bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal Structure of MpPR-1i, a SCP/TAPS protein from Moniliophthora perniciosa, the fungus that causes Witches’ Broom Disease of Cacao
Authors: Baroni Renata M. , Luo Zhipu , Darwiche Rabih , Hudspeth Elissa M. , Schneiter Roger , Pereira Gonçalo A. G. , Mondego Jorge M. C. , Asojo Oluwatoyin A. 
Published: August 2017

AbstractThe pathogenic fungi Moniliophthora perniciosa causes Witches’ Broom Disease (WBD) of cacao. The structure of MpPR-1i, a protein expressed by M. perniciosa when it infects cacao, are presented. This is the first reported de novo structure determined by single-wavelength anomalous dispersion phasing upon soaking with selenourea. Each monomer has flexible loop regions linking the core alpha-beta-alpha sandwich topology that comprise ~50% of the structure, making it difficult to generate an accurate homology model of the protein. MpPR-1i is monomeric in solution but is packed as a high ~70% solvent content, crystallographic heptamer. The greatest conformational flexibility between monomers is found in loops exposed to the solvent channel that connect the two longest strands. MpPR-1i lacks the conserved CAP tetrad and is incapable of binding divalent cations. MpPR-1i has the ability to bind lipids, which may have roles in its infection of cacao. These lipids likely bind in the palmitate binding cavity as observed in tablysin-15, since MpPR-1i binds palmitate with comparable affinity as tablysin-15. Further studies are required to clarify the possible roles and underlying mechanisms of neutral lipid binding, as well as their effects on the pathogenesis of M. perniciosa so as to develop new interventions for WBD.
Molecular Organization Induced Anisotropic Properties of Perylene – Silica Hybrid Nanoparticles
Authors: Sriramulu Deepa , Turaga Shuvan Prashant , Bettiol Andrew Anthony , Valiyaveettil Suresh 
Published: August 2017

AbstractOptically active silica nanoparticles are interesting owing to high stability and easy accessibility. Unlike previous reports on dye loaded silica particles, here we address an important question on how optical properties are dependent on the aggregation-induced segregation of perylene molecules inside and outside the silica nanoparticles. Three differentially functionalized fluorescent perylene - silica hybrid nanoparticles are prepared from appropriate ratios of perylene derivatives and tetraethyl orthosilicate (TEOS) and investigated the structure property correlation (P-ST, P-NP and P-SF). The particles differ from each other on the distribution, organization and intermolecular interaction of perylene inside or outside the silica matrix. Structure and morphology of all hybrid nanoparticles were characterized using a range of techniques such as electron microscope, optical spectroscopic measurements and thermal analysis. The organizations of perylene in three different silica nanoparticles were explored using steady-state fluorescence, fluorescence anisotropy, lifetime measurements and solid state polarized spectroscopic studies. The interactions and changes in optical properties of the silica nanoparticles in presence of different amines were tested and quantified both in solution and in vapor phase using fluorescence quenching studies. The synthesized materials can be regenerated after washing with water and reused for sensing of amines.
Superparamagnetic colloids in viscous fluids
Authors: Darras A. , Opsomer E. , Vandewalle N. , Lumay G. 
Published: August 2017

AbstractThe influence of a magnetic field on the aggregation process of superparamagnetic colloids has been well known on short time for a few decades. However, the influence of important parameters, such as viscosity of the liquid, has received only little attention. Moreover, the equilibrium state reached after a long time is still challenging on some aspects. Indeed, recent experimental measurements show deviations from pure analytical models in extreme conditions. Furthermore, current simulations would require several years of computing time to reach equilibrium state under those conditions. In the present paper, we show how viscosity influences the characteristic time of the aggregation process, with experimental measurements in agreement with previous theories on transient behaviour. Afterwards, we performed numerical simulations on equivalent systems with lower viscosities. Below a critical value of viscosity, a transition to a new aggregation regime is observed and analysed. We noticed this result can be used to reduce the numerical simulation time from several orders of magnitude, without modifying the intrinsic physical behaviour of the particles. However, it also implies that, for high magnetic fields, granular gases could have a very different behaviour from colloidal liquids.
Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations
Authors: Rydzewski J. , Nowak W. 
Published: August 2017

AbstractUnderstanding the mechanisms of ligand binding to enzymes is of paramount importance for the design of new drugs. Here, we report on the use of a novel biased molecular dynamics (MD) methodology to study the mechanism of camphor binding to cytochrome P450cam. Microsecond-long MD simulations allowed us to observe reaction coordinates characterizing ligand diffusion from the active site of cytochrome P450cam to solvent via three egress routes. These atomistic simulations were used to estimate thermodynamic quantities along the reaction coordinates and indicate diverse binding configurations. The results suggest that the diffusion of camphor along the pathway near the substrate recognition site (SRS) is thermodynamically preferred. In addition, we show that the diffusion near the SRS is triggered by a transition from a heterogeneous collection of closed ligand-bound conformers to the basin comprising the open conformations of cytochrome P450cam. The conformational change accompanying this switch is characterized by the retraction of the F and G helices and the disorder of the B′ helix. These results are corroborated by experimental studies and provide detailed insight into ligand binding and conformational behavior of the cytochrome family. The presented methodology is general and can be applied to other ligand-protein systems.
Kleptoplast photosynthesis is nutritionally relevant in the sea slug Elysia viridis
Authors: Cartaxana Paulo , Trampe Erik , Kühl Michael , Cruz Sónia 
Published: August 2017

AbstractSeveral sacoglossan sea slug species feed on macroalgae and incorporate chloroplasts into tubular cells of their digestive diverticula. We investigated the role of the “stolen” chloroplasts (kleptoplasts) in the nutrition of the sea slug Elysia viridis and assessed how their abundance, distribution and photosynthetic activity were affected by light and starvation. Elysia viridis individuals feeding on the macroalga Codium tomentosum were compared with starved specimens kept in dark and low light conditions. A combination of variable Chl a fluorescence and hyperspectral imaging, and HPLC pigment analysis was used to evaluate the spatial and temporal variability of photopigments and of the photosynthetic capacity of kleptoplasts. We show increased loss of weight and body length in dark-starved E. viridis as compared to low light-starved sea slugs. A more pronounced decrease in kleptoplast abundance and lower photosynthetic electron transport rates were observed in dark-starved sea slugs than in low light-starved animals. This study presents strong evidence of the importance of kleptoplast photosynthesis for the nutrition of E. viridis in periods of food scarcity. Deprived of photosynthates, E. viridis could accelerate the breakdown of kleptoplasts in the dark to satisfy its’ energy requirements.
Sunscreen products impair the early developmental stages of the sea urchin Paracentrotus lividus
Authors: Corinaldesi Cinzia , Damiani Elisabetta , Marcellini Francesca , Falugi Carla , Tiano Luca , Brugè Francesca , Danovaro Roberto 
Published: August 2017

AbstractMarine ecosystems are increasingly threatened by the release of personal care products. Among them, sunscreens are causing concern either for the effects on skin protection from UV radiation and for the potential impacts on marine life. Here, we assessed the UVA protective efficacy of three sunscreens on human dermal fibroblasts, including two common products in Europe and USA, and an eco-friendly product. The sunscreens’ effects were also tested on Paracentrotus lividus, a marine species possibly threatened by these contaminants. We found that all tested sunscreens had similar efficacy in protecting human fibroblasts from UVA radiation. Conversely, the sunscreens’ effects on embryo-larval development of P. lividus were dependent on the product tested. In particular, the USA sunscreen, containing benzophenone-3, homosalate and preservatives, caused the strongest impact on the sea urchin development, whereas the eco-friendly sunscreen determined the weakest effects. These results suggest that although the tested products protected human skin cells from UVA-induced damage, they might severely affect the success of recruitment and survival of the sea urchin. Our findings underline the importance of developing eco-friendly sunscreens for minimising or avoiding the impact on marine life while protecting human skin from UV damage.
Evidence of robust 2D transport and Efros-Shklovskii variable range hopping in disordered topological insulator (Bi2Se3) nanowires
Authors: Bhattacharyya Biplab , Sharma Alka , Sinha Bhavesh , Shah Kunjal , Jejurikar Suhas , Senguttuvan T. D. , Husale Sudhir 
Published: August 2017

AbstractWe report the experimental observation of variable range hopping conduction in focused-ion-beam (FIB) fabricated ultra-narrow nanowires of topological insulator (Bi2Se3). The value of the exponent (d + 1)−1 in the hopping equation was extracted as $$ \sim \frac{1}{2}\,\,$$
~

1
2

for different widths of nanowires, which is the proof of the presence of Efros-Shklovskii hopping transport mechanism in a strongly disordered system. High localization lengths (0.5 nm, 20 nm) were calculated for the devices. A careful analysis of the temperature dependent fluctuations present in the magnetoresistance curves, using the standard Universal Conductance Fluctuation theory, indicates the presence of 2D topological surface states. Also, the surface state contribution to the conductance was found very close to one conductance quantum. We believe that our experimental findings shed light on the understanding of quantum transport in disordered topological insulator based nanostructures.
ER/K linked GPCR-G protein fusions systematically modulate second messenger response in cells
Authors: Malik Rabia U. , Dysthe Matthew , Ritt Michael , Sunahara Roger K. , Sivaramakrishnan Sivaraj 
Published: August 2017

AbstractFRET and BRET approaches are well established for detecting ligand induced GPCR-G protein interactions in cells. Currently, FRET/BRET assays rely on co-expression of GPCR and G protein, and hence depend on the stoichiometry and expression levels of the donor and acceptor probes. On the other hand, GPCR-G protein fusions have been used extensively to understand the selectivity of GPCR signaling pathways. However, the signaling properties of fusion proteins are not consistent across GPCRs. In this study, we describe and characterize novel sensors based on the Systematic Protein Affinity Strength Modulation (SPASM) technique. Sensors consist of a GPCR and G protein tethered by an ER/K linker flanked by FRET probes. SPASM sensors are tested for the β2-, α1-, and α2- adrenergic receptors, and adenosine type 1 receptor (A1R), tethered to Gαs-XL, Gαi2, or Gαq subunits. Agonist stimulation of β2-AR and α2-AR increases FRET signal comparable to co-expressed FRET/BRET sensors. SPASM sensors also retain signaling through the endogenous G protein milieu. Importantly, ER/K linker length systematically tunes the GPCR-G protein interaction, with consequent modulation of second messenger signaling for cognate interactions. SPASM GPCR sensors serve the dual purpose of detecting agonist-induced changes in GPCR-G protein interactions, and linking these changes to downstream signaling.
Epicatechin oligomers longer than trimers have anti-cancer activities, but not the catechin counterparts
Authors: Takanashi Kohki , Suda Manato , Matsumoto Kiriko , Ishihara Chisato , Toda Kazuya , Kawaguchi Koichiro , Senga Shogo , Kobayashi Narumi , Ichikawa Mikihiro , Katoh Miyuki , Hattori Yasunao , Kawahara Sei-ichi , Umezawa Koji , Fujii Hiroshi , Makabe Hidefumi 
Published: August 2017

AbstractSince procyanidins (oligomeric catechin or epicatechin) were reported to exhibit health benefits, much attention has been paid to the synthesis of these compounds, especially those that are longer than trimers. In the present study, syntheses of cinnamtannin A3 (epicatechin pentamer), A4 (epicatechin hexamer), catechin tetramer, pentamer, arecatannin A2 (epicatechin-epicatechin-epicatechin-catechin) and A3 (epicatechin-epicatechin-epicatechin-epicatechin-catechin) were achieved. The key reaction was a Lewis acid mediated equimolar condensation. The antitumor effects of these synthesized compounds against a human prostate cancer cell line (PC-3) were investigated. Among the tested compounds, cinnamtannin A3, A4 and arecatannin A3, which possess epicatechin oligomers longer than tetramers as the basic scaffold, showed significant activities for suppression of cell growth, invasion and FABP5 (fatty acid-binding protein 5) gene expression. Effects on cell cycle distribution showed that cell cycle arrest in the G2 phase was induced. Furthermore, these epicatechin oligomers suppressed significantly the expression of the cancer-promoting gene, FABP5, which is related to cell proliferation and metastasis in various cancer cells. Interestingly, the suppressive activities were associated with the degree of oligomerization of epicatechin. Thus, synthetic studies clearly demonstrate that epicatechin oligomers longer than trimers have significant anti-tumorigenic activities, but not the catechin counterparts.
CYP2C19*2 and CYP2C19*17 variants and effect of tamoxifen on breast cancer recurrence: Analysis of the International Tamoxifen Pharmacogenomics Consortium dataset
Authors: Damkier Per , Kjærsgaard Anders , Barker Kimberly A. , Cronin-Fenton Deidre , Crawford Anatasha , Hellberg Ylva , Janssen Emilius A. M. , Langefeld Carl , Ahern Thomas P. , Lash Timothy L. 
Published: August 2017

AbstractThe role of cytochrome P450 drug metabolizing enzymes in the efficacy of tamoxifen treatment of breast cancer is subject to substantial interest and controversy. CYP2D6 have been intensively studied, but the role of CYP2C19 is less elucidated, and we studied the association of CYPC19 genotype and recurrence of breast cancer. We used outcome and genotyping data from the large publicly available International Tamoxifen Pharmacogenomics Consortium (ITPC) dataset. Cox regression was used to compute the hazard ratios (HRs) for recurrence. CYP2C19 genotype data was available for 2 423 patients and the final sample cohort comprised 2 102 patients. CYP2C19*2 or *19 alleles did not influence DFS. For the CYP2C19*2 allele, the HR was 1.05 (CI 0.78–1.42) and 0.79 (CI 0.32–1.94) for hetero- and homozygote carriers, respectively. The corresponding HR for hetero- and homozygote carriers of the CYP2C19*17 allele were 1.02 (CI 0.71–1.46) and 0.57 (CI 0.26–1.24), respectively. Accounting for CYP2D6 genotype status did not change these estimates. We found no evidence to support a clinically meaningful role of CYP2C19 polymorphisms and response to tamoxifen in breast cancer patients and, consequently, CYP2C19 genotype status should not be included in clinical decisions on tamoxifen treatment.
Assessing cell-nanoparticle interactions by high content imaging of biocompatible iron oxide nanoparticles as potential contrast agents for magnetic resonance imaging
Authors: Hachani Roxanne , Birchall Martin A. , Lowdell Mark W. , Kasparis Georgios , Tung Le D. , Manshian Bella B. , Soenen Stefaan J. , Gsell Willy , Himmelreich Uwe , Gharagouzloo Codi A. , Sridhar Srinivas , Thanh Nguyen T. K. 
Published: August 2017

AbstractStem cell tracking in cellular therapy and regenerative medicine is an urgent need, superparamagnetic iron oxide nanoparticles (IONPs) could be used as contrast agents in magnetic resonance imaging (MRI) that allows visualization of the implanted cells ensuring they reach the desired sites in vivo. Herein, we report the study of the interaction of 3,4-dihydroxyhydrocinnamic acid (DHCA) functionalized IONPs that have desirable properties for T2 - weighted MRI, with bone marrow-derived primary human mesenchymal stem cells (hMSCs). Using the multiparametric high-content imaging method, we evaluate cell viability, formation of reactive oxygen species, mitochondrial health, as well as cell morphology and determine that the hMSCs are minimally affected after labelling with IONPs. Their cellular uptake is visualized by transmission electron microscopy (TEM) and Prussian Blue staining, and quantified using an iron specific colourimetric method. In vitro and in vivo studies demonstrate that these IONPs are biocompatible and can produce significant contrast enhancement in T2-weighted MRI. Iron oxide nanoparticles are detected in vivo as hypointense regions in the liver up to two weeks post injection using 9.4 T MRI. These DHCA functionalized IONPs are promising contrast agents for stem cell tracking by T2-weighted MRI as they are biocompatible and show no evidence of cytotoxic effects on hMSCs.
Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs
Authors: Garcia-Elias Anna , Alloza Leonor , Puigdecanet Eulàlia , Nonell Lara , Tajes Marta , Curado Joao , Enjuanes Cristina , Díaz Oscar , Bruguera Jordi , Martí-Almor Julio , Comín-Colet Josep , Benito Begoña 
Published: August 2017

AbstractMicroRNAs (miRNAs) have emerged as promising biomarkers of disease. Their potential use in clinical practice requires standardized protocols with very low miRNA concentrations, particularly in plasma samples. Here we tested the most appropriate method for miRNA quantification and validated the performance of a hybridization platform using lower amounts of starting RNA. miRNAs isolated from human plasma and from a reference sample were quantified using four platforms and profiled with hybridization arrays and RNA sequencing (RNA-seq). Our results indicate that the Infinite® 200 PRO Nanoquant and Nanodrop 2000 spectrophotometers magnified the miRNA concentration by detecting contaminants, proteins, and other forms of RNA. The Agilent 2100 Bioanalyzer PicoChip and SmallChip gave valuable information on RNA profile but were not a reliable quantification method for plasma samples. The Qubit® 2.0 Fluorometer provided the most accurate quantification of miRNA content, although RNA-seq confirmed that only ~58% of small RNAs in plasma are true miRNAs. On the other hand, reducing the starting RNA to 70% of the recommended amount for miRNA profiling with arrays yielded results comparable to those obtained with the full amount, whereas a 50% reduction did not. These findings provide important clues for miRNA determination in human plasma samples.
Isoflurane produces antidepressant effects and induces TrkB signaling in rodents
Authors: Antila Hanna , Ryazantseva Maria , Popova Dina , Sipilä Pia , Guirado Ramon , Kohtala Samuel , Yalcin Ipek , Lindholm Jesse , Vesa Liisa , Sato Vinicius , Cordeira Joshua , Autio Henri , Kislin Mikhail , Rios Maribel , Joca Sâmia , Casarotto Plinio , Khiroug Leonard , Lauri Sari , Taira Tomi , Castrén Eero , Rantamäki Tomi 
Published: August 2017

AbstractA brief burst-suppressing isoflurane anesthesia has been shown to rapidly alleviate symptoms of depression in a subset of patients, but the neurobiological basis of these observations remains obscure. We show that a single isoflurane anesthesia produces antidepressant-like behavioural effects in the learned helplessness paradigm and regulates molecular events implicated in the mechanism of action of rapid-acting antidepressant ketamine: activation of brain-derived neurotrophic factor (BDNF) receptor TrkB, facilitation of mammalian target of rapamycin (mTOR) signaling pathway and inhibition of glycogen synthase kinase 3β (GSK3β). Moreover, isoflurane affected neuronal plasticity by facilitating long-term potentiation in the hippocampus. We also found that isoflurane increased activity of the parvalbumin interneurons, and facilitated GABAergic transmission in wild type mice but not in transgenic mice with reduced TrkB expression in parvalbumin interneurons. Our findings strengthen the role of TrkB signaling in the antidepressant responses and encourage further evaluation of isoflurane as a rapid-acting antidepressant devoid of the psychotomimetic effects and abuse potential of ketamine.
2D surface optical lattice formed by plasmon polaritons with application to nanometer-scale molecular deposition
Authors: Yin Yanning , Xu Supeng , Li Tao , Yin Yaling , Xia Yong , Yin Jianping 
Published: August 2017

AbstractSurface plasmon polaritons, due to their tight spatial confinement and high local intensity, hold great promises in nanofabrication which is beyond the diffraction limit of conventional lithography. Here, we demonstrate theoretically the 2D surface optical lattices based on the surface plasmon polariton interference field, and the potential application to nanometer-scale molecular deposition. We present the different topologies of lattices generated by simple configurations on the substrate. By explicit theoretical derivations, we explain their formation and characteristics including field distribution, periodicity and phase dependence. We conclude that the topologies can not only possess a high stability, but also be dynamically manipulated via changing the polarization of the excitation laser. Nanometer-scale molecular deposition is simulated with these 2D lattices and discussed for improving the deposition resolution. The periodic lattice point with a width resolution of 33.2 nm can be obtained when the fullerene molecular beam is well-collimated. Our study can offer a superior alternative method to fabricate the spatially complicated 2D nanostructures, with the deposition array pitch serving as a reference standard for accurate and traceable metrology of the SI length standard.
Responses of crop yield growth to global temperature and socioeconomic changes
Authors: Iizumi Toshichika , Furuya Jun , Shen Zhihong , Kim Wonsik , Okada Masashi , Fujimori Shinichiro , Hasegawa Tomoko , Nishimori Motoki 
Published: August 2017

AbstractAlthough biophysical yield responses to local warming have been studied, we know little about how crop yield growth—a function of climate and technology—responds to global temperature and socioeconomic changes. Here, we present the yield growth of major crops under warming conditions from preindustrial levels as simulated by a global gridded crop model. The results revealed that global mean yields of maize and soybean will stagnate with warming even when agronomic adjustments are considered. This trend is consistent across socioeconomic assumptions. Low-income countries located at low latitudes will benefit from intensive mitigation and from associated limited warming trends (1.8 °C), thus preventing maize, soybean and wheat yield stagnation. Rice yields in these countries can improve under more aggressive warming trends. The yield growth of maize and soybean crops in high-income countries located at mid and high latitudes will stagnate, whereas that of rice and wheat will not. Our findings underpin the importance of ambitious climate mitigation targets for sustaining yield growth worldwide.