bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infrared nanospectroscopy characterization of oligomeric and fibrillar aggregates during amyloid formation
Authors: Ruggeri F. S. , Longo G. , Faggiano S. , Lipiec E. , Pastore A. , Dietler G. 
Published: July 2015

AbstractAmyloids are insoluble protein fibrillar aggregates. The importance of characterizing their aggregation has steadily increased because of their link to human diseases and material science applications. In particular, misfolding and aggregation of the Josephin domain of ataxin-3 is implicated in spinocerebellar ataxia-3. Infrared nanospectroscopy, simultaneously exploiting atomic force microscopy and infrared spectroscopy, can characterize at the nanoscale the conformational rearrangements of proteins during their aggregation. Here we demonstrate that we can individually characterize the oligomeric and fibrillar species formed along the amyloid aggregation. We describe their secondary structure, monitoring at the nanoscale an α-to-β transition, and couple these studies with an independent measurement of the evolution of their intrinsic stiffness. These results suggest that the aggregation of Josephin proceeds from the monomer state to the formation of spheroidal intermediates with a native structure. Only successively, these intermediates evolve into misfolded aggregates and into the final fibrils.
PTEN mediates Notch-dependent stalk cell arrest in angiogenesis
Authors: Serra Helena , Chivite Iñigo , Angulo-Urarte Ana , Soler Adriana , Sutherland James D. , Arruabarrena-Aristorena Amaia , Ragab Anan , Lim Radiance , Malumbres Marcos , Fruttiger Marcus , Potente Michael , Serrano Manuel , Fabra Àngels , Viñals Francesc , Casanovas Oriol , Pandolfi Pier Paolo , Bigas Anna , Carracedo Arkaitz , Gerhardt Holger , Graupera Mariona 
Published: July 2015

AbstractCoordinated activity of VEGF and Notch signals guides the endothelial cell (EC) specification into tip and stalk cells during angiogenesis. Notch activation in stalk cells leads to proliferation arrest via an unknown mechanism. By using gain- and loss-of-function gene-targeting approaches, here we show that PTEN is crucial for blocking stalk cell proliferation downstream of Notch, and this is critical for mouse vessel development. Endothelial deletion of PTEN results in vascular hyperplasia due to a failure to mediate Notch-induced proliferation arrest. Conversely, overexpression of PTEN reduces vascular density and abrogates the increase in EC proliferation induced by Notch blockade. PTEN is a lipid/protein phosphatase that also has nuclear phosphatase-independent functions. We show that both the catalytic and non-catalytic APC/C-Fzr1/Cdh1-mediated activities of PTEN are required for stalk cells’ proliferative arrest. These findings define a Notch–PTEN signalling axis as an orchestrator of vessel density and implicate the PTEN-APC/C-Fzr1/Cdh1 hub in angiogenesis.
Single-atom electron energy loss spectroscopy of light elements
Authors: Senga Ryosuke , Suenaga Kazu 
Published: July 2015

AbstractLight elements such as alkali metal (lithium, sodium) or halogen (fluorine, chlorine) are present in various substances and indeed play significant roles in our life. Although atomic behaviours of these elements are often a key to resolve chemical or biological activities, they are hardly visible in transmission electron microscope because of their smaller scattering power and higher knock-on probability. Here we propose a concept for detecting light atoms encaged in a nanospace by means of electron energy loss spectroscopy using inelastically scattered electrons. In this method, we demonstrate the single-atom detection of lithium, fluorine, sodium and chlorine with near-atomic precision, which is limited by the incident probe size, signal delocalization and atomic movement in nanospace. Moreover, chemical shifts of lithium K-edge have been successfully identified with various atomic configurations in one-dimensional lithium compounds.
[NiFe]-hydrogenase is essential for cyanobacterium Synechocystis sp. PCC 6803 aerobic growth in the dark
Authors: De Rosa Edith , Checchetto Vanessa , Franchin Cinzia , Bergantino Elisabetta , Berto Paola , Szabò Ildikò , Giacometti Giorgio M. , Arrigoni Giorgio , Costantini Paola 
Published: July 2015

AbstractThe cyanobacterium Synechocystis sp. PCC 6803 has a bidirectional [NiFe]-hydrogenase (Hox hydrogenase) which reversibly reduces protons to H2. This enzyme is composed of a hydrogenase domain and a diaphorase moiety, which is distinctly homologous to the NADH input module of mitochondrial respiratory Complex I. Hox hydrogenase physiological function is still unclear, since it is not required for Synechocystis fitness under standard growth conditions. We analyzed the phenotype under prolonged darkness of three Synechocystis knock-out strains, lacking either Hox hydrogenase (ΔHoxE-H) or one of the proteins responsible for the assembly of its NiFe active site (ΔHypA1 and ΔHypB1). We found that Hox hydrogenase is required for Synechocystis growth under this condition, regardless of the functional status of its catalytic site, suggesting an additional role beside hydrogen metabolism. Moreover, quantitative proteomic analyses revealed that the expression levels of several subunits of the respiratory NADPH/plastoquinone oxidoreductase (NDH-1) are reduced when Synechocystis is grown in the dark. Our findings suggest that the Hox hydrogenase could contribute to electron transport regulation when both photosynthetic and respiratory pathways are down-regulated and provide a possible explanation for the close evolutionary relationship between mitochondrial respiratory Complex I and cyanobacterial [NiFe]-hydrogenases.
Invasion Expansion: Time since introduction best predicts global ranges of marine invaders
Authors: Byers James E. , Smith Rachel S. , Pringle James M. , Clark Graeme F. , Gribben Paul E. , Hewitt Chad L. , Inglis Graeme J. , Johnston Emma L. , Ruiz Gregory M. , Stachowicz John J. , Bishop Melanie J. 
Published: July 2015

AbstractStrategies for managing biological invasions are often based on the premise that characteristics of invading species and the invaded environment are key predictors of the invader’s distribution. Yet, for either biological traits or environmental characteristics to explain distribution, adequate time must have elapsed for species to spread to all potential habitats. We compiled and analyzed a database of natural history and ecological traits of 138 coastal marine invertebrate species, the environmental conditions at sites to which they have been introduced and their date of first introduction. We found that time since introduction explained the largest fraction (20%) of the variability in non-native range size, while traits of the species and environmental variables had significant, but minimal, influence on non-native range size. The positive relationship between time since introduction and range size indicates that non-native marine invertebrate species are not at equilibrium and are still spreading, posing a major challenge for management of coastal ecosystems.
Rechargeable magnesium-ion battery based on a TiSe2-cathode with d-p orbital hybridized electronic structure
Authors: Gu Yunpeng , Katsura Yukari , Yoshino Takafumi , Takagi Hidenori , Taniguchi Kouji 
Published: July 2015

AbstractRechargeable ion-batteries, in which ions such as Li+carry charges between electrodes, have been contributing to the improvement of power-source performance in a wide variety of mobile electronic devices. Among them, Mg-ion batteries are recently attracting attention due to possible low cost and safety, which are realized by abundant natural resources and stability of Mg in the atmosphere. However, only a few materials have been known to work as rechargeable cathodes for Mg-ion batteries, owing to strong electrostatic interaction between Mg2+and the host lattice. Here we demonstrate rechargeable performance of Mg-ion batteries at ambient temperature by selecting TiSe2as a model cathode by focusing on electronic structure. Charge delocalization of electrons in a metal-ligand unit throughd-porbital hybridization is suggested as a possible key factor to realize reversible intercalation of Mg2+into TiSe2. The viewpoint from the electronic structure proposed in this study might pave a new way to design electrode materials for multivalent-ion batteries.
The relationship between nociceptive brain activity, spinal reflex withdrawal and behaviour in newborn infants
Authors: Hartley Caroline , Goksan Sezgi , Poorun Ravi , Brotherhood Kelly , Mellado Gabriela Schmidt , Moultrie Fiona , Rogers Richard , Adams Eleri , Slater Rebeccah 
Published: July 2015

AbstractMeasuring infant pain is complicated by their inability to describe the experience. While nociceptive brain activity, reflex withdrawal and facial grimacing have been characterised, the relationship between these activity patterns has not been examined. As cortical and spinally mediated activity is developmentally regulated, it cannot be assumed that they are predictive of one another in the immature nervous system. Here, using a new experimental paradigm, we characterise the nociceptive-specific brain activity, spinal reflex withdrawal and behavioural activity following graded intensity noxious stimulation and clinical heel lancing in 30 term infants. We show that nociceptive-specific brain activity and nociceptive reflex withdrawal are graded with stimulus intensity (p < 0.001), significantly correlated (r = 0.53, p = 0.001) and elicited at an intensity that does not evoke changes in clinical pain scores (p = 0.55). The strong correlation between reflex withdrawal and nociceptive brain activity suggests that movement of the limb away from a noxious stimulus is a sensitive indication of nociceptive brain activity in term infants. This could underpin the development of new clinical pain assessment measures.
Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei
Authors: Vega Fernando E. , Brown Stuart M. , Chen Hao , Shen Eric , Nair Mridul B. , Ceja-Navarro Javier A. , Brodie Eoin L. , Infante Francisco , Dowd Patrick F. , Pain Arnab 
Published: July 2015

AbstractThe coffee berry borer, Hypothenemus hampei, is the most economically important insect pest of coffee worldwide. We present an analysis of the draft genome of the coffee berry borer, the third genome for a Coleopteran species. The genome size is ca. 163 Mb with 19,222 predicted protein-coding genes. Analysis was focused on genes involved in primary digestion as well as gene families involved in detoxification of plant defense molecules and insecticides, such as carboxylesterases, cytochrome P450, gluthathione S-transferases, ATP-binding cassette transporters and a gene that confers resistance to the insecticide dieldrin. A broad range of enzymes capable of degrading complex polysaccharides were identified. We also evaluated the pathogen defense system and found homologs to antimicrobial genes reported in the Drosophila genome. Ten cases of horizontal gene transfer were identified with evidence for expression, integration into the H. hampei genome and phylogenetic evidence that the sequences are more closely related to bacterial rather than eukaryotic genes. The draft genome analysis broadly expands our knowledge on the biology of a devastating tropical insect pest and suggests new pest management strategies.
Insulin-degrading enzyme prevents α-synuclein fibril formation in a nonproteolytical manner
Authors: Sharma Sandeep K. , Chorell Erik , Steneberg Pär , Vernersson-Lindahl Emma , Edlund Helena , Wittung-Stafshede Pernilla 
Published: July 2015

AbstractThe insulin-degrading enzyme (IDE) degrades amyloidogenic proteins such as Amyloid β (Αβ) and Islet Amyloid Polypeptide (IAPP), i.e. peptides associated with Alzheimer’s disease and type 2 diabetes, respectively. In addition to the protease activity normally associated with IDE function an additional activity involving the formation of stable, irreversible complexes with both Αβ and α-synuclein, an amyloidogenic protein involved in Parkinson’s disease, was recently proposed. Here, we have investigated the functional consequences of IDE-α-synuclein interactions in vitro. We demonstrate that IDE in a nonproteolytic manner and at sub-stoichiometric ratios efficiently inhibits α-synuclein fibril formation by binding to α-synuclein oligomers making them inert to amyloid formation. Moreover, we show that, within a defined range of α-synuclein concentrations, interaction with α-synuclein oligomers increases IDE’s proteolytic activity on a fluorogenic substrate. We propose that the outcomes of IDE-α-synuclein interactions, i.e. protection against α-synuclein amyloid formation and stimulated IDE protease activity, may be protective in vivo.
BaFe12O19-chitosan Schiff-base Ag (I) complexes embedded in carbon nanotube networks for high-performance electromagnetic materials
Authors: Zhao Jie , Xie Yu , Guan Dongsheng , Hua Helin , Zhong Rong , Qin Yuancheng , Fang Jing , Liu Huilong , Chen Junhong 
Published: July 2015

AbstractThe multiwalled carbon nanotubes/BaFe12O19-chitosan (MCNTs/BF-CS) Schiff base Ag (I) complex composites were synthesized successfully by a chemical bonding method. The morphology and structures of the composites were characterized with electron microscopy, Fourier transform infrared spectroscopy and X-ray diffraction techniques. Their conductive properties were measured using a four-probe conductivity tester at room temperature and their magnetic properties were tested by a vibrating sample magnetometer. The results show that the BF-CS Schiff base Ag (I) complexes are embedded into MCNT networks. When the mass ratio of MCNTs and BF-CS Schiff base is 0.95:1, the conductivity, Ms (saturation magnetization), Mr (residual magnetization) and Hc (coercivity) of the BF-CS Schiff base composites reach 1.908 S cm−1, 28.20 emu g−1, 16.66 emu g−1 and 3604.79 Oe, respectively. Finally, a possible magnetic mechanism of the composites has also been proposed.
Tunable Dipole Surface Plasmon Resonances of Silver Nanoparticles by Cladding Dielectric Layers
Authors: Liu Xiaotong , Li Dabing , Sun Xiaojuan , Li Zhiming , Song Hang , Jiang Hong , Chen Yiren 
Published: July 2015

AbstractThe tunability of surface plasmon resonance can enable the highest degree of localised surface plasmon enhancement to be achieved, based on the emitting or absorbing wavelength. In this article, tunable dipole surface plasmon resonances of Ag nanoparticles (NPs) are realized by modification of the SiO2dielectric layer thicknesses. SiO2layers both beneath and over the Ag NPs affected the resonance wavelengths of local surface plasmons (LSPs). By adjusting the SiO2thickness beneath the Ag NPs from 5 nm to 20 nm, the dipole surface plasmon resonances shifted from 470 nm to 410 nm. Meanwhile, after sandwiching the Ag NPs by growing SiO2before NPs fabrication and then overcoating the NPs with various SiO2thicknesses from 5 nm to 20 nm, the dipole surface plasmon resonances changed from 450 nm to 490 nm. The SiO2cladding dielectric layer can tune the Ag NP surface charge, leading to a change in the effective permittivity of the surrounding medium and thus to a blueshift or redshift of the resonance wavelength. Also, the quadrupole plasmon resonances were suppressed by the SiO2cladding layer because the dielectric SiO2can suppress level splitting of surface plasmon resonances caused by the Ag NP coupling effect.
Bi-photon spectral correlation measurements from a silicon nanowire in the quantum and classical regimes
Authors: Jizan Iman , Helt L. G. , Xiong Chunle , Collins Matthew J. , Choi Duk-Yong , Joon Chae Chang , Liscidini Marco , Steel M. J. , Eggleton Benjamin J. , Clark Alex S. 
Published: July 2015

AbstractThe growing requirement for photon pairs with specific spectral correlations in quantum optics experiments has created a demand for fast, high resolution and accurate source characterisation. A promising tool for such characterisation uses classical stimulated processes, in which an additional seed laser stimulates photon generation yielding much higher count rates, as recently demonstrated for a χ(2) integrated source in A. Eckstein et al. Laser Photon. Rev. 8, L76 (2014). In this work we extend these results to χ(3) integrated sources, directly measuring for the first time the relation between spectral correlation measurements via stimulated and spontaneous four wave mixing in an integrated optical waveguide, a silicon nanowire. We directly confirm the speed-up due to higher count rates and demonstrate that this allows additional resolution to be gained when compared to traditional coincidence measurements without any increase in measurement time. As the pump pulse duration can influence the degree of spectral correlation, all of our measurements are taken for two different pump pulse widths. This allows us to confirm that the classical stimulated process correctly captures the degree of spectral correlation regardless of pump pulse duration and cements its place as an essential characterisation method for the development of future quantum integrated devices.
Functional ferroelectric tunnel junctions on silicon
Authors: Guo Rui , Wang Zhe , Zeng Shengwei , Han Kun , Huang Lisen , Schlom Darrell G. , Venkatesan T. , Ariando  , Chen Jingsheng 
Published: July 2015

AbstractThe quest for solid state non-volatility memory devices on silicon with high storage density, high speed, low power consumption has attracted intense research on new materials and novel device architectures. Although flash memory dominates in the non-volatile memory market currently, it has drawbacks, such as low operation speed and limited cycle endurance, which prevents it from becoming the “universal memory”. In this report, we demonstrate ferroelectric tunnel junctions (Pt/BaTiO3/La0.67Sr0.33MnO3) epitaxially grown on silicon substrates. X-ray diffraction spectra and high resolution transmission electron microscope images prove the high epitaxial quality of the single crystal perovskite films grown on silicon. Furthermore, the write speed, data retention and fatigue properties of the device compare favorably with flash memories. The results prove that the silicon-based ferroelectric tunnel junction is a very promising candidate for application in future non-volatile memories.
Opening the conformation is a master switch for the dual localization and phosphatase activity of PTEN
Authors: Nguyen Hoai-Nghia , Yang Jr-Ming , Miyamoto Takafumi , Itoh Kie , Rho Elmer , Zhang Qiang , Inoue Takanari , Devreotes Peter N. , Sesaki Hiromi , Iijima Miho 
Published: July 2015

AbstractTumor suppressor PTEN mainly functions at two subcellular locations, the plasma membrane and the nucleus. At the plasma membrane, PTEN dephosphorylates the tumorigenic second messenger PIP3, which drives cell proliferation and migration. In the nucleus, PTEN controls DNA repair and genome stability independently of PIP3. Whereas the concept that a conformational change regulates protein function through post-translational modifications has been well established in biology, it is unknown whether a conformational change simultaneously controls dual subcellular localizations of proteins. Here, we discovered that opening the conformation of PTEN is the crucial upstream event that determines its key dual localizations of this crucial tumor suppressor. We identify a critical conformational switch that regulates PTEN’s localization. Most PTEN molecules are held in the cytosol in a closed conformation by intramolecular interactions between the C-terminal tail and core region. Dephosphorylation of the tail opens the conformation and exposes the membrane-binding regulatory interface in the core region, recruiting PTEN to the membrane. Moreover, a lysine at residue 13 is also exposed and when ubiquitinated, transports PTEN to the nucleus. Thus, opening the conformation of PTEN is a key mechanism that enhances its dual localization and enzymatic activity, providing a potential therapeutic strategy in cancer treatments.
Genome-wide whole blood microRNAome and transcriptome analyses reveal miRNA-mRNA regulated host response to foodborne pathogen Salmonella infection in swine
Authors: Bao Hua , Kommadath Arun , Liang Guanxiang , Sun Xu , Arantes Adriano S. , Tuggle Christopher K. , Bearson Shawn M.D. , Plastow Graham S. , Stothard Paul , Guan Le Luo 
Published: July 2015

AbstractTo understand the role of miRNAs in regulating genes involved in host response to bacterial infection and shedding of foodborne pathogens, a systematic profiling of miRNAs and mRNAs from the whole blood of pigs upon Salmonella challenge was performed. A total of 62 miRNAs were differentially expressed post infection (false discovery rate <0.1). An integrative analysis of both the differentially expressed miRNAs and mRNAs using sequence-based miRNA target prediction and negative correlation of miRNA-mRNA profiles helped identify miRNA-mRNA networks that may potentially regulate host response to Salmonella infection. From these networks, miR-214 and miR-331-3p were identified as new candidates potentially associated with Salmonella infection. An miRNA seed sequence analysis suggested that these miRNAs regulate several critical immune-related genes including SLC11A1, PIGE-108A11.3 and VAV2. We showed that challenged pigs had reduced miR-214 expression and increased miR-331-3p expression in the whole blood. Furthermore, the expression of the proposed targets of miR-214 (SLC11A1 and PIGE-108A11.3) increased while that of the proposed target of miR-331-3p (VAV2) decreased following challenge (expression changes confirmed by in vitro assays). Based on these observations, we propose potential roles for miR-214 and miR-331-3p in regulation of immune responses to Salmonella infection.
Colokinetic effect of noradrenaline in the spinal defecation center: implication for motility disorders
Authors: Naitou Kiyotada , Shiina Takahiko , Kato Kurumi , Nakamori Hiroyuki , Sano Yuuki , Shimizu Yasutake 
Published: July 2015

AbstractChronic abdominal pain in irritable bowel syndrome (IBS) usually appears in combination with disturbed bowel habits, but the etiological relationship between these symptoms remains unclear. Noradrenaline is a major neurotransmitter controlling pain sensation in the spinal cord. To test the hypothesis that the descending noradrenergic pathway from the brain stem moderates gut motility, we examined effects of intrathecal application of noradrenaline to the spinal defecation center on colorectal motility. Colorectal intraluminal pressure and expelled volume were recorded in vivo in anesthetized rats. Intrathecal application of noradrenaline into the L6-S1 spinal cord, where the lumbosacral defecation center is located, caused propulsive contractions of the colorectum. Inactivation of spinal neurons by tetrodotoxin blocked the effect of noradrenaline. Pharmacological experiments showed that the effect of noradrenaline is mediated primarily by alpha-1 adrenoceptors. The enhancement of colorectal motility by intrathecal noradrenaline was abolished by severing of the pelvic nerves. Our results demonstrate that noradrenaline acting on sacral parasympathetic preganglionic neurons through alpha-1 adrenoceptors causes propulsive motility of the colorectum in rats. Considering that visceral pain activates the descending inhibitory pathways including noradrenergic neurons, our results provide a rational explanation of the concurrent appearance of chronic abdominal pain and colonic motility disorders in IBS patients.