bluuebunny/crossref_metadata_2025_split huggingface dataset:
Force-induced chemical reactions on the metal centre in a single metalloprotein molecule
Authors: Zheng Peng , Arantes Guilherme M. , Field Martin J. , Li Hongbin 
Published: June 2015

AbstractMetalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions.
Gender differences in brain structure and resting-state functional connectivity related to narcissistic personality
Authors: Yang Wenjing , Cun Lingli , Du Xue , Yang Junyi , Wang Yanqiu , Wei Dongtao , Zhang Qinglin , Qiu Jiang 
Published: June 2015

AbstractAlthough cognitive and personality studies have observed gender differences in narcissism, the neural bases of these differences remain unknown. The current study combined the voxel-based morphometry and resting state functional connectivity (rsFC) analyses to explore the sex-specific neural basis of narcissistic personality. The VBM results showed that the relationship between narcissistic personality and regional gray matter volume (rGMV) differed between sexes. Narcissistic scores had a significant positive correlation with the rGMV of the right SPL in females, but not in males. Further analyses were conducted to investigate the sex-specific relationship between rsFC and narcissism, using right SPL/frontal eye fields (FEF) as the seed regions (key nodes of the dorsal attention network, DAN). Interestingly, decreased anticorrelations between the right SPL/FEF and areas of the precuneus and middle frontal gyrus (key nodes of the the default mode network, DMN) were associated with higher narcissistic personality scores in males, whereas females showed the opposite tendency. The findings indicate that gender differences in narcissism may be associated with differences in the intrinsic and dynamic interplay between the internally-directed DMN and the externally-directed TPN. Morphometry and functional connectivity analyses can enhance our understanding of the neural basis of sex-specific narcissism.
Heat stress induced apoptosis is triggered by transcription-independent p53, Ca2+ dyshomeostasis and the subsequent Bax mitochondrial translocation
Authors: Gu Z. T. , Li L. , WU F. , Zhao P. , Yang H. , Liu Y. S. , Geng Y. , Zhao M. , Su L. 
Published: June 2015

AbstractIn this study, We demonstrated that Bax mitochondrial translocation plays a vital role in the initiation of the mitochondrial signaling pathway upon activation by heat stress. In addition, both p53 mitochondrial translocation and Ca2+ signal mediated MPTP opening activate Bax mitochondrial translocation. Employing pifithrin-α (a p53 mitochondrial translocation inhibitor) and CsA (a permeability transition pore (MPTP) inhibitor), we found that heat stress induced Bax mitochondrial translocation was significantly inhibited in cells pretreated with both PFT and CsA. Furthermore, we demonstrated that generation of reactive oxygen species (ROS) is a critical mediator in heat stress induced apoptosis and that the antioxidant MnTBAP significantly decreased heat stress induced p53 mitochondrial translocation and Ca2+ signal mediated MPTP opening, as well as the subsequent Bax mitochondrial translocation and activation of the caspase cascade. Taken together, our results indicate that heat stress induces apoptosis through the mitochondrial pathway with ROS dependent mitochondrial p53 translocation and Ca2+ dyshomeostasis and the ensuing intro Bax mitochondrial translocation as the upstream events involved in triggering the apoptotic process observed upon cellular exposure to heat stress.
Scattering of Sculpted Light in Intact Brain Tissue, with implications for Optogenetics
Authors: Favre-Bulle Itia A. , Preece Daryl , Nieminen Timo A. , Heap Lucy A. , Scott Ethan K. , Rubinsztein-Dunlop Halina 
Published: June 2015

AbstractOptogenetics uses light to control and observe the activity of neurons, often using a focused laser beam. As brain tissue is a scattering medium, beams are distorted and spread with propagation through neural tissue and the beam’s degradation has important implications in optogenetic experiments. To address this, we present an analysis of scattering and loss of intensity of focused laser beams at different depths within the brains of zebrafish larvae. Our experimental set-up uses a 488 nm laser and a spatial light modulator to focus a diffraction-limited spot of light within the brain. We use a combination of experimental measurements of back-scattered light in live larvae and computational modelling of the scattering to determine the spatial distribution of light. Modelling is performed using the Monte Carlo method, supported by generalised Lorenz–Mie theory in the single-scattering approximation. Scattering in areas rich in cell bodies is compared to that of regions of neuropil to identify the distinct and dramatic contributions that cell nuclei make to scattering. We demonstrate the feasibility of illuminating individual neurons, even in nucleus-rich areas, at depths beyond 100 μm using a spatial light modulator in combination with a standard laser and microscope optics.
Experimental Realization of Extreme Heat Flux Concentration with Easy-to-Make Thermal Metamaterials
Authors: Chen Fei , Yuan Lei Dang 
Published: June 2015

AbstractThe ability to harvest thermal energy and manipulate heat fluxes has recently attracted a great deal of research interest because this is critical to achieve efficient solar-to-thermal energy conversion in the technology of concentrated solar thermal collectors. Thermal metamaterials with engineered thermal conduction are often utilized to control the diffusive heat flow in ways otherwise not possible with naturally occurring materials. In this work, we adopt the transformation thermodynamics approach to design an annular fan-shaped thermal metamaterial which is capable of guiding heat fluxes and concentrating thermal energy to the central region of the metamaterial device without disturbing the temperature profile outside the structure – a fascinating and unique feature impossibly achieved with homogeneous materials. In experiment, this rationally-designed metamaterial structure demonstrates extreme heat flux compression from both line-shaped and point thermal sources with measured concentration efficiency up to 83.1%, providing the first experimental realization of our recent theoretical prediction (T. Han et al., Energy Environ. Sci., 2013, 6, 3537-3541). These unprecedented results may open up new possibilities for engineering thermal materials with desired properties that can be used for dramatically enhancing the efficiency of the existing solar thermal collectors.
iRhom1 regulates proteasome activity via PAC1/2 under ER stress
Authors: Lee WonJae , Kim YoungDoo , Park Jisu , Shim SangMi , Lee Jieun , Hong Se-hoon , Ahn Hye-Hyun , Lee Huikyong , Jung Yong-Keun 
Published: June 2015

AbstractProteasome is a protein degradation complex that plays a major role in maintaining cellular homeostasis. Despite extensive efforts to identify protein substrates that are degraded through ubiquitination, the regulation of proteasome activity itself under diverse signals is poorly understood. In this study, we have isolated iRhom1 as a stimulator of proteasome activity from genome-wide functional screening using cDNA expression and an unstable GFP-degron. Downregulation of iRhom1 reduced enzymatic activity of proteasome complexes and overexpression of iRhom1 enhanced it. Native-gel and fractionation analyses revealed that knockdown of iRhom1 expression impaired the assembly of the proteasome complexes. The expression of iRhom1 was increased by endoplasmic reticulum (ER) stressors, such as thapsigargin and tunicamycin, leading to the enhancement of proteasome activity, especially in ER-containing microsomes. iRhom1 interacted with the 20S proteasome assembly chaperones PAC1 and PAC2, affecting their protein stability. Moreover, knockdown of iRhom1 expression impaired the dimerization of PAC1 and PAC2 under ER stress. In addition, iRhom1 deficiency in D. melanogaster accelerated the rough-eye phenotype of mutant Huntingtin, while transgenic flies expressing either human iRhom1 or Drosophila iRhom showed rescue of the rough-eye phenotype. Together, these results identify a novel regulator of proteasome activity, iRhom1, which functions via PAC1/2 under ER stress.
Revealing patterns of local species richness along environmental gradients with a novel network tool
Authors: Baudena Mara , Sánchez Angel , Georg Co-Pierre , Ruiz-Benito Paloma , Rodríguez Miguel Á. , Zavala Miguel A. , Rietkerk Max 
Published: June 2015

AbstractHow species richness relates to environmental gradients at large extents is commonly investigated aggregating local site data to coarser grains. However, such relationships often change with the grain of analysis, potentially hiding the local signal. Here we show that a novel network technique, the “method of reflections”, could unveil the relationships between species richness and climate without such drawbacks. We introduced a new index related to potential species richness, which revealed large scale patterns by including at the local community level information about species distribution throughout the dataset (i.e., the network). The method effectively removed noise, identifying how far site richness was from potential. When applying it to study woody species richness patterns in Spain, we observed that annual precipitation and mean annual temperature explained large parts of the variance of the newly defined species richness, highlighting that, at the local scale, communities in drier and warmer areas were potentially the species richest. Our method went far beyond what geographical upscaling of the data could unfold and the insights obtained strongly suggested that it is a powerful instrument to detect key factors underlying species richness patterns and that it could have numerous applications in ecology and other fields.
The effect of land-use on the diversity and mass-abundance relationships of understory avian insectivores in Sri Lanka and southern India
Authors: Sreekar Rachakonda , Srinivasan Umesh , Mammides Christos , Chen Jin , Manage Goodale Uromi , Wimalabandara Kotagama Sarath , Sidhu Swati , Goodale Eben 
Published: June 2015

AbstractUnderstory avian insectivores are especially sensitive to deforestation, although regional differences in how these species respond to human disturbance may be linked to varying land-use histories. South Asia experienced widespread conversion of forest to agriculture in the nineteenth century, providing a comparison to tropical areas deforested more recently. In Sri Lanka and the Western Ghats of India, we compared understory insectivores to other guilds and to insectivores with different vertical strata preferences, both inside mixed-species flocks and for the whole bird community. Overall species richness did not change across the land-use gradient, although there was substantial turnover in species composition between land-use types. We found that the proportion of species represented by insectivores was ~1.14 times higher in forest compared to agriculture and the proportion of insectivores represented by understory species was ~1.32 times higher in forests. Mass-abundance relationships were very different when analyzed on mixed-species flocks compared to the total community, perhaps indicating reduced competition in these mutualisms. We show that South Asia fits the worldwide pattern of understory insectivores declining with increased land-use intensity and conclude that these species can be used globally as indicator and/or umbrella species for conservation across different disturbance time scales.
Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts
Authors: Morel Guillaume , Sterck Lieven , Swennen Dominique , Marcet-Houben Marina , Onesime Djamila , Levasseur Anthony , Jacques Noémie , Mallet Sandrine , Couloux Arnaux , Labadie Karine , Amselem Joëlle , Beckerich Jean-Marie , Henrissat Bernard , Van de Peer Yves , Wincker Patrick , Souciet Jean-Luc , Gabaldón Toni , Tinsley Colin R. , Casaregola Serge 
Published: June 2015

AbstractThe evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi–yeasts split concomitant with the yeasts’ genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
Achieving synchronization with active hybrid materials: Coupling self-oscillating gels and piezoelectric films
Authors: Yashin Victor V. , Levitan Steven P. , Balazs Anna C. 
Published: June 2015

AbstractLightweight, deformable materials that can sense and respond to human touch and motion can be the basis of future wearable computers, where the material itself will be capable of performing computations. To facilitate the creation of “materials that compute”, we draw from two emerging modalities for computation: chemical computing, which relies on reaction-diffusion mechanisms to perform operations and oscillatory computing, which performs pattern recognition through synchronization of coupled oscillators. Chemical computing systems, however, suffer from the fact that the reacting species are coupled only locally; the coupling is limited by diffusion as the chemical waves propagate throughout the system. Additionally, oscillatory computing systems have not utilized a potentially wearable material. To address both these limitations, we develop the first model for coupling self-oscillating polymer gels to a piezoelectric (PZ) micro-electro-mechanical system (MEMS). The resulting transduction between chemo-mechanical and electrical energy creates signals that can be propagated quickly over long distances and thus, permits remote, non-diffusively coupled oscillators to communicate and synchronize. Moreover, the oscillators can be organized into arbitrary topologies because the electrical connections lift the limitations of diffusive coupling. Using our model, we predict the synchronization behavior that can be used for computational tasks, ultimately enabling “materials that compute”.
Does the passage of seeds through frugivore gut affect their storage: A case study on the endangered plant Euryodendron excelsum
Authors: Shikang Shen , Fuqin Wu , Yuehua Wang 
Published: June 2015

AbstractPlant-frugivore mutualism serves an important function in multiple ecological processes. Although previous studies have highlighted the effect of frugivore gut passage on fresh seed germinability, no study has investigated the effect on seed storage after frugivore gut passage. We used the endangered plant, Euryodendron excelsum, to determine the combined effects of frugivore gut passage and storage conditions on the germination percentage and rate of seeds. In particular, three treatments that included storage periods, storage methods and seed types were designed in the experiment. We hypothesized that seeds that passed through the gut will exhibit enhanced germination capacity and rate during storage. Results showed that the final germination percentage decreased in seeds that passed through the gut, whereas the germination rate increased during seed storage. Germination decreased in most types of seeds under both dry and wet storage after 6 months compared with storage after 1 and 3 months. The results suggest that after frugivore gut passage, E. excelsum seeds cannot form persistent soil seed bank in the field and were not suitable for species germplasm storage. These finding underscore that seeds that passed through frugivore gut have long-term impact on their viability and germination performance.
Function and evolution of Magnaporthe oryzae avirulence gene AvrPib responding to the rice blast resistance gene Pib
Authors: Zhang Shulin , Wang Ling , Wu Weihuai , He Liyun , Yang Xianfeng , Pan Qinghua 
Published: June 2015

AbstractMagnaporthe oryzae (Mo) is the causative pathogen of the damaging disease rice blast. The effector gene AvrPib, which confers avirulence to host carrying resistance gene Pib, was isolated via map-based cloning. The gene encodes a 75-residue protein, which includes a signal peptide. Phenotyping and genotyping of 60 isolates from each of five geographically distinct Mo populations revealed that the frequency of virulent isolates, as well as the sequence diversity within the AvrPib gene increased from a low level in the far northeastern region of China to a much higher one in the southern region, indicating a process of host-driven selection. Resequencing of the AvrPiballele harbored by a set of 108 diverse isolates revealed that there were four pathoways, transposable element (TE) insertion (frequency 81.7%), segmental deletion (11.1%), complete absence (6.7%) and point mutation (0.6%), leading to loss of the avirulence function. The lack of any TE insertion in a sample of non-rice infecting Moisolates suggested that it occurred after the host specialization of Mo. Both the deletions and the functional point mutation were confined to the signal peptide. The reconstruction of 16 alleles confirmed seven functional nucleotide polymorphisms for the AvrPiballeles, which generated three distinct expression profiles.
Ongoing dynamics in large-scale functional connectivity predict perception
Authors: Sadaghiani Sepideh , Poline Jean-Baptiste , Kleinschmidt Andreas , D’Esposito Mark 
Published: June 2015

SignificanceMost brain activity is not directly evoked by specific external events. This ongoing activity is correlated across distant brain regions within large-scale networks. This correlation or functional connectivity may reflect communication across brain regions. Strength and spatial organization of functional connectivity changes dynamically over seconds to minutes. Using functional MRI, we show that these ongoing changes correlate with behavior. The connectivity state before playback of a faint sound predicted whether the participant was going to perceive the sound on that trial. Connectivity states preceding missed sounds showed weakened modular structure, in which connectivity was more random and less organized across brain regions. These findings suggest that ongoing brain connectivity dynamics contribute to explaining behavioral variability.
Biocatalytic synthesis of starch esters by immobilized lipase on magnetic microparticles
Authors: Prasertpornsakun Nattanun , Raita Marisa , Laosiripojana Navadol , Champreda Verawat 
Published: June 2015

Abstract
Enzymatic esterification is an efficient approach for modifying starch to functionalized biomaterials. In this study, conversion of cassava starch to fatty acid acyl esters using immobilized Thermomyces lanuginosus lipase on Fe3O4 microparticles modified with 3-aminopropyltriethoxysilane and covalently linked by 1-ethyl-3-(3-dimethyl aminopropyl) carbodiimide and N-hydroxysuccinimide (Fe3O4-AP-ED-lipase) in a solvent-free system was studied. An optimized reaction containing 5% w/v gelatinized starch, 1% v/v Triton X-100, and 1% w/v biocatalyst with 2.5% w/v of fatty acids (palmitic, oleic, or linoleic acid) resulted in esterified products with a degree of substitution (DS) of 0.12–0.14, while a slightly lower DS was observed using crude palm fatty acid distillate as the acyl donor with 42.9–59.6% recovery yield. Increasing DS led to lower glass transition temperature and higher viscosity of the esterified products. The enzyme showed high operational stability with 85% retaining in activity after recycling in three consecutive batches with simple separation by magnetization, leading to improved process economics.
Characterization of a feruloyl esterase B from Talaromyces cellulolyticus
Authors: Watanabe Masahiro , Yoshida Erika , Fukada Hiroaki , Inoue Hiroyuki , Tokura Mitsunori , Ishikawa Kazuhiko 
Published: June 2015

Abstract
A feruloyl esterase catalyzes the hydrolysis of the 4-hydroxy-3-methoxycinnamoyl (feruloyl) group from esterified sugars in plant cell walls. Talaromyces cellulolyticus is a high cellulolytic-enzyme producing fungus. However, there is no report for feruloyl esterase activity of T. cellulolyticus. Analysis of the genome database of T. cellulolyticus identified a gene encoding a putative feruloyl esterase B. The recombinant enzyme was prepared using a T. cellulolyticus homologous expression system and characterized. The purified enzyme exhibited hydrolytic activity toward p-nitrophenyl acetate, p-nitrophenyl trans-ferulate, methyl ferulate, rice husk, and bagasse. HPLC assays showed that the enzyme released ferulic acid and p-coumaric acid from hydrothermal-treated rice husk and bagasse. Trichoderma sp. is well-known high cellulolytic-enzyme producing fungus useful for the lignocellulosic biomass saccharification. Interestingly, no feruloyl esterase has been reported from Trichoderma sp. The results show that this enzyme is expected to be industrially useful for biomass saccharification.