
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