bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinetic Studies on sec‐Alcohol Racemization with Dicarbonylchloro(pentabenzylcyclopentadienyl)‐ and Dicarbonylchloro(pentaphenylcyclopentadienyl)ruthenium Catalysts
Authors: Mavrynsky Denys , Murzin Dmitry Yu. , Leino Reko
Published: May 2013

Pentasubstituted cyclopentadienyl complexes of ruthenium R5CpRu(CO)2Cl (R=Ph, benzyl) form, upon activation with tBuOK, highly active catalysts for racemization of chiral sec‐alcohols. In combination with suitable resolving enzymes, such catalyst systems can efficiently be utilized for dynamic kinetic resolution reactions providing chiral alcohols, after hydrolysis of the corresponding acetates, in high yields and high enantiomeric purities. Here, three such ruthenium complexes were first characterized by NMR spectroscopy and cyclic voltammetry analysis (CVA) for elucidating their electronic characteristics in detail. Then, accurate kinetic studies were performed providing for the first time the calculated racemization rate constants for such catalyst systems. Furthermore, the dependence of the racemization rate on the electronic structure of the catalyst was investigated from the Hammett constants, substitution patterns of the substrate, and by isotopic labeling studies. The results obtained support the earlier suggested racemization reaction mechanism and indicated that the electron‐rich catalyst Bn5CpRu(CO)2Cl (Bn=benzyl) racemizes electron‐rich substrates more efficiently and in most cases faster than its pentaphenyl substituted analogue, formerly often considered as the leading catalyst candidate for dynamic kinetic resolution applications. The electron‐deficient catalyst Ph5CpRu(CO)2Cl, in turn, is more efficient for electron‐poor substrates.
Multistimuli‐Responsive Supramolecular Organogels Formed by Low‐Molecular‐Weight Peptides Bearing Side‐Chain Azobenzene Moieties
Authors: Fatás Paola , Bachl Jürgen , Oehm Stefan , Jiménez Ana I. , Cativiela Carlos , Díaz Díaz David
Published: May 2013

This work demonstrates that the incorporation of azobenzene residues into the side chain of low‐molecular‐weight peptides can modulate their self‐assembly process in organic solvents leading to the formation of stimuli responsive physical organogels. The major driving forces for the gelation process are hydrogen bonding and π–π interactions, which can be triggered either by thermal or ultrasound external stimuli, affording materials having virtually the same properties. In addition, a predictive model for gelation of polar protic solvent was developed by using Kamlet–Taft solvent parameters and experimental data. The obtained viscoelastic materials exhibited interconnected multistimuli responsive behaviors including thermal‐, photo‐, chemo‐ and mechanical responses. All of them displayed thermoreversability with gel‐to‐sol transition temperatures established between 33–80 °C and gelation times from minutes to several hours. Structure–property relationship studies of a designed peptide library have demonstrated that the presence and position of the azobenzene residue can be operated as a versatile regulator to reduce the critical gelation concentration and enhance both the thermal stability and mechanical strength of the gels, as demonstrated by comparative dynamic rheology. The presence of N‐Boc protecting group in the peptides showed also a remarkable effect on the formation and properties of the gels. Despite numerous examples of peptide‐based gelators known in the literature, this is the first time in which low‐molecular‐weight peptides bearing side chain azobenzene units are used for the synthesis of “intelligent” supramolecular organogels. Compared with other approaches, this strategy is advantageous in terms of structural flexibility since it is compatible with a free, unprotected amino terminus and allows placement of the chromophore at any position of the peptide sequence.
Ion‐Pair‐Based Assemblies Comprising Pyrrole–Pyrazole Hybrids
Authors: Maeda Hiromitsu , Chigusa Kengo , Sakurai Tsuneaki , Ohta Kazuchika , Uemura Shinobu , Seki Shu
Published: May 2013

Modified 3,5‐dipyrrolylpyrazole (DPP) derivatives in their protonated form produce planar [2+2]‐type complexes with trifluoroacetate (TFA) ions. These complexes serve as constituent components of ion‐pair‐based assemblies. An essential strategy for the construction of dimension‐controlled organized structures based on these [2+2]‐type complexes is the introduction of aryl rings bearing long alkyl chains, which enables the formation of 2D patterns at interfaces, supramolecular gels, and mesophases.
Salimabromide: Unexpected Chemistry from the Obligate Marine Myxobacterium Enhygromyxa salina
Authors: Felder Stephan , Dreisigacker Sandra , Kehraus Stefan , Neu Edith , Bierbaum Gabriele , Wright Patrick R. , Menche Dirk , Schäberle Till F. , König Gabriele M.
Published: May 2013

Marine myxobacteria (Enhygromyxa, Plesiocystis, Pseudoenhygromyxa, Haliangium) are phylogenetically distant from their terrestrial counterparts. Salimabromide is the first natural product from the Plesiocystis/Enhygromyxa clade of obligatory marine myxobacteria. Salimabromide has a new tetracyclic carbon skeleton, comprising a brominated benzene ring, a furano lactone residue, and a cyclohexane ring, bridged by a seven‐membered cyclic moiety. The absolute configuration was deduced from experimental and calculated CD data. Salimabromide revealed antibiotic activity towards Arthrobacter cristallopoietes.
All‐pass dispersion synthesis using microwave C‐sections
Authors: Gupta Shulabh , Sounas Dimitrios , Zhang Qingfeng , Caloz Christophe
Published: May 2013

A closed‐form iterative procedure for synthesizing quasi‐arbitrary phase responses with cascaded microwave C‐section all‐pass phasers is presented. The synthesis consists in mapping the transmission poles of the cascaded C‐section structure onto the transmission poles of the specified transfer function, where the latter poles are computed using a closed‐form polynomial generation method. The real and complex transmission poles of the specified transfer function are realized using C‐sections of different lengths and different couplings coefficients. The proposved synthesis is validated by both full‐wave analysis and measured multilayer prototypes. Copyright © 2013 John Wiley & Sons, Ltd.
Expression of EphA8‐Fc in transgenic mouse embryos induces apoptosis of neural epithelial cells during brain development
Authors: Kim Yujin , Park Eunjeong , Noh Hyuna , Park Soochul
Published: May 2013

EphAs and ephrin‐As are expressed in multiple regions of the developing brain and have been implicated in regulating brain size. Here, we report the identification of a novel mechanism in which reverse signaling through ephrin‐As controls neural epithelial cell number in the developing brain. Ectopic expression of EphA8‐Fc in transgenic embryos induced apoptosis of neural epithelial cells, which was accompanied by a dramatic decrease in brain size. The number of ephrin‐A5‐expressing cells was significantly reduced in the brain region where EphA8‐Fc was ectopically expressed. Furthermore,in vitroculture of the dissociated neuroepithelial cells revealed that EphA8‐Fc enhanced apoptotic cell death of the ephrinA5‐expressing cells in a caspase‐dependent manner. Thus, our results suggest that reverse signaling through ephrin‐As is biochemically linked with caspase‐dependent proapoptotic signaling during early brain development. © 2013 Wiley Periodicals, Inc. Develop Neurobiol 73: 702–712, 2013
Delimiting shades of gray: phylogeography of theNorthernFulmar,Fulmarus glacialis
Authors: Kerr Kevin C. R. , Dove Carla J.
Published: May 2013

TheNorthernFulmar (Fulmarus glacialis) is a common tube‐nosed seabird with a disjunctHolarctic range. Taxonomic divisions within theNorthernFulmar have historically been muddled by geographical variation notably including highly polymorphic plumage. Recent molecular analyses (i.e.,DNAbarcoding) have suggested that genetic divergence betweenAtlantic andPacific populations could be on par with those typically observed between species. We employ a multigene phylogenetic analysis to better explore the level of genetic divergence between these populations and to test an old hypothesis on the origin of the modern distribution of color morphs across their range. Additionally, we test whether mutations in the melanocortin‐1 receptor gene (MC1R) are associated with dark plumage in theNorthernFulmar. We confirmed that mitochondrial lineages in theAtlantic andPacific populations are highly divergent, but nuclear markers revealed incomplete lineage sorting. Genetic divergence between these populations is consistent with that observed between many species ofProcellariiformes and we recommend elevating these two forms to separate species. We also find thatMC1Rvariation is not associated with color morph but rather is better explained by geographical divergence.
CEACAM1 on activated NK cells inhibits NKG2D‐mediated cytolytic function and signaling
Authors: Hosomi Shuhei , Chen Zhangguo , Baker Kristi , Chen Lanfen , Huang Yu‐Hwa , Olszak Torsten , Zeissig Sebastian , Wang Jing H. , Mandelboim Ofer , Beauchemin Nicole , Lanier Lewis L. , Blumberg Richard S.
Published: May 2013

Carcinoembryonic antigen‐related cell adhesion molecule 1 (CEACAM1) is expressed on activated natural killer (NK) cells wherein it inhibits lysis of CEACAM1‐bearing tumor cell lines. The mechanism for this is unknown. Here, we show that interleukin‐2‐induced expression of CEACAM1 on both mouse and primary human NK cells impairs the ability of NK gene complex group 2 member D (NKG2D) to stimulate cytolysis of CEACAM1‐bearing cells. This process requires the expression of CEACAM1 on the NK cells and on the tumor cells, which is consistent with the involvement of trans‐homophilic interactions between CEACAM1. Mechanistically, co‐engagement of NKG2D and CEACAM1 results in a biochemical association between these two surface receptors and the recruitment of Src homology phosphatase 1 by CEACAM1 that leads to dephosphorylation of the guanine nucleotide exchange factor Vav1 and blockade of downstream signaling that is associated with the initiation of cytolysis. Thus, CEACAM1 on activated NK cells functions as an inhibitory receptor for NKG2D‐mediated cytolysis, which has important implications for understanding the means by which CEACAM1 expression adversely affects tumor immunity.
Analysis of the Hysteretic Behaviour of 3D Spin Crossover Compounds by Using an Ising‐Like Model
Authors: Chiruta Daniel , Linares Jorge , Garcia Yann , Dahoo Pierre Richard , Dimian Mihai
Published: May 2013

In this contribution, we use a recently developed Monte Carlo technique to investigate the impact of ferro‐, antiferromagnetic interactions for different thermodynamic parameters in a three‐dimensional Ising‐like model. We present the role of temperature and pressure on the first‐order phase‐transition between a low‐spin and a high‐spin state and identify different response curves. The analysis of one‐ and two‐step spin‐crossover behaviour has been performed by using a self‐consistent approach, because it is known that for a system with both short‐ and long‐range interactions, the Hamiltonian does not have an exact solution. However, by constructing the distributions of the states with Monte Carlo entropic sampling and by taking into account the temperature degeneracy dependence between low‐spin and high‐spin states, we could solve the Hamiltonian. We provide herein a systematic comparison to our previous experimental works and as part of our continuous interest in spin crossover nanosystems, we present a size effect study.
Quantification of the Nucleophilic Reactivities of Ethyl Arylacetate Anions
Authors: Corral‐Bautista Francisco , Mayr Herbert
Published: May 2013

The kinetics of the reactions of substituted ethyl arylacetates with quinone methides and structurally related diethyl benzylidenemalonates have been studied in DMSO. The second‐order rate constants (lg k2) correlated linearly with the electrophilicities E according to the linear free‐energy relationship lg k2 = sN(N + E), allowing us to determine the nucleophilicity parameters N and sN for these anions. The nucleophilic reactivities of the carbanions vary from N = 27.5 for the parent compound to N = 20.0 for the 4‐nitro‐substituted derivative.
Genotoxicity induced by Taenia solium and its reduction by immunization with calreticulin in a hamster model of taeniosis
Authors: Salazar Ana María , Mendlovic Fela , Cruz‐Rivera Mayra , Chávez‐Talavera Oscar , Sordo Monserrat , Avila Guillermina , Flisser Ana , Ostrosky‐Wegman Patricia
Published: May 2013

Genotoxicity induced by neurocysticercosis has been demonstrated in vitro and in vivo in humans. The adult stage of Taenia solium lodges in the small intestine and is the main risk factor to acquire neurocysticercosis, nevertheless its carcinogenic potential has not been evaluated. In this study, we determined the genotoxic effect of T. solium infection in the hamster model of taeniosis. In addition, we assessed the effect of oral immunization with recombinant T. solium calreticulin (rTsCRT) plus cholera toxin as adjuvant on micronuclei induction, as this protein has been shown to induce 33–44% protection in the hamster model of taeniosis. Blood samples were collected from the orbital venous plexus of noninfected and infected hamsters at different days postinfection, as well as from orally immunized animals, to evaluate the frequency of micronucleated reticulocytes as a measure of genotoxicity induced by parasite exposure and rTsCRT vaccination. Our results indicate that infection with T. solium caused time‐dependent DNA damage in vivo and that rTsCRT immunization reduced the genotoxic damage induced by the presence of the tapeworms. Environ. Mol. Mutagen. 54:347–353, 2013. © 2013 Wiley Periodicals, Inc.
A reductionist mechanistic model for bioconcentration of neutral and weakly polar organic compounds in fish
Authors: Kuo Dave T.F. , Di Toro Dominic M.
Published: May 2013

The bioconcentration factor (BCF) of neutral and weakly polar organic chemicals in fish is modeled using independently calibrated models of chemical partitioning (freely dissolved fraction of chemical in the aqueous phase [φsys] and wet-weight fish–water partition coefficient [KFW]), respiratory exchange (respiratory update rate constant [k1], and respiratory elimination rate constant [k2 = k1/KFW]), and biotransformation (whole-body biotransformation rate constant [kM]) as BCF = φsysKFW/(1 + kM/k2). Existing k1 models tend to overestimate for chemicals with log KOW < 3.5, which constituted 30% to 50% of the examined chemicals. A revised k1 model covering a wider log KOW range (0–8.5) is presented k1 = (5.46 × 10−6 MW + 0.261/KOW)−1, where MW is the molecular weight. The biotransformation rate constant kM is modeled using biota internal partitioning and Abraham parameters as reactivity descriptors. The reductionist model was tested using 3 different BCF data sets (US Environmental Protection Agency's Estimation Programs Interface [EPI], n = 548; Hertfordshire, n = 210; Arnot–Gobas, n = 1855) and compared with the following 3 state-of-the-art models: 1) the EPI Suite BCFBAF module, 2) the European Commision's Computer Assisted Evaluation of industrial chemical Substances According to Regulations (CAESAR), and 3) the EPI/Arnot mechanistic kinetic model. The reductionist model performed comparably with the alternative models (root mean square errors [RMSEs] = 0.72–0.77), with only 5 fitting parameters and no training against experimental BCFs. Respiratory elimination and biotransformation dominate the total depuration (i.e., [k2 + kM]/kT ≥ 0.8) for approximately 98% of the data entries, thus validating the reductionist approximation. Mechanistic models provide greater insights into bioaccumulation and are more sensitive to biological variation. All three BCF data sets and relevant properties and checkpoint values necessary for reproducing predictions of the reductionist model have been documented. The present study shows that a streamlined mechanistic model of BCF is possible for assessment purposes. Environ Toxicol Chem 2013;32:2089–2099. © 2013 SETAC
Invasive dreissenid mussels and round gobies: A benthic pathway for the trophic transfer of microcystin
Authors: Poste Amanda E. , Ozersky Ted
Published: May 2013

In the present preliminary study, the authors identify 2 pathways through which invasive dreissenid mussels can transfer microcystin to higher trophic levels: either directly, through consumption by benthivorous fish such as the round goby; or indirectly, through their biodeposits, which are an important food source for benthic invertebrates. The results suggest that dreissenid mussels represent a potentially important benthic pathway for the food web transfer of microcystin. Environ Toxicol Chem 2013;32:2159–2164. © 2013 SETAC
Enzymatic biomarkers as tools to assess environmental quality: A case study of exposure of the honeybee Apis mellifera to insecticides
Authors: Carvalho Stephan M. , Belzunces Luc P. , Carvalho Geraldo A. , Brunet Jean-Luc , Badiou-Beneteau Alexandra
Published: May 2013

The present study was intended to evaluate the responses of enzymes in the honeybee Apis mellifera after exposure to deltamethrin, fipronil, and spinosad and their use as biomarkers. After determination of the median lethal doses (LD50), honeybees were exposed at doses of 5.07 ng/bee and 2.53 ng/bee for deltamethrin, 0.58 ng/bee and 0.29 ng/bee for fipronil, and 4.71 ng/bee and 2.36 ng/bee for spinosad (equivalent to 1/10th [LD50/10] and 1/20th [LD50/20] of the LD50, respectively). The responses of acetylcholinesterase (AChE), carboxylesterases (CaEs-1–3), glutathione-S-transferase (GST), catalase (CAT), and alkaline phosphatase (ALP) were assessed. The results showed that deltamethrin, fipronil, and spinosad modulated these biomarkers differentially. For the enzyme involved in the defense against oxidative stress, fipronil and spinosad induced CAT activity. For the remaining enzymes, 3 response profiles were identified. First, exposure to deltamethrin induced slight effects and modulated only CaE-1 and CaE-2, with opposite effects. Second, spinosad exhibited an induction profile for most of the biomarkers, except AChE. Third, fipronil did not modulate AChE, CaE-2, or GST, increased CAT and CaE-1, and decreased ALP. Thus, this set of honeybee biomarkers appears to be a promising tool to evaluate environmental and honeybee health, and it could generate fingerprints to characterize exposures to pesticides. Environ Toxicol Chem 2013;32:2117–2124. © 2013 SETAC
Re–Os geochronology, fluid inclusions and genesis of the 0.85 Ga Tumen molybdenite–fluorite deposit in Eastern Qinling, China: implications for pre‐Mesozoic Mo enrichment and tectonic setting
Authors: Deng Xiao‐Hua , Chen Yan‐Jing , Santosh M. , Yao Jun‐Ming
Published: May 2013

The East Qinling Molybdenum Belt (EQMB), central China, hosting tens of Mesozoic magmatic hydrothermal Mo deposits, is one of the largest molybdenum belts in the world. Recently, a new type of Mo mineralization characterized by molybdenite–fluorite veins was discovered with ongoing prospecting at the Tumen area in the Huaxiong block, representing the southernmost tectonic unit of the North China Craton. The molybdenite–fluorite veins occur in faults or ductile shear zones cross‐cutting the Neoproterozoic Luanchuan Group. At the Tumen deposit, CO2‐rich, aqueous and daughter mineral‐bearing fluid inclusions are observed in fluorite. These fluid inclusions resemble those reported from magmatic hydrothermal Mo systems formed in intracontinental tectonic settings and yield homogenization temperatures up to 450 °C, with salinities up to 39.8 wt.% NaCl equiv, suggesting that the mineralization resulted from a magmatic fluid system. Seven molybdenite analyses from the molybdenite–fluorite veins yield Re–Os isotope ages ranging from 845.8 ± 7.3 to 965.3 ± 7.2 Ma, with an isochron age of 847.4 ± 7.3 Ma (2σ, MSWD = 23), marking the timing of mineralization as Neoproterozoic. These ages are broadly comparable with the 844.3 ± 1.6 Ma age reported from the Shuangshan syenite located near the mining area, and theca. 830 Ma gabbros occurring within the same tectonic unit, indicating that the deposit was possibly related to Neoproterozoic rifting at the southern margin of the North China Craton. The age data correspond to the transition from the culmination of the assembly of the Neoproterozoic supercontinent Rodinia to the beginning of its break‐up. Our results provide new insights into the regional tectonics and show that the Mo mineralization is not related to the much younger Mesozoic Yanshanian magmatism as considered in previous studies. Copyright © 2013 John Wiley & Sons, Ltd.
Towards the Investigation of Heat Transfer Characteristics in a Viscous Dissipative Shear Driven Flow Through an Annulus: An Analytical Study
Authors: Mondal Pranab Kumar , Mukherjee Sanchayan
Published: May 2013

In the present study, the laminar forced convective heat transfer of a shear‐driven flow through an annulus in a viscous dissipative environment is investigated. The temperature distribution for different constant heat flux boundary conditions is studied, and so are the heat transfer characteristics of a Newtonian fluid under consideration. Following an analytical methodology, closed‐form expressions of the Nusselt number on both walls of the annulus have been devised. It is shown that the effect of viscous dissipation significantly alters the temperature profile, and the consequential effect is reflected in the variation of the Nusselt number. In most of the cases, variation of the Nusselt number exhibits a discontinuity in behavior at different locations within the annulus where an equilibrium state between the energy is attained due to shear heating and the heat supplied by the wall. However, it has been observed that the greater viscous dissipative heat causes a rise in the temperature and consequently a fall in the rate of heat transfer. © 2013 Wiley Periodicals, Inc. Heat Trans Asian Res, 42(7): 569–588, 2013; Published online in Wiley Online Library (wileyonlinelibrary.com/journal/htj). DOI 10.1002/htj.21057
TYPIFYING IRRIGATED AREAS TO SUPPORT POLICY DESIGN AND IMPLEMENTATION: THE CASE OF THE GUADALQUIVIR RIVER BASIN
Authors: Gómez‐Limón J. A. , Arriaza M. , Villanueva A. J.
Published: May 2013

Irrigated agriculture in the Guadalquivir River Basin (GRB, southern Spain) has changed dramatically over the last decade, both in terms of the type of crops grown and also irrigation technology (water use efficiency). The main cause for this has been the irruption of modern olive groves, characterized by lower water demand (around 1500 m3 ha‐1) and the use of drip irrigation systems. In addition to the increase in olive plantations, accounting for approximately half of the 850 000 ha irrigated in the GRB, there has also been an intense process of modernization and intensification of irrigated agriculture, as shown by the latest Inventory of Irrigated Areas of Andalusia (2008). All these changes make it necessary to redefine irrigated areas, not only on the basis of their crop mix, but also taking into account a full array of key variables, such as irrigated area managerial features (water allotments, water pricing, etc.) and farm structural features (irrigation systems, etc.). This study classifies the irrigation areas in the GRB into five homogeneous clusters by means of factor and cluster analysis. This full typology of irrigated areas could provide useful information for policymakers to improve the design and the implementation of agricultural and water planning policies. Copyright © 2013 John Wiley & Sons, Ltd.
TRADITIONAL IRRIGATION AND WATER MANAGEMENT PRACTICES IN HIGHLAND ETHIOPIA: CASE STUDY IN DANGILA WOREDA
Authors: Belay Mehretie , Bewket Woldeamlak
Published: May 2013

This paper examines traditional irrigation practices and their contribution to rural livelihoods in Dangila woreda (district) in the north‐western highlands of Ethiopia. Data were collected from November 2010 to May 2011 through a questionnaire survey of 126 irrigators and field observation of irrigation practices. The results show that over 90% of the irrigators used furrow systems. Around 54% of them reported that irrigation had contributed 11–20% to their household incomes in the past 12 years (1999/2000–2010/2011). The majority of the farmers agreed that the use of irrigation has increased in area coverage, crop outputs and contribution to household incomes over the past two decades. Water was distributed on rotation turns headed by water committees that were headed by individuals locally referred to as Yewha Abat (water fathers). Over 60% of the respondents indicated that they faced water and irrigable land shortages where the latter significantly influence households' irrigation income (significant at p < 0.0005). Although traditional irrigation has been known in the study area for many years, the attention offered to it from state agencies has not been encouraging. The study recommends appropriate institutional support to be provided to smallholder irrigators to improve the overall performance of traditional irrigation schemes. Copyright © 2013 John Wiley & Sons, Ltd.
Synthesis and Characterization of Chitosan Tripolyphosphate Nanoparticles and its Encapsulation Efficiency Containing Russell's Viper Snake Venom
Authors: Venkatesan C. , Vimal S. , Hameed A. S. Sahul
Published: May 2013

Chitosan Tripolyphosphate (CS/TPP) nanoparticle is a biodegradable and nontoxic polysaccharide, used as a carrier for drug delivery. The morphology and particle‐size measurements of the nanoparticles were studied by field emission scanning electron microscopy and Fourier Transform Infrared Spectroscopy (FTIR). This study aims to evaluate the impact of Russell's viper venom encapsulation on various factors and loading capacity, in addition to explore the physicochemical structure of nanoparticles. FTIR confirmed that tripolyphosphoric groups of TPP linked with ammonium groups of CS in the nanoparticles. Our results showed that CS can react with TPP to form stable cationic nanoparticles. The results also showed that encapsulation efficiency of venom at different concentrations of 20, 40, 60, 500, and 1000 µg/mL were achieved for CS/TPP nanoparticles at different concentrations of 1.5, 2, and 3 mg/mL. The cytotoxicity of CS/TPP nanoparticles was evaluated by MTT (‐3 (4, 5‐Dimethylthiazol‐2‐yl)‐2, 5‐diphenyltetrazolium bromide, a tetrazole) assay. © 2013 Wiley Periodicals, Inc. J BiochemMol Toxicol 27:406‐411, 2013; View this article online at wileyonlinelibrary.com. DOI 10.1002/jbt.21502
High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models
Authors: Moore Benjamin L. , Kelley Lawrence A. , Barber James , Murray James W. , MacDonald James T.
Published: May 2013

Coarse‐grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full‐atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log‐likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full‐atom models using Rosetta which has implications for multiscale protein modeling using coarse‐grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/. © 2013 Wiley Periodicals, Inc.
Binding affinity of substituted ureido‐benzenesulfonamide ligands to the carbonic anhydrase receptor: A theoretical study of enzyme inhibition
Authors: Sahu Chandan , Sen Kaushik , Pakhira Srimanta , Mondal Bhaskar , Das Abhijit K.
Published: May 2013

The binding properties of a series of benzenesulfonamide inhibitors (4‐substituted‐ureido‐benzenesulfonamides, UBSAs) of human carbonic anhydrase II (hCA II) enzyme with active site residues have been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) model. To account for the important docking interactions between the UBSAs ligand and hCA II enzyme, a molecular docking program AutoDock Vina is used. The molecular docking results obtained by AutoDock Vina revealed that the docked conformer has root mean square deviation value less than 1.50 Å compared to X‐ray crystal structures. The inhibitory activity of UBSA ligands against hCA II is found to be in good agreement with the experimental results. The thermodynamic parameters for inhibitor binding show that hydrogen bonding, hydrophilic, and hydrophobic interactions play a major role in explaining the diverse inhibitory range of these derivatives. Additionally, natural bond orbital analysis is performed to characterize the ligand–metal charge transfer stability. The insights gained from this study have great potential to design new hCA‐II inhibitor, 4‐[3‐(1‐p‐Tolyl‐4‐trifluoromethyl‐1H‐pyrazol‐3‐yl)‐ureido]‐benzenesulfonamide, which belongs to the family of UBSA inhibitors and shows similar type of inhibitor potency with hCA II. This work also reveals that a QM/MM model and molecular docking method are computationally feasible and accurate for studying substrate–protein inhibition. © 2013 Wiley Periodicals, Inc.
High‐energy X‐ray tomography analysis of a metal packing biofilm reactor for the production of lipopeptides byBacillus subtilis
Authors: Zune Quentin , Soyeurt Delphine , Toye Dominique , Ongena Marc , Thonart Philippe , Delvigne Frank
Published: May 2013

BACKGROUND

Whereas multi‐species biofilm reactors are commonly used for the treatment of liquid and solid wastes, new strategies are progressing for the development of single species biofilm for the production of high‐value metabolites. Technically, this new concept relies on the design of bioreactors able to promote biofilm formation and on the identification of the key physico‐chemical parameters involved in biofilm formation.

RESULTS

An experimental setting comprising a liquid continuously recirculated on a metal structured packing has been used to promoteBacillus subtilisGA1biofilm formation. The colonization of the packing has been visualized non‐invasively by X‐ray tomography. This analysis revealed an uneven, conical, distribution of the biofilm inside the packing. Compared with a submerged culture carried out in a stirred tank reactor, significant modification of the lipopeptide profile has been observed in the biofilm reactor with the disappearance of fengycin and iturin fractions and an increase of the surfactin fraction. In addition, considering the biofilm reactor design, no foam formation has been observed during the culture.

CONCLUSIONS

The configuration of this biofilm reactor set‐up allows for a higher surfactin production by comparison with a submerged culture while avoiding foam formation. Additionally, scale‐up could easily be performed by increasing the number of packing elements. © 2013 Society of Chemical Industry
Long‐term changes in solar quiet (Sq) geomagnetic variations related to Earth's magnetic field secular variation
Authors: de Haro Barbas Blas F. , Elias Ana G. , Cnossen Ingrid , Zossi de Artigas Marta
Published: May 2013

The daily amplitude of the solar quiet (Sq) magnetic variation of the horizontal intensity, H, of observatories at low and midlatitudes is analyzed, in search of significant long‐term trends. These trends are expected based on secular variations of the Earth's magnetic field (B) and increasing concentrations of greenhouse gases which can affect Sq for instance through their effect on ionospheric conductivities and E‐region electron concentration. The hourly horizontal geomagnetic field component, H, measured at Apia, Fredericksburg, Hermanus, Bangui, and Trivandrum was analyzed for the period 1960–2000. The solar activity effect was filtered out from the daily Sq amplitude of H, and then linear trends were calculated and compared to trend values obtained from the Coupled Magnetosphere‐Ionosphere‐Thermosphere model. Linear trends were calculated separately for periods of different secular trends in the magnetic field intensity, B. We found significant trends in experimental data for Apia, Fredericksburg, Hermanus, and for the period 1960–1983 for Bangui. There is reasonable quantitative agreement between experimental and simulated trends, and a qualitative agreement with trends expected from the secular trend in B.
Absorption characteristics of optically complex inland waters: Implications for water optical classification
Authors: Shi Kun , Li Yunmei , Li Lin , Lu Heng
Published: May 2013

Multiple bio‐optical measurements were conducted in inland waters of China, including Lake Taihu [spring and autumn], Lake Chaohu, Lake Dianchi, and Three Gorges Reservoirs. The variations in the absorption characteristics of chromophoric dissolved organic matter (CDOM), phytoplankton, and non‐algal particles (NAP) and their relative contributions to total absorption among these waters were analyzed. The obtained results indicated that these areas are representative of the optically complex inland waters characterized by strong regional variations of their absorption properties. By means of the relative contributions of NAP and phytoplankton to the total water absorption at 550 and 675 nm, these waters were classified into three optical water types, each one having specific biogeochemical and optical properties. Two of the types were distinct and corresponded to waters that are optically controlled by NAP (Type I) and dominated by phytoplankton (Type III). Type II was related to relatively optically mixed waters where the absorption properties are controlled by NAP and phytoplankton. Additionally, the differences in remote‐sensing reflectance (Rrs) spectra among the three classified water types were clarified to establish optical criteria for identifying these water types. On this basis, the classification criteria for MERIS images were developed, which allowed one to cluster every Rrs spectrum into one of the three water types by comparing the values from band 6, band 8, and band 9 of MERIS images. The proposed criteria were subsequently conducted to map the water types of Lake Taihu using MERIS images.
The sensitivity of forest water use to the timing of precipitation and snowmelt recharge in the California Sierra: Implications for a warming climate
Authors: Tague Christina , Peng Hui
Published: May 2013

Forest responses to warming, in the absence of changes in vegetation structure, reflect the balance between the increased atmospheric demand for water and changes in water availability. This study uses a coupled hydroecologic model applied to a snow‐dominated mountain watershed to demonstrate how complex topography and interannual variation in climate drivers combine to alter the balance between moisture availability and energy demand. We focus specifically on how often and under what conditions changes in the timing of soil water recharge as precipitation or snowmelt are a significant control on forest actual evapotranspiration (AET) in the Central California Sierra. We show that while interannual variation in precipitation is the dominant control on interannual variation in AET, how much of that recharge accumulates as a seasonal snowpack can act as a second‐order control. This sensitivity of AET to snow accumulation and melt occurs across a substantial elevation range (1800–2700 m) and at both aggregate watershed and 90 m patch scales. Model results suggest that the variation in AET due to recharge timing is greatest for patches and years with moderate levels of precipitation or patches that receive substantial lateral moisture inputs. For a 3°C warming scenario, the annual AET increases in some years due to warmer temperatures but decreases by as much as 40% in other years due to an earlier timing of snowmelt. These results help to clarify the conditions under which water availability for forests decreases and highlight scenarios that may lead to increased drought stress under a warming climate in snow‐dominated mountain regions.
Effectiveness of micron‐sized superparamagnetic iron oxide particles as markers for detection of migration of bone marrow‐derived mesenchymal stromal cells in a stroke model
Authors: Tarulli Emidio , Chaudhuri Joydeep D. , Gretka Voytek , Hoyles Amy , Morshead Cindi M. , Stanisz G.J.
Published: May 2013

Purpose:

To evaluate the feasibility of using micron‐sized superparamagnetic iron oxide particles (MPIOs) as an effective labeling agent for monitoring bone marrow‐derived mesenchymal stromal cell (BMSC) migration in the brain using magnetic resonance imaging (MRI) in a rat model of stroke and whether the accumulation of MPIO‐labeled BMSCs can be differentiated from the accumulation of free MPIO particles or hemoglobin breakdown at a site of neuronal damage.

Materials and Methods:

In this study BMSCs were labeled with iron oxide and their pattern of migration following intravenous injection in a rat stroke model was monitored using a clinical MRI system followed by standard histopathology. The migration pattern was compared between intravenous injection of BMSCs alone, BMSCs labeled with MPIOs, and MPIO particles alone.

Results:

The results demonstrated that while MRI was highly sensitive in the detection of iron oxide particle‐containing cells in areas of neuronal ischemia, the true origin of cells containing iron oxide particles remains ambiguous. Therefore, detection of iron particles may not be a suitable strategy for the detection of BMSCs in the brain in a stroke model.

Conclusion:

This study suggests that the use of MPIOs as labeling agents are insufficient to conclusively determine the localization of iron within cells in regions of neuronal ischemia and hemorrhage. J. Magn. Reson. Imaging 2013;37:1409–1418. © 2012 Wiley Periodicals, Inc.
Evolving role of MRI in Crohn's disease
Authors: Yacoub Joseph H. , Obara Piotr , Oto Aytekin
Published: May 2013

MR enterography is playing an evolving role in the evaluation of small bowel Crohn's disease (CD). Standard MR enterography includes a combination of rapidly acquired T2 sequence, balanced steady‐state acquisition, and contrast enhanced T1‐weighted gradient echo sequence. The diagnostic performance of these sequences has been shown to be comparable, and in some respects superior, to other small bowel imaging modalities. The findings of CD on MR enterography have been well described in the literature. New and emerging techniques such as diffusion‐weighted imaging (DWI), dynamic contrast enhanced MRI (DCE‐MRI), cinematography, and magnetization transfer, may lead to improved accuracy in characterizing the disease. These advanced techniques can provide quantitative parameters that may prove to be useful in assessing disease activity, severity, and response to treatment. In the future, MR enterography may play an increasing role in management decisions for patients with small bowel CD; however, larger studies are needed to validate these emerging MRI parameters as imaging biomarkers. J. Magn. Reson. Imaging 2013;37:1277–1289. © 2013 Wiley Periodicals, Inc.
An ultrasonic method for separation of epiphytic microbes from freshwater submerged macrophytes
Authors: Cai Xianlei , Gao Guang , Yang Jing , Tang Xiangming , Dai Jiangyu , Chen Dan , Song Yuzhi
Published: May 2013

Epiphytic microbes are common inhabitants of freshwater submerged macrophytes, which play an important role in aquatic ecosystems. An important precondition for studying the epiphytic microbes is having an effective method of separating the attached microbes from the host macrophytes. We developed an ultrasound‐based method for separating epiphytic microbes from freshwater submerged macrophytes, optimized the conditions of ultrasonic separation with an orthogonal experimental design, and compared the optimized ultrasonic method with manual separation. This method can be particularly useful for freshwater submerged macrophytes having a complex morphology.
Simulation of present and future climate of Saudi Arabia using a regional climate model (PRECIS)
Authors: Almazroui Mansour
Published: May 2013

In this article, climate parameters (rainfall and temperature) are simulated for Saudi Arabia by downscaling the European Centre for Medium‐Range Weather Forecasts (ECMWF) 40‐year reanalysis (ERA40) and the European Community − Hamburg Atmospheric Model (ECHAM5) data using the UK Met Office Regional Climate Model PRECIS (Providing REgional Climates for Impacts Studies). Simulations are performed for a present climate of 30 years (1971–2000) using ERA40 and ECHAM5, and future climate is predicted for a period of 50 years (2021–2070) using ECHAM5 A1B emissions scenario. The results show that the spatial distribution of the present‐day rainfall and temperature simulated by PRECIS are consistent with the observed dataset. In addition, their annual cycle and interannual variability are reasonably well reproduced. The dry precipitation and warm temperature biases exhibited in the driving fields (compared with the observations) are reduced because of the improvements in specific humidity and in the wind field within the PRECIS simulations compared with the driving fields. The projection using the calibrated national average temperature exhibits a positive trend in mean temperature of around 0.65 °C per decade. For rainfall projection, the results show that the coastal areas along the central parts of the Red Sea and the south‐southwestern areas of Saudi Arabia may experience more extreme rainfall events, whereas the northern and central parts of the country may undergo a drying trend. © 2013 The Authors. International Journal of Climatology published by John Wiley & Sons Ltd on behalf of the Royal Meteorological Society.
Effects of Topography and Surface Soil Cover on Erosion for Mining Reclamation: The Experimental Spoil Heap at El Machorro Mine (Central Spain)
Authors: Martín‐Moreno Cristina , Martín Duque José Francisco , Nicolau Ibarra José Manuel , Hernando Rodríguez Néstor , Sanz Santos Miguel Ángel , Sánchez Castillo Lázaro
Published: May 2013

Mining reclamation tries to reduce environmental impacts, including accelerated runoff, erosion and sediment load in the nearby fluvial networks and their ecosystems. This study compares the effects of topography and surface soil cover on erosion on man‐made slopes coming from surface mining reclamation in Central Spain. Two topographic profiles, linear and concave, with two surface soil covers, subsoil and topsoil, were monitored for two hydrologic years. Sediment load, rill development and plant colonization from the four profiles were measured under field conditions. The results show that, in the case of this experiment, a thick and non‐compacted topsoil cover on a linear slope yielded less sediment than carbonate colluvium or topsoil cover on a concave slope. This study also shows that vegetation establishment, which plays an important role in erosion control, depends on topography. Plant cover was more widespread and more homogeneous on linear profiles with topsoil cover. On concave slopes, plant establishment was severely limited on the steepest upper part and favoured in the bottom. This study suggests that management of topography and surface soil cover should be approached systematically, taking three outcomes into consideration: (i) topsoil can lead to a successful mining reclamation regardless of topography, (ii) created concave slopes can lead to a successful mining reclamation and (iii) topography determines the vegetation colonization pattern. Copyright © 2013 John Wiley & Sons, Ltd.
Untangling the web: The diverse functions of the PIWI/piRNA pathway
Authors: Mani Sneha Ramesh , Juliano Celina E.
Published: May 2013

Small RNAs impact several cellular processes through gene regulation. Argonaute proteins bind small RNAs to form effector complexes that control transcriptional and post‐transcriptional gene expression. PIWI proteins belong to the Argonaute protein family, and bind PIWI‐interacting RNAs (piRNAs). They are highly abundant in the germline, but are also expressed in some somatic tissues. The PIWI/piRNA pathway has a role in transposon repression in Drosophila, which occurs both by epigenetic regulation and post‐transcriptional degradation of transposon mRNAs. These functions are conserved, but clear differences in the extent and mechanism of transposon repression exist between species. Mutations in piwi genes lead to the upregulation of transposon mRNAs. It is hypothesized that this increased transposon mobilization leads to genomic instability and thus sterility, although no causal link has been established between transposon upregulation and genome instability. An alternative scenario could be that piwi mutations directly affect genomic instability, and thus lead to increased transposon expression. We propose that the PIWI/piRNA pathway controls genome stability in several ways: suppression of transposons, direct regulation of chromatin architecture and regulation of genes that control important biological processes related to genome stability. The PIWI/piRNA pathway also regulates at least some, if not many, protein‐coding genes, which further lends support to the idea that piwi genes may have broader functions beyond transposon repression. An intriguing possibility is that the PIWI/piRNA pathway is using transposon sequences to coordinate the expression of large groups of genes to regulate cellular function. Mol. Reprod. Dev. 80:632–664, 2013. © 2013 Wiley Periodicals, Inc.
An embedded four‐channel receive‐only RF coil array for fMRI experiments of the somatosensory pathway in conscious awake marmosets
Authors: Papoti Daniel , Yen Cecil Chern‐Chyi , Mackel Julie B. , Merkle Hellmut , Silva Afonso C.
Published: May 2013

fMRI has established itself as the main research tool in neuroscience and brain cognitive research. The common marmoset (Callithrix jacchus) is a non‐human primate model of increasing interest in biomedical research. However, commercial MRI coils for marmosets are not generally available. The present work describes the design and construction of a four‐channel receive‐only surface RF coil array with excellent signal‐to‐noise ratio (SNR) specifically optimized for fMRI experiments in awake marmosets in response to somatosensory stimulation. The array was designed as part of a helmet‐based head restraint system used to prevent motion during the scans. High SNR was obtained by building the coil array using a thin and flexible substrate glued to the inner surface of the restraint helmet, so as to minimize the distance between the array elements and the somatosensory cortex. Decoupling between coil elements was achieved by partial geometrical overlapping and by connecting them to home‐built low‐input‐impedance preamplifiers. In vivo images show excellent coverage of the brain cortical surface with high sensitivity near the somatosensory cortex. Embedding the coil elements within the restraint helmet allowed fMRI data in response to somatosensory stimulation to be collected with high sensitivity and reproducibility in conscious, awake marmosets. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.