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https://www.readbyqxmd.com/read/29223076/the-impact-of-soil-erosion-on-soil-fertility-and-vine-vigor-a-multidisciplinary-approach-based-on-field-laboratory-and-remote-sensing-approaches
#1
Agata Novara, Antonino Pisciotta, Mario Minacapilli, Antonino Maltese, Fulvio Capodici, Artemi Cerdà, Luciano Gristina
Soil erosion processes in vineyards, beyond surface runoff and sediment transport, have a strong effect on soil organic carbon (SOC) loss and redistribution along the slope. Variation in SOC across the landscape can determine differences in soil fertility and vine vigor. The goal of this research was to analyze the interactions among vines vigor, sediment delivery and SOC in a sloping vineyard located in Sicily. Six pedons were studied along the slope by digging 6 pits up to 60cm depth. Soil was sampled every 10cm and SOC, water extractable organic carbon (WEOC) and specific ultraviolet absorbance (SUVA) were analyzed...
December 6, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29222970/relaxation-of-structural-constraints-during-amicyanin-unfolding
#2
John J Kozak, Harry B Gray, Roberto A Garza-López
We study the thermal unfolding of amicyanin by quantifying the resiliency of the native state to structural perturbations. Three signatures characterizing stages of unfolding are identified. The first signature, lateral extension of the polypeptide chain, is calculated directly from the reported crystallographic data. Two other signatures, the radial displacement of each residue from Cu(II) and the angular spread in the chain as the protein unfolds, are calculated using crystallographic data in concert with a geometrical model we introduced previously (J...
November 22, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/29222332/stabilization-of-the-gp120-v3-loop-through-hydrophobic-interactions-reduces-the-immunodominant-v3-directed-non-neutralizing-response-to-hiv-1-envelope-trimers
#3
Steven W de Taeye, Alba Torrents de la Peña, Andrea Vecchione, Enzo Scutigliani, Kwinten Sliepen, Judith A Burger, Patricia van der Woude, Anna Schorcht, Edith E Schermer, Marit J van Gils, Celia C LaBranche, David C Montefiori, Ian A Wilson, John P Moore, Andrew B Ward, Rogier W Sanders
To provide protective immunity against circulating primary HIV-1 strains, a vaccine most likely has to induce broadly neutralizing antibodies (bNAbs) to the HIV-1 envelope (Env) glycoprotein spike. Recombinant Env trimers such as the prototype BG505 SOSIP.664 that closely mimic the native Env spike can induce autologous neutralizing antibodies (NAbs) against relatively resistant (tier-2) primary viruses. Ideally, Env immunogens should present bNAb epitopes, but limit the presentation of immunodominant non-NAb epitopes that might induce off-target and potentially interfering responses...
December 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29221988/modulations-of-keap1-nrf2-signaling-axis-by-tiia-ameliorated-the-oxidative-stress-induced-myocardial-apoptosis
#4
Shi-Hai Yan, Ning-Wei Zhao, Zhi-Rong Geng, Jia-Yin Shen, Fu-Ming Liu, Dong Yan, Jie Zhou, Chao Nie, Cheng-Cai Huang, Zhu-Yuan Fang
Mounting evidence has strongly implicated oxidative stress in the development of cardiac dysfunction, and myocardial apoptosis contributes to the pathogenesis of heart failure. Quantitative cardiac proteomics data revealed that pressure load by TAC resulted in a significant decline in mitochondrial metabolic activity, where TIIA (Tanshinone IIA sulfonate) treatment reversed it in vivo, which might be mediated by Nrf2. In NRVMs, TIIA treatment ameliorated H2O2-induced caspase-3/9 activations through the suppression of p38 and mTOR signaling pathways, where caspase-mediated cleavage of YY1 and PARP resulted in the defects in mitochondrial biogenesis and DNA repair, and this event finally led to cardiomyocyte apoptosis...
December 5, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29221408/exploring-a-multi-scale-method-for-molecular-simulation-in-continuum-solvent-model-explicit-simulation-of-continuum-solvent-as-an-incompressible-fluid
#5
Li Xiao, Ray Luo
We explored a multi-scale algorithm for the Poisson-Boltzmann continuum solvent model for more robust simulations of biomolecules. In this method, the continuum solvent/solute interface is explicitly simulated with a numerical fluid dynamics procedure, which is tightly coupled to the solute molecular dynamics simulation. There are multiple benefits to adopt such a strategy as presented below. At this stage of the development, only nonelectrostatic interactions, i.e., van der Waals and hydrophobic interactions, are included in the algorithm to assess the quality of the solvent-solute interface generated by the new method...
December 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29221394/mesoscale-simulations-of-confined-nafion-thin-films
#6
P Vanya, J Sharman, J A Elliott
The morphology and transport properties of thin films of the ionomer Nafion, with thicknesses on the order of the bulk cluster size, have been investigated as a model system to explain the anomalous behaviour of catalyst/electrode-polymer interfaces in membrane electrode assemblies. We have employed dissipative particle dynamics (DPD) to investigate the interaction of water and fluorocarbon chains, with carbon and quartz as confining materials, for a wide range of operational water contents and film thicknesses...
December 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29221146/swertiajaponin-inhibits-skin-pigmentation-by-dual-mechanisms-to-suppress-tyrosinase
#7
Bonggi Lee, Kyoung Mi Moon, Bong-Seon Lee, Ju-Hye Yang, Kwang Il Park, Won-Kyung Cho, Jin Yeul Ma
Many skin-whitening compounds target tyrosinase because it catalyzes two rate-limiting steps in melanin synthesis. Although many tyrosinase inhibitors are currently available for a skin-whitening purpose, undesirable adverse effects are also reported. Thus, numerous efforts have been made to develop safer tyrosinase inhibitors from natural products. In line with this, we tested fifty flavonoids, a group of naturally occurring antioxidants and metal chelators, and screened swertiajaponin as the strongest tyrosinase inhibitor in cell-free experiments...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29220758/interaction-of-a-digestive-protease-candida-rugosa-lipase-with-three-surfactants-investigated-by-spectroscopy-molecular-docking-and-enzyme-activity-assay
#8
Rui Zhang, Yang Liu, Xinran Huang, Mengchen Xu, Rutao Liu, Wansong Zong
The extensive use of surfactants in food, laundry products and agriculture has caused concern about their biosafety. However, few studies have been done on their potential effect on the lipase which has always been used with surfactants in food and laundry industry. Herein, we investigated the interaction of three surfactants (sodium dodecyl sulfate (SDS), sodium dodecyl benzene sulfonate (SDBS), sodium lauryl sulfonate (SLS)) with Candida rugosa lipase (CRL), which is a popular biocatalyst used regularly with surfactants...
December 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29219839/efficient-exfoliation-of-layered-materials-by-waste-liquor
#9
Jiheng Ding, Hongran Zhao, Yan Zheng, Qiaolei Wang, Hao Chen, Huimin Dou, Haibin Yu
Based on the unique material properties, two-dimensional (2D) nanomaterials such as graphene, molybdenum disulfide (MoS2), and boron nitride (BN) have been attracting increasing research interest. The potential of 2D materials in the form of nanoplatelets used as new materials will be important to both nanomaterials and advanced materials. Usually water is considered as the ideal dispersed medium, while the essential hydrophobicity of 2D nanoplatelets and limitation of mass production became the quite serious obstacles for the usage in various fields...
December 8, 2017: Nanotechnology
https://www.readbyqxmd.com/read/29219743/building-a-polysaccharide-hydrogel-capsule-delivery-system-for-control-release-of-ibuprofen
#10
Zhi Chen, Ting Wang, Qing Yan
Development of a delivery system which can effectively carry hydrophobic drugs and have pH response is becoming necessary. Here we demonstrate that through preparation of β-cyclodextrin polymer (β-CDP), a hydrophobic drug molecule of ibuprofen (IBU) was incorporated into our prepared β-CDP inner cavities, aiming to improve the poor water solubility of IBU. A core-shell capsule structure has been designed for achieving the drug pH targeted and sustained release. This delivery system was built with polysaccharide polymer of Sodium alginate (SA), sodium carboxymethylcellulose (CMC) and hydroxyethyl cellulose (HEC) by physical cross-linking...
December 8, 2017: Journal of Biomaterials Science. Polymer Edition
https://www.readbyqxmd.com/read/29218946/-metabolism-of-inula-cappa-extract-by-rat-intestinal-bacteria-in-vitro
#11
Zi-Peng Gong, Jing-Yu Hou, Mei Li, Lin-Lin Wu, Ting-Ting Chen, Yong-Jun Li, Ai-Min Wang, Yan-Yu Lan, Yong-Lin Wang
To investigate the metabolism of major components in Inula cappa by rat intestinal bacteria in vitro. I. cappa extract was incubated for 24 h with rat intestinal bacteria under anaerobic environment. After the samples were precipitated by n-butanol, UPLC-Q-TOF-MS/MS was applied for the qualitative analysis of the metabolites, combined with data software such as Metabolite Tools, Data Analysis and so on. The potential metabolites in rat intestinal bacteria were analyzed by comparing the total ion current of the test samples and blank samples and analyzing the quasi-molecular ion and fragment ion of all chromatograms...
September 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29218757/local-and-global-anatomy-of-antibody-protein-antigen-recognition
#12
Meryl Wang, David Zhu, Jianwei Zhu, Ruth Nussinov, Buyong Ma
Deciphering antibody-protein antigen recognition is of fundamental and practical significance. We constructed an antibody structural dataset, partitioned it into human and murine subgroups, and compared it with nonantibody protein-protein complexes. We investigated the physicochemical properties of regions on and away from the antibody-antigen interfaces, including net charge, overall antibody charge distributions, and their potential role in antigen interaction. We observed that amino acid preference in antibody-protein antigen recognition is entropy driven, with residues having low side-chain entropy appearing to compensate for the high backbone entropy in interaction with protein antigens...
December 8, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29218636/incorporation-of-second-coordination-sphere-d-amino-acids-alters-cd-ii-geometries-in-designed-thiolate-rich-proteins
#13
Leela Ruckthong, Aniruddha Deb, Lars Hemmingsen, James E Penner-Hahn, Vincent L Pecoraro
We use a de Novo protein design strategy to demonstrate that the second coordination sphere of a metal site plays a key role in controlling coordination geometries of Cd(II)-tris-thiolate complexes. Specifically, we show that alteration of chirality within the core hydrophobic packing region of a three-stranded coiled coil (3SCC) can control the coordination number of Cd(II) by limiting steric encumbrance to the metal center. Within a specific class of 3SCCs [Ac-G-(LKALEEK) n -G-NH2], where n = 4 is TRI and n = 5 is GRAND, one L-Leu may be substituted by L-Cys to generate a planar tris-thiolate array capable of metal binding...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218629/design-of-artificial-metalloproteins-metalloenzymes-by-tuning-noncovalent-interactions
#14
REVIEW
Shun Hirota, Ying-Wu Lin
Noncovalent weak interactions [hydrophobic interaction and hydrogen (H)-bond] play crucial roles in controlling the functions of biomolecules, and thus have been used to design artificial metalloproteins/metalloenzymes during the past few decades. In this review, we focus on the recent progresses in protein design by tuning the noncovalent interactions, including hydrophobic and H-bonding interactions. The topics include redesign and reuse of the heme pocket and other protein scaffolds, design of the heme protein interface, and de novo design of metalloproteins...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218505/antibacterial-and-antibiofilm-activity-of-lactic-acid-bacteria-isolated-from-traditional-artisanal-milk-cheese-from-northeast-china-against-enteropathogenic-bacteria
#15
Xingyang Cui, Yunjia Shi, Shanshan Gu, Xin Yan, Hongyan Chen, Junwei Ge
The present study aims to investigate the probiotic properties of novel strains of lactic acid bacteria isolated from traditional artisanal milk cheese from Northeast China and to explore their antibacterial activity against enteropathogenic bacteria. Of the 321 isolates, 86 exhibited survival in low pH, resistance to pancreatin, and tolerance to bile salts; of these, 12 inhibited the growth of more than seven enteropathogenic bacteria and exhibited antibiofilm activities against Staphylococcus aureus CMCC26003 and/or Escherichia coli CVCC230...
December 7, 2017: Probiotics and Antimicrobial Proteins
https://www.readbyqxmd.com/read/29218491/a-specific-amino-acid-residue-in-the-catalytic-site-of-dandelion-polyphenol-oxidases-acts-as-selector-for-substrate-specificity
#16
Sarah M Prexler, Ratna Singh, Bruno M Moerschbacher, Mareike E Dirks-Hofmeister
Successful site-directed mutagenesis combined with in silico modeling and docking studies for the first time offers experimental proof of the role of the 'substrate selector' residue in plant polyphenol oxidases. The plant and fungi enzymes responsible for tissue browning are called polyphenol oxidases (PPOs). In plants, PPOs often occur as families of isoenzymes which are differentially expressed, but little is known about their physiological roles or natural substrates. In a recent study that explored these structure-function relationships, the eleven known dandelion (Taraxacum officinale) PPOs were shown to separate into two different phylogenetic groups differing in catalytic cavity architecture, kinetic parameters, and substrate range...
December 7, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29218352/an-ultra-low-frictional-interface-combining-fdts-sams-with-molybdenum-disulfide
#17
Xing'an Cao, Xuehui Gan, Yitian Peng, Yongxia Wang, Xingzhong Zeng, Haojie Lang, Jinan Deng, Kun Zou
Interfacial friction is of crucial importance to ensure the friction-reducing and anti-wear properties of mechanical microstructures in micro/nanoelectromechanical systems (MEMS/NEMS). An ultra-low frictional interface combining hydrophobic 1H,1H,2H,2H-perfluorodecyltrichlorosilane (FDTS) self-assembled monolayers (SAMs) coated on an AFM tip with mechanically exfoliated molybdenum disulfide (MoS2) nanosheets deposited on a planar Si/SiO2 substrate was achieved. The FDTS SAMs/MoS2 interface between the FDTS SAMs and the MoS2 nanosheets exhibits an ultra-low friction force that is independent of the relative humidity...
December 8, 2017: Nanoscale
https://www.readbyqxmd.com/read/29218350/comment-on-thermal-compaction-of-the-intrinsically-disordered-protein-tau-entropic-structural-and-hydrophobic-factors-by-a-battisti-g-ciasca-a-grottesi-and-a-tenenbaum-phys-chem-chem-phys-2017-19-8435
#18
Giuseppe Graziano
In a recent article, A. Battisti et al., Phys. Chem. Chem. Phys., 2017, 19, 8435, results from SAXS measurements, metadynamic trajectories and classic MD trajectories at different temperatures have been used to study the temperature-induced compaction of the intrinsically disordered protein tau. The analysis, though technically sound, does not provide a clear explanation of hydrophobic interaction strengthening on increasing the temperature and its relationship with the population increase of secondary structural elements...
December 8, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29218349/core-hydrophobicity-tuning-of-a-self-assembled-particle-results-in-efficient-lipid-reduction-and-favorable-organ-distribution
#19
Bhabatosh Banik, Ru Wen, Sean Marrache, Anil Kumar, Nagesh Kolishetti, Elizabeth W Howerth, Shanta Dhar
Atherosclerosis, the deadliest disease in the United States, arises due to the build up of plaques in the arteries as a result of excessive cholesterol deposition and an impaired cholesterol removal process. High density lipoproteins (HDL), popularly known as "good cholesterol", are naturally occurring nano-sized particles that, along with apolipoproteins, are deployed to maintain cholesterol homeostasis in the body. Both cholesterol efflux, from the fat-laden macrophages in the arteries, and intracellular lipid transport, to deliver cholesterol to the mitochondria of liver cells for metabolism, hold key responsibilities to maintain healthy lipid levels inside the body...
December 8, 2017: Nanoscale
https://www.readbyqxmd.com/read/29218041/mrp-antiporters-have-important-roles-in-diverse-bacteria-and-archaea
#20
REVIEW
Masahiro Ito, Masato Morino, Terry A Krulwich
Mrp (Multiple resistance and pH) antiporter was identified as a gene complementing an alkaline-sensitive mutant strain of alkaliphilic Bacillus halodurans C-125 in 1990. At that time, there was no example of a multi-subunit type Na+/H+ antiporter comprising six or seven hydrophobic proteins, and it was newly designated as the monovalent cation: proton antiporter-3 (CPA3) family in the classification of transporters. The Mrp antiporter is broadly distributed among bacteria and archaea, not only in alkaliphiles...
2017: Frontiers in Microbiology
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