bluuebunny/crossref_metadata_2025 huggingface dataset:
Impacts of Conformational Geometries in Fluorinated Alkanes
Authors: Brandenburg Tim , Golnak Ronny , Nagasaka Masanari , Atak Kaan , Sreekantan Nair Lalithambika Sreeju , Kosugi Nobuhiro , Aziz Emad F.
Published: August 2016

Research of blood substitute formulations and their base materials is of high scientific interest. Especially fluorinated microemulsions based on perfluorocarbons, with their interesting chemical properties, offer opportunities for applications in biomedicine and physical chemistry. In this work, carbon K-edge absorption spectra of liquid perfluoroalkanes and their parent hydrocarbons are presented and compared. Based on soft X-ray absorption, a comprehensive picture of the electronic structure is provided with the aid of time dependent density functional theory. We have observed that conformational geometries mainly influence the chemical and electronic interactions in the presented liquid materials, leading to a direct association of conformational geometries to the dissolving capacity of the presented perfluorocarbons with other solvents like water and possibly gases like oxygen.
Shape-Controlled Synthesis of Pt Nanopeanuts
Authors: Zhang Xuemei , Xia Zengzilu , Huang Yingzhou , Jia Yunpeng , Sun Xiaonan , Li Yu , Li Xueming , Wu Rui , Liu Anping , Qi Xueqiang , Wang Shuxia , Wen Weijia
Published: August 2016

Exploring the novel shape of Pt nanoparticles is one of the most useful ways to improve the electrocatalytic performance of Pt in fuel cells. In this work, the Pt nanopeanuts consisting of two nanospheres grown together have been fabricated through a two-step polyol method. The high resolution scanning electron microscope (SEM) images and energy dispersive x-ray (EDX) spectrum collected at adjacent part point out the Pt nanopeanut is apparently different from the two physical attached nanospheres. To understand the growth mechanism of this nanopeanut, the final products in different synthesis situations are studied. The results indicate the interesting morphology of Pt nanopeanuts mainly benefit from the chemical reagent (FeCl3) while the size and homogeneity are greatly affected by the temperature. Furthermore, the electrocatalytic activity of the Pt nanopeanuts has also been demonstrated here. Our two-step synthesis of Pt nanopeanuts not only enlarges the group of Pt nanoparticles, but also provides a beneficial strategy for the synthesis of novel metal nanoparticles.
The use of DAPI fluorescence lifetime imaging for investigating chromatin condensation in human chromosomes
Authors: Estandarte Ana Katrina , Botchway Stanley , Lynch Christophe , Yusuf Mohammed , Robinson Ian
Published: August 2016

Chromatin undergoes dramatic condensation and decondensation as cells transition between the different phases of the cell cycle. The organization of chromatin in chromosomes is still one of the key challenges in structural biology. Fluorescence lifetime imaging (FLIM), a technique which utilizes a fluorophore’s fluorescence lifetime to probe changes in its environment, was used to investigate variations in chromatin compaction in fixed human chromosomes. Fixed human metaphase and interphase chromosomes were labeled with the DNA minor groove binder, DAPI, followed by measurement and imaging of the fluorescence lifetime using multiphoton excitation. DAPI lifetime variations in metaphase chromosome spreads allowed mapping of the differentially compacted regions of chromatin along the length of the chromosomes. The heteromorphic regions of chromosomes 1, 9, 15, 16 and Y, which consist of highly condensed constitutive heterochromatin, showed statistically significant shorter DAPI lifetime values than the rest of the chromosomes. Differences in the DAPI lifetimes for the heteromorphic regions suggest differences in the structures of these regions. DAPI lifetime variations across interphase nuclei showed variation in chromatin compaction in interphase and the formation of chromosome territories. The successful probing of differences in chromatin compaction suggests that FLIM has enormous potential for application in structural and diagnostic studies.
Exploratory Metabolomics Profiling in the Kainic Acid Rat Model Reveals Depletion of 25-Hydroxyvitamin D3 during Epileptogenesis
Authors: Heischmann Svenja , Quinn Kevin , Cruickshank-Quinn Charmion , Liang Li-Ping , Reisdorph Rick , Reisdorph Nichole , Patel Manisha
Published: August 2016

Currently, no reliable markers are available to evaluate the epileptogenic potential of a brain injury. The electroencephalogram is the standard method of diagnosis of epilepsy; however, it is not used to predict the risk of developing epilepsy. Biomarkers that indicate an individual’s risk to develop epilepsy, especially those measurable in the periphery are urgently needed. Temporal lobe epilepsy (TLE), the most common form of acquired epilepsy, is characterized by spontaneous recurrent seizures following brain injury and a seizure-free “latent” period. Elucidation of mechanisms at play during epilepsy development (epileptogenesis) in animal models of TLE could enable the identification of predictive biomarkers. Our pilot study using liquid chromatography-mass spectrometry metabolomics analysis revealed changes (p-value ≤ 0.05, ≥1.5-fold change) in lipid, purine, and sterol metabolism in rat plasma and hippocampus during epileptogenesis and chronic epilepsy in the kainic acid model of TLE. Notably, disease development was associated with dysregulation of vitamin D3 metabolism at all stages and plasma 25-hydroxyvitamin D3 depletion in the acute and latent phase of injury-induced epileptogenesis. These data suggest that plasma VD3 metabolites reflect the severity of an epileptogenic insult and that a panel of plasma VD3 metabolites may be able to serve as a marker of epileptogenesis.
microRNA regulatory circuits in a mouse model of inherited retinal degeneration
Authors: Palfi Arpad , Hokamp Karsten , Hauck Stefanie M. , Vencken Sebastian , Millington-Ward Sophia , Chadderton Naomi , Carrigan Mathew , Kortvely Elod , Greene Catherine M. , Kenna Paul F. , Farrar G. Jane
Published: August 2016

miRNA dysregulation is a hallmark of many neurodegenerative disorders, including those involving the retina. Up-regulation of miR-1/133 and miR-142, and down-regulation of miR-183/96/182 has been described in the RHO-P347S mouse retina, a model for a common form of inherited blindness. High-throughput LC-MS/MS was employed to analyse the protein expression of predicted targets for these miRNAs in RHO-P347S mouse retinas; 133 potential target genes were identified. Pathway over-representation analysis suggests G-protein signaling/visual transduction, and synaptic transmission for miR-1, and transmembrane transport, cell-adhesion, signal transduction and apoptosis for miR-183/96/182 as regulated functions in retina. Validation of miRNA-target mRNA interactions for miR-1, miR-96/182 and miR-96 targeting Ctbp2, Rac1 and Slc6a9, respectively, was demonstrated in vitro. In vivo interaction of miR-183/96/182 and Rac1 mRNA in retina was confirmed using miR-CATCH. Additional miRNAs (including miR-103-3p, miR-9-5p) were both predicted to target Rac1 mRNA and enriched by Rac1-miR-CATCH. Other Rac1-miR-CATCH-enriched miRNAs (including miR-125a/b-5p, miR-378a-3p) were not predicted to target Rac1. Furthermore, levels of ~25% of the retinal Rac1 interactors were determined by LC-MS/MS; expression of Rap1gds1 and Cav1 was elevated. Our data suggest significant utilisation of miRNA-based regulation in retina. Possibly more than 30 miRNAs interact with Rac1 in retina, targeting both UTRs and coding regions.
Neutrons describe ectoine effects on water H-bonding and hydration around a soluble protein and a cell membrane
Authors: Zaccai Giuseppe , Bagyan Irina , Combet Jérôme , Cuello Gabriel J. , Demé Bruno , Fichou Yann , Gallat François-Xavier , Galvan Josa Victor M. , von Gronau Susanne , Haertlein Michael , Martel Anne , Moulin Martine , Neumann Markus , Weik Martin , Oesterhelt Dieter
Published: August 2016

Understanding adaptation to extreme environments remains a challenge of high biotechnological potential for fundamental molecular biology. The cytosol of many microorganisms, isolated from saline environments, reversibly accumulates molar concentrations of the osmolyte ectoine to counterbalance fluctuating external salt concentrations. Although they have been studied extensively by thermodynamic and spectroscopic methods, direct experimental structural data have, so far, been lacking on ectoine-water-protein interactions. In this paper,in vivodeuterium labeling, small angle neutron scattering, neutron membrane diffraction and inelastic scattering are combined with neutron liquids diffraction to characterize the extreme ectoine-containing solvent and its effects on purple membrane ofH. salinarumandE. colimaltose binding protein. The data reveal that ectoine is excluded from the hydration layer at the membrane surface and does not affect membrane molecular dynamics, and prove a previous hypothesis that ectoine is excluded from a monolayer of dense hydration water around the soluble protein. Neutron liquids diffraction to atomic resolution shows how ectoine enhances the remarkable properties of H-bonds in water—properties that are essential for the proper organization, stabilization and dynamics of biological structures.
Precipitation overrides warming in mediating soil nitrogen pools in an alpine grassland ecosystem on the Tibetan Plateau
Authors: Lin Li , Zhu Biao , Chen Chengrong , Zhang Zhenhua , Wang Qi-Bing , He Jin-Sheng
Published: August 2016

Soils in the alpine grassland store a large amount of nitrogen (N) due to slow decomposition. However, the decomposition could be affected by climate change, which has profound impacts on soil N cycling. We investigated the changes of soil total N and five labile N stocks in the topsoil, the subsoil and the entire soil profile in response to three years of experimental warming and altered precipitation in a Tibetan alpine grassland. We found that warming significantly increased soil nitrate N stock and decreased microbial biomass N (MBN) stock. Increased precipitation reduced nitrate N, dissolved organic N and amino acid N stocks, but increased MBN stock in the topsoil. No change in soil total N was detected under warming and altered precipitation regimes. Redundancy analysis further revealed that soil moisture (26.3%) overrode soil temperature (10.4%) in explaining the variations of soil N stocks across the treatments. Our results suggest that precipitation exerted stronger influence than warming on soil N pools in this mesic and high-elevation grassland ecosystem. This indicates that the projected rise in future precipitation may lead to a significant loss of dissolved soil N pools by stimulating the biogeochemical processes in this alpine grassland.
A multi-similarity spectral clustering method for community detection in dynamic networks
Authors: Qin Xuanmei , Dai Weidi , Jiao Pengfei , Wang Wenjun , Yuan Ning
Published: August 2016

Community structure is one of the fundamental characteristics of complex networks. Many methods have been proposed for community detection. However, most of these methods are designed for static networks and are not suitable for dynamic networks that evolve over time. Recently, the evolutionary clustering framework was proposed for clustering dynamic data, and it can also be used for community detection in dynamic networks. In this paper, a multi-similarity spectral (MSSC) method is proposed as an improvement to the former evolutionary clustering method. To detect the community structure in dynamic networks, our method considers the different similarity metrics of networks. First, multiple similarity matrices are constructed for each snapshot of dynamic networks. Then, a dynamic co-training algorithm is proposed by bootstrapping the clustering of different similarity measures. Compared with a number of baseline models, the experimental results show that the proposed MSSC method has better performance on some widely used synthetic and real-world datasets with ground-truth community structure that change over time.
Structural and physical properties of the dust particles in Qatar and their influence on the PV panel performance
Authors: Aïssa Brahim , Isaifan Rima J. , Madhavan Vinod E. , Abdallah Amir A.
Published: August 2016

Recently, extensive R&D has been conducted, both by industry and academia, to significantly raise the conversion efficiency of commercial photovoltaic (PV) modules. The installation of PV systems aimed at optimizing solar energy yield is primarily dictated by its geographic location and installation design to maximize solar exposure. However, even when these characteristics have been addressed appropriately, there are other factors that adversely affect the performance of PV systems, namely the temperature-induced voltage decrease leading to a PV power loss and the dust accumulation (soiling). The latter is the lesser acknowledged factor that significantly influences the performance of PV installations especially in the Middle East region. In this paper we report on the investigation of the structural and physical properties of the desert-dust particles in the State of Qatar. The dust particles were collected directly from the PV panels installed in desert environment and characterized by different techniques, including scanning electron, optical and atomic force microscopies, X-ray diffraction, energy-dispersive, UV-Vis, micro-Raman and Fourier transform infrared spectroscopy. The vibrating sample magnetometry analyses were also conducted to study the magnetic properties of the dust particles. The influence of the dust accumulation on the PV panel performance was also presented and discussed.
Folding analysis of the most complex Stevedore’s protein knot
Authors: Wang Iren , Chen Szu-Yu , Hsu Shang-Te Danny
Published: August 2016

DehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the most complex 61 Stevedore’s protein knot within its folding topology. To examine how DehI attains such an intricate knotted topology we combined far-UV circular dichroism (CD), intrinsic fluorescence spectroscopy and small angle X-ray scattering (SAXS) to investigate its folding mechanism. Equilibrium unfolding of DehI by chemical denaturation indicated the presence of two highly populated folding intermediates, I and I’. While the two intermediates vary in secondary structure contents and tertiary packing according to CD and intrinsic fluorescence, respectively, their overall dimension and compactness are similar according to SAXS. Three single-tryptophan variants (W34, W53, and W196) were generated to probe non-cooperative unfolding events localized around the three fluorophores. Kinetic fluorescence measurements indicated that the transition from the intermediate I’ to the unfolded state is rate limiting. Our multiparametric folding analyses suggest that DehI unfolds through a linear folding pathway with two distinct folding intermediates by initial hydrophobic collapse followed by nucleation condensation, and that knotting precedes the formation of secondary structures.
A self-enhanced transport mechanism through long noncoding RNAs for X chromosome inactivation
Authors: Li Chunhe , Hong Tian , Webb Chiu-Ho , Karner Heather , Sun Sha , Nie Qing
Published: August 2016

X-chromosome inactivation (XCI) is the mammalian dosage compensation strategy for balancing sex chromosome content between females and males. While works exist on initiation of symmetric breaking, the underlying allelic choice mechanisms and dynamic regulation responsible for the asymmetric fate determination of XCI remain elusive. Here we combine mathematical modeling and experimental data to examine the mechanism of XCI fate decision by analyzing the signaling regulatory circuit associated with long noncoding RNAs (lncRNAs) involved in XCI. We describe three plausible gene network models that incorporate features of lncRNAs in their localized actions and rapid transcriptional turnovers. In particular, we show experimentally that Jpx (a lncRNA) is transcribed biallelically, escapes XCI and is asymmetrically dispersed between two X’s. Subjecting Jpx to our test of model predictions against previous experimental observations, we identify that a self-enhanced transport feedback mechanism is critical to XCI fate decision. In addition, the analysis indicates that an ultrasensitive response of Jpx signal on CTCF is important in this mechanism. Overall, our combined modeling and experimental data suggest that the self-enhanced transport regulation based on allele-specific nature of lncRNAs and their temporal dynamics provides a robust and novel mechanism for bi-directional fate decisions in critical developmental processes.
Expanding the molecular toolkit for the homoacetogen Clostridium ljungdahlii
Authors: Molitor Bastian , Kirchner Kristina , Henrich Alexander W. , Schmitz Simone , Rosenbaum Miriam A.
Published: August 2016

Increasing interest in homoacetogenic bacteria for the production of biochemicals and biofuels requisites the development of new genetic tools for these atypical production organisms. An attractive host for the conversion of synthesis gas or electricity into multi-carbon compounds is Clostridium ljungdahlii. So far only limited achievements in modifying this organism towards the production of industrially relevant compounds have been made. Therefore, there is still a strong need for developing new and optimizing existing genetic tools to efficiently access its metabolism. Here, we report on the development of a stable and reproducible transformation protocol that is applicable to C. ljungdahlii and several other clostridial species. Further, we demonstrate the functionality of a temperature-sensitive origin of replication in combination with a fluorescence marker system as important tools for future genetic engineering of this host for microbial bioproduction.
Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data
Authors: Blekhman Ran , Tang Karen , Archie Elizabeth A. , Barreiro Luis B. , Johnson Zachary P. , Wilson Mark E. , Kohn Jordan , Yuan Michael L. , Gesquiere Laurence , Grieneisen Laura E. , Tung Jenny
Published: August 2016

Field studies of wild vertebrates are frequently associated with extensive collections of banked fecal samples—unique resources for understanding ecological, behavioral and phylogenetic effects on the gut microbiome. However, we do not understand whether sample storage methods confound the ability to investigate interindividual variation in gut microbiome profiles. Here, we extend previous work on storage methods for gut microbiome samples by comparing immediate freezing, the gold standard of preservation, to three methods commonly used in vertebrate field studies: lyophilization, storage in ethanol and storage in RNAlater. We found that the signature of individual identity consistently outweighed storage effects: alpha diversity and beta diversity measures were significantly correlated across methods and while samples often clustered by donor, they never clustered by storage method. Provided that all analyzed samples are stored the same way, banked fecal samples therefore appear highly suitable for investigating variation in gut microbiota. Our results open the door to a much-expanded perspective on variation in the gut microbiome across species and ecological contexts.
Optical Addressing of Multi-Colour Photochromic Material Mixture for Volumetric Display
Authors: Hirayama Ryuji , Shiraki Atsushi , Naruse Makoto , Nakamura Shinichiro , Nakayama Hirotaka , Kakue Takashi , Shimobaba Tomoyoshi , Ito Tomoyoshi
Published: August 2016

This is the first study to demonstrate that colour transformations in the volume of a photochromic material (PM) are induced at the intersections of two control light channels, one controlling PM colouration and the other controlling decolouration. Thus, PM colouration is induced by position selectivity and therefore, a dynamic volumetric display may be realised using these two control lights. Moreover, a mixture of multiple PM types with different absorption properties exhibits different colours depending on the control light spectrum. Particularly, the spectrum management of the control light allows colour-selective colouration besides position selectivity. Therefore, a PM-based, full-colour volumetric display is realised. We experimentally construct a mixture of two PM types and validate the operating principles of such a volumetric display system. Our system is constructed simply by mixing multiple PM types; therefore, the display hardware structure is extremely simple and the minimum size of a volume element can be as small as the size of a molecule. Volumetric displays can provide natural three-dimensional (3D) perception; therefore, the potential uses of our system include high-definition 3D visualisation for medical applications, architectural design, human–computer interactions, advertising and entertainment.
Quantifying the evolution of flow boiling bubbles by statistical testing and image analysis: toward a general model
Authors: Xiao Qingtai , Xu Jianxin , Wang Hua
Published: August 2016

A new index, the estimate of the error variance, which can be used to quantify the evolution of the flow patterns when multiphase components or tracers are difficultly distinguishable, was proposed. The homogeneity degree of the luminance space distribution behind the viewing windows in the direct contact boiling heat transfer process was explored. With image analysis and a linear statistical model, the F-test of the statistical analysis was used to test whether the light was uniform and a non-linear method was used to determine the direction and position of a fixed source light. The experimental results showed that the inflection point of the new index was approximately equal to the mixing time. The new index has been popularized and applied to a multiphase macro mixing process by top blowing in a stirred tank. Moreover, a general quantifying model was introduced for demonstrating the relationship between the flow patterns of the bubble swarms and heat transfer. The results can be applied to investigate other mixing processes that are very difficult to recognize the target.
De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure
Authors: Hill Camilla Beate , Cassin Andrew , Keeble-Gagnère Gabriel , Doblin Monika S. , Bacic Antony , Roessner Ute
Published: August 2016

Plant roots are the first organs sensing and responding to salinity stress, manifested differentially between different root types, and also at the individual tissue and cellular level. High genetic diversity and the current lack of an assembled map-based sequence of the barley genome severely limit barley research potential. We used over 580 and 600 million paired-end reads, respectively, to create twode novoassemblies of a barley landrace (Sahara) and a malting cultivar (Clipper) with known contrasting responses to salinity. Generalized linear models were used to statistically access spatial, treatment-related, and genotype-specific responses. This revealed a spatial gene expression gradient along the barley root, with more differentially expressed transcripts detected between different root zones than between treatments. The root transcriptome also showed a gradual transition from transcripts related to sugar-mediated signaling at the root meristematic zone to those involved in cell wall metabolism in the elongation zone, and defense response-related pathways toward the maturation zone, with significant differences between the two genotypes. The availability of these additional transcriptome reference sets will serve as a valuable resource to the cereal research community, and may identify valuable traits to assist in breeding programmes.
The loss of ATP2C1 impairs the DNA damage response and induces altered skin homeostasis: Consequences for epidermal biology in Hailey-Hailey disease
Authors: Cialfi Samantha , Le Pera Loredana , De Blasio Carlo , Mariano Germano , Palermo Rocco , Zonfrilli Azzurra , Uccelletti Daniela , Palleschi Claudio , Biolcati Gianfranco , Barbieri Luca , Screpanti Isabella , Talora Claudio
Published: August 2016

Mutation of the Golgi Ca2+-ATPase ATP2C1 is associated with deregulated calcium homeostasis and altered skin function. ATP2C1 mutations have been identified as having a causative role in Hailey-Hailey disease, an autosomal-dominant skin disorder. Here, we identified ATP2C1 as a crucial regulator of epidermal homeostasis through the regulation of oxidative stress. Upon ATP2C1 inactivation, oxidative stress and Notch1 activation were increased in cultured human keratinocytes. Using RNA-seq experiments, we found that the DNA damage response (DDR) was consistently down-regulated in keratinocytes derived from the lesions of patients with Hailey-Hailey disease. Although oxidative stress activates the DDR, ATP2C1 inactivation down-regulates DDR gene expression. We showed that the DDR response was a major target of oxidative stress-induced Notch1 activation. Here, we show that this activation is functionally important because early Notch1 activation in keratinocytes induces keratinocyte differentiation and represses the DDR. These results indicate that an ATP2C1/NOTCH1 axis might be critical for keratinocyte function and cutaneous homeostasis, suggesting a plausible model for the pathological features of Hailey-Hailey disease.
Overexpression of the Eggplant (Solanum melongena) NAC Family Transcription Factor SmNAC Suppresses Resistance to Bacterial Wilt
Authors: Na Chen , Shuanghua Wu , Jinglong Fu , Bihao Cao , Jianjun Lei , Changming Chen , Jin Jiang
Published: August 2016

Bacterial wilt (BW) is a serious disease that affects eggplant (Solanum melongena) production. Although resistance to this disease has been reported, the underlying mechanism is unknown. In this study, we identified a NAC family transcription factor (SmNAC) from eggplant and characterized its expression, its localization at the tissue and subcellular levels, and its role in BW resistance. To this end, transgenic eggplant lines were generated in which the expression of SmNAC was constitutively up regulated or suppressed using RNAi. The results indicated that overexpression of SmNAC decreases resistance to BW. Moreover, SmNAC overexpression resulted in the reduced accumulation of the plant immune signaling molecule salicylic acid (SA) and reduced expression of ICS1 (a gene that encode isochorismate synthase 1, which is involved in SA biosynthesis). We propose that reduced SA content results in increased bacterial wilt susceptibility in the transgenic lines. Our results provide important new insights into the regulatory mechanisms of bacterial wilt resistance in eggplant.
Social context affects tail displays by Phrynocephalus vlangalii lizards from China
Authors: Peters Richard A. , Ramos Jose A. , Hernandez Juan , Wu Yayong , Qi Yin
Published: August 2016

Competition between animals for limited resources often involves signaling to establish ownership or dominance. In some species, the defended resource relates to suitable thermal conditions and refuge from predators. This is particularly true of burrow-dwelling lizards such as the Qinghai toad-headed agama (Phrynocephalus vlangalii), which are found on the Tibetan plateau of western China. Male and female lizards occupy separate burrows, which are vital for anti-predator behaviour during warmer months when lizards are active and, crucially, provide shelter from harsh winter conditions. These lizards are readily observed signaling by means of tail displays on the sand dunes they inhabit. Given the selective pressure to hold such a resource, both males and females should exhibit territorial behaviour and we considered this study system to examine in detail how social context influences motion based territorial signaling. We confirmed that territorial signaling was used by both sexes and by adopting a novel strategy that permitted 3D reconstruction of tail displays, we identified significant variation due to social context. However, signal structure was not related to lizard morphology. Clearly, the burrow is a highly valued resource and we suggest that additional variation in signaling behaviour might be mediated by resource quality.
Astrocytic Acid-Sensing Ion Channel 1a Contributes to the Development of Chronic Epileptogenesis
Authors: Yang Feng , Sun Xiaolong , Ding Yinxiu , Ma Hui , Yang Tangpeng Ou , Ma Yue , Wei Dong , Li Wen , Xu Tianle , Jiang Wen
Published: August 2016

Unraveling mechanisms underlying epileptogenesis after brain injury is an unmet medical challenge. Although histopathological studies have revealed that reactive astrogliosis and tissue acidosis are prominent features in epileptogenic foci, their roles in epileptogenesis remain unclear. Here, we explored whether astrocytic acid-sensing ion channel-1a (ASIC1a) contributes to the development of chronic epilepsy. High levels of ASIC1a were measured in reactive astrocytes in the hippocampi of patients with temporal lobe epilepsy (TLE) and epileptic mice. Extracellular acidosis caused a significant Ca2+ influx in cultured astrocytes, and this influx was sensitive to inhibition by the ASIC1a-specific blocker psalmotoxin 1 (PcTX1). In addition, recombinant adeno-associated virus (rAAV) vectors carrying a GFAP promoter in conjunction with ASIC1a shRNA or cDNA were generated to suppress or restore, respectively, ASIC1a expression in astrocytes. Injection of rAAV-ASIC1a-shRNA into the dentate gyrus of the wide type TLE mouse model resulted in the inhibition of astrocytic ASIC1a expression and a reduction in spontaneous seizures. By contrast, rAAV-ASIC1a-cDNA restored astrocytic ASIC1a expression in an ASIC1a knock-out TLE mouse model and increased the frequency of spontaneous seizures. Taken together, our results reveal that astrocytic ASIC1a may be an attractive new target for the treatment of epilepsy.
Inhibition of methane and natural gas hydrate formation by altering the structure of water with amino acids
Authors: Sa Jeong-Hoon , Kwak Gye-Hoon , Han Kunwoo , Ahn Docheon , Cho Seong Jun , Lee Ju Dong , Lee Kun-Hong
Published: August 2016

Natural gas hydrates are solid hydrogen-bonded water crystals containing small molecular gases. The amount of natural gas stored as hydrates in permafrost and ocean sediments is twice that of all other fossil fuels combined. However, hydrate blockages also hinder oil/gas pipeline transportation, and, despite their huge potential as energy sources, our insufficient understanding of hydrates has limited their extraction. Here, we report how the presence of amino acids in water induces changes in its structure and thus interrupts the formation of methane and natural gas hydrates. The perturbation of the structure of water by amino acids and the resulting selective inhibition of hydrate cage formation were observed directly. A strong correlation was found between the inhibition efficiencies of amino acids and their physicochemical properties, which demonstrates the importance of their direct interactions with water and the resulting dissolution environment. The inhibition of methane and natural gas hydrate formation by amino acids has the potential to be highly beneficial in practical applications such as hydrate exploitation, oil/gas transportation, and flow assurance. Further, the interactions between amino acids and water are essential to the equilibria and dynamics of many physical, chemical, biological, and environmental processes.
High Efficient Photo-Fenton Catalyst of α-Fe2O3/MoS2 Hierarchical Nanoheterostructures: Reutilization for Supercapacitors
Authors: Yang Xijia , Sun Haiming , Zhang Lishu , Zhao Lijun , Lian Jianshe , Jiang Qing
Published: August 2016

A novel three-dimensional (3D) α-Fe2O3/MoS2 hierarchical nanoheterostructure is effectively synthesized via a facile hydrothermal method. The zero-dimensional (0D) Fe2O3 nanoparticles guide the growth of two-dimensional (2D) MoS2 nanosheets and formed 3D flower-like structures, while MoS2 facilitates the good dispersion of porous Fe2O3 with abundant oxygen vacancies. This charming 3D-structure with perfect match of non-equal dimension exhibits high recyclable photo-Fenton catalytic activity for Methyl orange pollutant and nice specific capacity in reusing as supercapacitor after catalysis. The synergistic effect between Fe2O3 and MoS2, the intermediate nanointerfaces, the 3D porous structures, and the abundant oxygen vacancies both contribute to highly active catalysis, nice electrochemical performance and stable cycling. This strategy is simple, cheap, and feasible for maximizing the value of the materials, as well as eliminating the secondary pollution.
Transcriptomic analysis of heteromorphic stamens in Cassia biscapsularis L.
Authors: Luo Zhonglai , Hu Jin , Zhao Zhongtao , Zhang Dianxiang
Published: August 2016

Hermaphroditic flowers have evolved primarily under the selection on male function. Evolutionary modification often leads to stamen differentiation within flowers, or “heteranthery”, a phenomenon intrigued scientists since the 18th century until recently. However, the genetic basis and molecular regulation mechanism has barely been touched. Here we conducted comparative transcriptome profiling in Cassia biscapsularis L., a heterantherous species with representative patterns of stamen differentiation. Numerous differentially expressed genes (DEGs) were detected between the staminodes (the degenerated stamens) and fertile stamens, while much fewer genes differentially expressed among the three sets of fertile stamens. GO term enrichment and KEGG pathway analysis characterized functional properties of DEGs in different stamen types. Transcripts showing close correlation between expression pattern and stamen types were identified. Transcription factors from the bHLH family were suggested to have taken crucial part in the formation of staminodes. This first global transcriptomic analysis focusing on stamen differentiation opens the door toward a more comprehensive understanding on the molecular regulation of floral organ evolution. Especially, the generated unigene resource would be valuable for developing male sterile lines in agronomy.
Structurally novel steroidal spirooxindole by241 potently inhibits tumor growth mainly through ROS-mediated mechanisms
Authors: Shi Xiao-Jing , Yu Bin , Wang Jun-Wei , Qi Ping-Ping , Tang Kai , Huang Xin , Liu Hong-Min
Published: August 2016

Cancer cells always have increased ROS levels, thus making them more vulnerable to persistent endogenous oxidative stress. The biochemical difference between cancer and normal cells could be exploited to achieve selective cancer cell killing by exogenous ROS-producing agents. Herein we described a structurally novel steroidal spirooxindole by241 and its anticancer efficacy. By241 exhibited potent inhibition against human cancer cells and less toxic to normal cells. By241 concentration-dependently induced apoptosis of MGC-803 and EC9706 cells, accompanied with the mitochondrial dysfunction and increased ROS levels. NAC can completely restore the decreased cell viability of MGC-803 cells caused by by241, suggesting ROS-mediated mechanisms. The expression levels of proteins involved in the mitochondrion-related pathways were detected, showing increased expression of proapoptotic proteins and decreased expression of anti-apoptotic proteins and activation of caspases-9/-3, but without activating caspase-8 expression. Pretreatment with Z-VAD-FMK partially rescued by241-induced apoptosis of MGC-803 cells. Additionally, by241 inhibited mTOR, activated p53 and its downstream proteins, cleaved MDM2 and PI3K/AKT as well as NF-κB signaling pathway. In vivo experiments showed that by241 did not have significant acute oral toxicity and exerted good anticancer efficacy against MGC-803 bearing mice models. Therefore, by241 may serve as a lead for further development for cancer therapy.
Ce3+-ion-induced visible-light photocatalytic degradation and electrochemical activity of ZnO/CeO2 nanocomposite
Authors: Rajendran Saravanan , Khan Mohammad Mansoob , Gracia F. , Qin Jiaqian , Gupta Vinod Kumar , Arumainathan Stephen
Published: August 2016

In this study, pure ZnO, CeO2 and ZnO/CeO2 nanocomposites were synthesized using a thermal decomposition method and subsequently characterized using different standard techniques. High-resolution X-ray photoelectron spectroscopy measurements confirmed the oxidation states and presence of Zn2+, Ce4+, Ce3+ and different bonded oxygen species in the nanocomposites. The prepared pure ZnO and CeO2 as well as the ZnO/CeO2 nanocomposites with various proportions of ZnO and CeO2 were tested for photocatalytic degradation of methyl orange, methylene blue and phenol under visible-light irradiation. The optimized and highly efficient ZnO/CeO2 (90:10) nanocomposite exhibited enhanced photocatalytic degradation performance for the degradation of methyl orange, methylene blue and phenol as well as industrial textile effluent compared to ZnO, CeO2 and the other investigated nanocomposites. Moreover, the recycling results demonstrate that the ZnO/CeO2 (90:10) nanocomposite exhibited good stability and long-term durability. Furthermore, the prepared ZnO/CeO2 nanocomposites were used for the electrochemical detection of uric acid and ascorbic acid. The ZnO/CeO2 (90:10) nanocomposite also demonstrated the best detection, sensitivity and performance among the investigated materials in this application. These findings suggest that the synthesized ZnO/CeO2 (90:10) nanocomposite could be effectively used in various applications.
Laquinimod rescues striatal, cortical and white matter pathology and results in modest behavioural improvements in the YAC128 model of Huntington disease
Authors: Garcia-Miralles Marta , Hong Xin , Tan Liang Juin , Caron Nicholas S. , Huang Yihui , To Xuan Vinh , Lin Rachel Yanping , Franciosi Sonia , Papapetropoulos Spyros , Hayardeny Liat , Hayden Michael R. , Chuang Kai-Hsiang , Pouladi Mahmoud A.
Published: August 2016

Increasing evidence supports a role for abnormal immune activation and inflammatory responses in Huntington disease (HD). In this study, we evaluated the therapeutic potential of laquinimod (1 and 10 mg/kg), a novel immunomodulatory agent shown to be protective in a number of neuroinflammatory conditions, in the YAC128 mouse model of HD. Treatment with laquinimod for 6 months rescued atrophy in the striatum, in certain cortical regions, and in the corpus callosum of YAC128 HD mice. Diffusion tensor imaging showed that white matter microstructural abnormalities in the posterior corpus callosum were improved following treatment with low dose (1 mg/kg) laquinimod, and were paralleled by reduced levels of interleukin-6 in the periphery of YAC128 HD mice. Functionally, treatment with laquinimod (1 and 10 mg/kg) led to modest improvements in motor function and in depressive-like behaviour. Taken together, these results suggest that laquinimod may improve some features of pathology in HD, and provides support for the role of immune activation in the pathogenesis of HD.
Crystallization characteristics in supercooled liquid zinc during isothermal relaxation: A molecular dynamics simulation study
Authors: Zhou Li-li , Liu Rang-su , Tian Ze-an , Liu Hai-rong , Hou Zhao-yang , Peng Ping
Published: August 2016

The crystallization characteristics in supercooled liquid Zn during isothermal relaxation were investigated using molecular dynamics simulations by adopting the cluster-type index method (CTIM) and the tracing method. Results showed that the crystallization process undergo three different stages. The size of the critical nucleus was found to be approximately 90–150 atoms in this system; the growth of nuclei proceeded via the successive formation of hcp and fcc structures with a layered distribution; and finally, the system evolved into a much larger crystal with a distinct layered distribution of hcp and fcc structures with an 8R stacking sequence of ABCBACAB by adjusting all of the atoms in the larger clusters according to a certain rule.
TLR4-Upregulated IL-1β and IL-1RI Promote Alveolar Macrophage Pyroptosis and Lung Inflammation through an Autocrine Mechanism
Authors: He Xingying , Qian Yongbing , Li Zhigang , Fan Erica K. , Li Yuehua , Wu Liang , Billiar Timothy R. , Wilson Mark A. , Shi Xueyin , Fan Jie
Published: August 2016

Acute lung injury (ALI) is a major component of multiple organ dysfunction syndrome (MODS) following pulmonary infection. Alveolar macrophages (AM) are at the center of the pathogenesis of the development of ALI. Interleukin-1β (IL-1β) is one of the key pro-inflammatory mediators and its maturation is tightly controlled by the formation and activation of the inflammasome. The biological effects of IL-1β are mediated through IL-1 receptor (IL-1R). In this study, we investigated the influence of LPS-induced IL-1β release and IL-1RI upregulation on the development of lung inflammation. We demonstrated that in AM, LPS-TLR4 signaling not only activates Nlrp3 inflammasome activation and subsequent release of IL-1β, but also up-regulates IL-1RI expression on AM surface through MyD88 and NF-κB dependent signaling. The upregulated IL-1RI, therefore, sensitizes AM to IL-1β and results in pyroptosome formation, which in turn leads to AM pyroptosis, a type of caspase-1-dependent inflammatory cell death. We further showed that AM pyroptosis exaggerates lung inflammation. The present study demonstrates a novel mechanism underlying LPS-induced innate immunity; that is, a secondary upregulation of IL-1β-IL-1RI signaling is responsible for AM pyroptosis and augmented lung injury in response to LPS.
Penguins reduced olfactory receptor genes common to other waterbirds
Authors: Lu Qin , Wang Kai , Lei Fumin , Yu Dan , Zhao Huabin
Published: August 2016

The sense of smell, or olfaction, is fundamental in the life of animals. However, penguins (Aves: Sphenisciformes) possess relatively small olfactory bulbs compared with most other waterbirds such as Procellariiformes and Gaviiformes. To test whether penguins have a reduced reliance on olfaction, we analyzed the draft genome sequences of the two penguins, which diverged at the origin of the order Sphenisciformes; we also examined six closely related species with available genomes and identified 29 one-to-one orthologous olfactory receptor genes (i.e. ORs) that are putatively functionally conserved and important across the eight birds. To survey the 29 one-to-one orthologous ORs in penguins and their relatives, we newly generated 34 sequences that are missing from the draft genomes. Through the analysis of totaling 378 OR sequences, we found that, of these functionally important ORs common to other waterbirds, penguins have a significantly greater percentage of OR pseudogenes than other waterbirds, suggesting a reduction of olfactory capability. The penguin-specific reduction of olfactory capability arose in the common ancestor of penguins between 23 and 60 Ma, which may have resulted from the aquatic specializations for underwater vision. Our study provides genetic evidence for a possible reduction of reliance on olfaction in penguins.
Correction: Corrigendum: Metal - Insulator Transition Driven by Vacancy Ordering in GeSbTe Phase Change Materials
Authors: Bragaglia Valeria , Arciprete Fabrizio , Zhang Wei , Mio Antonio Massimiliano , Zallo Eugenio , Perumal Karthick , Giussani Alessandro , Cecchi Stefano , Boschker Jos Emiel , Riechert Henning , Privitera Stefania , Rimini Emanuele , Mazzarello Riccardo , Calarco Raffaella
Published: August 2016

Scientific Reports 6: Article number: 23843; published online: 01 April 2016; updated: 16 August 2016 In this Article, Stefania Privitera and Emanuele Rimini are incorrectly listed as being affiliated with ‘Paul-Drude-Institut für Festkörperelektronik, Hausvogteiplatz 5-7, 10117 Berlin, Germany’. The correct affiliation is listed below:
Erratum: Isotropic plasticity of β-type Ti-29Nb-13Ta-4.6Zr alloy single crystals for the development of single crystalline β-Ti implants
Authors: Hagihara Koji , Nakano Takayoshi , Maki Hideaki , Umakoshi Yukichi , Niinomi Mitsuo
Published: August 2016

Scientific Reports 6: Article number: 29779; published online: 15 July 2016; updated: 16 August 2016 This Article contains typographical errors in Table 1. In the column ‘Slip (twinning) system’, the seventh {332} <113> twin value “(3 3) [1 3 1]” is incorrectly given as “(3 3) [1 1 3]”. In addition, the tenth {332} <113> twin value “( 3 3) [3 1 1]” is incorrectly given as “( 3 3) [1 1 3]”.
Proteomics tools reveal startlingly high amounts of oxytocin in plasma and serum
Authors: Brandtzaeg Ole Kristian , Johnsen Elin , Roberg-Larsen Hanne , Seip Knut Fredrik , MacLean Evan L. , Gesquiere Laurence R. , Leknes Siri , Lundanes Elsa , Wilson Steven Ray
Published: August 2016

The neuropeptide oxytocin (OT) is associated with a plethora of social behaviors and is a key topic at the intersection of psychology and biology. However, tools for measuring OT are still not fully developed. We describe a robust nano liquid chromatography-mass spectrometry (nanoLC-MS) platform for measuring the total amount of OT in human plasma/serum. OT binds strongly to plasma proteins, but a reduction/alkylation (R/A) procedure breaks this bond, enabling ample detection of total OT. The method (R/A + robust nanoLC-MS) was used to determine total OT plasma/serum levels to startlingly high concentrations (high pg/mL-ng/mL). Similar results were obtained when combining R/A and ELISA. Compared to measuring free OT, measuring total OT can have advantages in e.g. biomarker studies.
New insights into the mode of action of the lantibiotic salivaricin B
Authors: Barbour Abdelahhad , Tagg John , Abou-Zied Osama K. , Philip Koshy
Published: August 2016

Salivaricin B is a 25 amino acid polycyclic peptide belonging to the type AII lantibiotics and first shown to be produced by Streptococcus salivarius. In this study we describe the bactericidal mode of action of salivaricin B against susceptible Gram-positive bacteria. The killing action of salivaricin B required micro-molar concentrations of lantibiotic whereas the prototype lantibiotic nisin A was shown to be potent at nano-molar levels. Unlike nisin A, salivaricin B did not induce pore formation or dissipate the membrane potential in susceptible cells. This was established by measuring the fluorescence of the tryptophan residue at position 17 when salivaricin B interacted with bacterial membrane vesicles. The absence of a fluorescence blue shift indicates a failure of salivaricin B to penetrate the membranes. On the other hand, salivaricin B interfered with cell wall biosynthesis, as shown by the accumulation of the final soluble cell wall precursor UDP-MurNAc-pentapeptide which is the backbone of the bacterial peptidoglycan. Transmission electron microscopy of salivaricin B-treated cells showed a reduction in cell wall thickness together with signs of aberrant septum formation in the absence of visible changes to cytoplasmic membrane integrity.