bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular basis for the thermostability of Newcastle disease virus
Authors: Wen Guoyuan , Hu Xiao , Zhao Kang , Wang Hongling , Zhang Zhenyu , Zhang Tengfei , Yang Jinlong , Luo Qingping , Zhang Rongrong , Pan Zishu , Shao Huabin , Yu Qingzhong 
Published: March 2016

AbstractThermostable Newcastle disease virus (NDV) vaccines have been used widely to protect village chickens against Newcastle disease, due to their decreased dependence on cold chain for transport and storage. However, the genetic basis underlying the NDV thermostability is poorly understood. In this study, we generated chimeric viruses by exchanging viral genes between the thermostable TS09-C strain and thermolabile LaSota strain using reverse genetics technology. Evaluations of these chimeric NDVs demonstrated that the thermostability of NDV was dependent on the origin of HN protein. Chimeras bearing the HN protein derived from thermostable virus exhibited a thermostable phenotype and vice versa. Both hemagglutinin and neuraminidase activities of viruses bearing the TS09-C HN protein were more thermostable than those containing LaSota HN protein. Furthermore, the newly developed thermostable virus rLS-T-HN, encoding the TS09-C HN protein in LaSota backbone, induced significantly higher antibody response than the TS09-C virus and conferred complete protection against virulent NDV challenge. Taken together, the data suggest that the HN protein of NDV is a crucial determinant of thermostability and the HN gene from a thermostable NDV could be engineered into a thermolabile NDV vaccine strain for developing novel thermostable NDV vaccine.
Mimicking titration experiments with MD simulations: A protocol for the investigation of pH-dependent effects on proteins
Authors: Socher Eileen , Sticht Heinrich 
Published: March 2016

AbstractProtein structure and function are highly dependent on the environmental pH. However, the temporal or spatial resolution of experimental approaches hampers direct observation of pH-induced conformational changes at the atomic level. Molecular dynamics (MD) simulation strategies (e.g. constant pH MD) have been developed to bridge this gap. However, one frequent problem is the sampling of unrealistic conformations, which may also lead to poor pKa predictions. To address this problem, we have developed and benchmarked the pH-titration MD (pHtMD) approach, which is inspired by wet-lab titration experiments. We give several examples how the pHtMD protocol can be applied for pKa calculation including peptide systems, Staphylococcus nuclease (SNase), and the chaperone HdeA. For HdeA, pHtMD is also capable of monitoring pH-dependent dimer dissociation in accordance with experiments. We conclude that pHtMD represents a versatile tool for pKa value calculation and simulation of pH-dependent effects in proteins.
Extended string-like binding of the phosphorylated HP1α N-terminal tail to the lysine 9-methylated histone H3 tail
Authors: Shimojo Hideaki , Kawaguchi Ayumi , Oda Takashi , Hashiguchi Nobuto , Omori Satoshi , Moritsugu Kei , Kidera Akinori , Hiragami-Hamada Kyoko , Nakayama Jun-ichi , Sato Mamoru , Nishimura Yoshifumi 
Published: March 2016

AbstractThe chromodomain of HP1α binds directly to lysine 9-methylated histone H3 (H3K9me). This interaction is enhanced by phosphorylation of serine residues in the N-terminal tail of HP1α by unknown mechanism. Here we show that phosphorylation modulates flexibility of HP1α’s N-terminal tail, which strengthens the interaction with H3. NMR analysis of HP1α’s chromodomain with N-terminal tail reveals that phosphorylation does not change the overall tertiary structure, but apparently reduces the tail dynamics. Small angle X-ray scattering confirms that phosphorylation contributes to extending HP1α’s N-terminal tail. Systematic analysis using deletion mutants and replica exchange molecular dynamics simulations indicate that the phosphorylated serines and following acidic segment behave like an extended string and dynamically bind to H3 basic residues; without phosphorylation, the most N-terminal basic segment of HP1α inhibits interaction of the acidic segment with H3. Thus, the dynamic string-like behavior of HP1α’s N-terminal tail underlies the enhancement in H3 binding due to phosphorylation.
A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge
Authors: Meyer Julie L. , Jaekel Ulrike , Tully Benjamin J. , Glazer Brian T. , Wheat C. Geoffrey , Lin Huei-Ting , Hsieh Chih-Chiang , Cowen James P. , Hulme Samuel M. , Girguis Peter R. , Huber Julie A. 
Published: March 2016

AbstractThe rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere.
Fingerprints of Multiple Electron Scatterings in Single-Layer Graphene
Authors: Jung Minbok , Sohn So-Dam , Park Jonghyun , Lee Keun-U , Shin Hyung-Joon 
Published: March 2016

AbstractThe electrons in graphene exhibit unusual behaviours, which can be described by massless Dirac quasiparticles. Understanding electron scattering in graphene has been of significant importance for its future application in electronic devices because electron scattering determines electrical properties such as resistivity and electron transport. There are two types of electron scatterings in graphene: intervalley scattering and intravalley scattering. In single-layer graphene, to date, it has been difficult to observe intravalley scattering because of the suppression of backscattering resulting from the chiral nature of the electrons in graphene. Here, we report the multiple electron scattering behaviours in single-layer graphene on a metallic substrate. By applying one- and two-dimensional Fourier transforms to maps of the local density of states, we can distinguish individual scattering processes from complex interference patterns. These techniques enable us to provide direct evidence of intravalley scattering, revealing a linear dispersion relation with a Fermi velocity of ~7.4 × 105 m/s.
Inhibition of cyclooxygenase-2 by NS398 attenuates noise-induced hearing loss in mice
Authors: Sun Yu , Yu Jintao , Lin Xi , Tang Wenxue 
Published: March 2016

AbstractNoise-induced hearing loss (NIHL) is an important occupational disorder. However, the molecular mechanisms underlying NIHL have not been fully clarified; therefore, the condition lacks effective therapeutic methods. Cyclooxygenase-2 (Cox-2) is an inducible enzyme involved in the synthesis of prostaglandins, and has been implicated in many pathophysiological events, such as oxidative stress and inflammation. In this study, we investigated the possible role of Cox-2 in the mechanisms of NIHL and the therapeutic effect of the Cox-2 inhibitor NS398 on NIHL using a mouse model. We demonstrated that Cox-2 is constitutively expressed in the mouse cochlea, and its expression could be dramatically up-regulated by high levels of noise exposure. Furthermore, we demonstrated that pre-treatment with the Cox-2 inhibitor NS398 could inhibit Cox-2 expression during noise overstimulation; and could attenuate noise-induced hearing loss and hair cell damage. Our results suggest that Cox-2 is involved in the pathogenesis of NIHL; and pharmacological inhibition of Cox-2 has considerable therapeutic potential in NIHL.
Oscillation control of carbon nanotube mechanical resonator by electrostatic interaction induced retardation
Authors: Yasuda Masaaki , Takei Kuniharu , Arie Takayuki , Akita Seiji 
Published: March 2016

AbstractDespite the superb intrinsic properties of carbon nanotube mechanical resonators, the quality factors at room temperature are 1,000 or less, even in vacuum, which is much lower than that of mechanical resonators fabricated using a top-down approach. This study demonstrates the improvement of the quality factor and the control of nonlinearity of the mechanical resonance of the cantilevered nanotube by electrostatic interaction. The apparent quality factor of the nanotube supported by insulator is improved drastically from approximately 630 to 3200 at room temperature. Results show that retardation of the electrostatic force induced by the contact resistance between the nanotube and the insulator support improves the quality factor. Finite element method calculation reveals that the nonuniform pileup charge on the insulator support strongly influences the nonlinearity of the resonance.
Germplasm dynamics: the role of ecotypic diversity in shaping the patterns of genetic variation in Lolium perenne
Authors: Blackmore T. , Thorogood D. , Skøt L. , McMahon R. , Powell W. , Hegarty M. 
Published: March 2016

AbstractPerennial ryegrass (Lolium perenne) is the most widely grown temperate grass species globally. Intensive plant breeding in ryegrass compared to many other crops species is a relatively recent exercise (last 100 years) and provides an interesting experimental system to trace the extent, impact and trajectory of undomesticated ecotypic variation represented in modern ryegrass cultivars. To explore germplasm dynamics in Lolium perenne, 2199 SNPs were genotyped in 716 ecotypes sampled from 90 European locations together with 249 cultivars representing 33 forage/amenity accessions. In addition three pseudo-cross mapping populations (450 individual recombinants) were genotyped to create a consensus genetic linkage map. Multivariate analyses revealed strong differentiation between cultivars with a small proportion of the ecotypic variation captured in improved cultivars. Ryegrass cultivars generated as part of a recurrent selection programme (RSP) are strongly associated with a small number of geographically localised Italian ecotypes which were among the founders of the RSP. Changes in haplotype frequency revealed signatures of selection in genes putatively involved in water-soluble carbohydrate (WSC) accumulation (a trait selected in the RSP). Retrospective analysis of germplasm in breeding programmes (germplasm dynamics) provides an experimental framework for the identification of candidate genes for novel traits such as WSC accumulation in ryegrass.
Perinatal Exposure to Neuregulin-1 Results in Disinhibition of Adult Midbrain Dopaminergic Neurons: Implication in Schizophrenia Modeling
Authors: Namba Hisaaki , Okubo Takeshi , Nawa Hiroyuki 
Published: March 2016

AbstractAberrant neuregulin-1 (NRG1) signals are suggested to associate with the neuropathophysiology of schizophrenia. Employing a mouse schizophrenia model established by neonatal neuregulin-1 challenge, we analysed postpubertal consequence of the NRG1 pretreatment for the electrophysiological property of nigral dopamine neurons. In vivo single unit recordings from anaesthetized NRG1-pretreated mice revealed increased spike bursting of nigral dopamine neurons. In slice preparations from NRG1-pretreated mice, spontaneous firing was elevated relative to controls. The relative increase in firing rates was abolished by a GABAA receptor antagonist. Whole-cell recording showed that perinatal NRG1 pretreatment diminished inhibitory miniature synaptic currents as well as GABAA receptor sensitivity. These results collectively suggest that perinatal exposure to neuregulin-1 results in the disinhibition of nigral dopamine neurons to influence their firing properties at the adult stage when the behavioral deficits are evident.
Habitat-based cetacean density models for the U.S. Atlantic and Gulf of Mexico
Authors: Roberts Jason J. , Best Benjamin D. , Mannocci Laura , Fujioka Ei , Halpin Patrick N. , Palka Debra L. , Garrison Lance P. , Mullin Keith D. , Cole Timothy V. N. , Khan Christin B. , McLellan William A. , Pabst D. Ann , Lockhart Gwen G. 
Published: March 2016

AbstractCetaceans are protected worldwide but vulnerable to incidental harm from an expanding array of human activities at sea. Managing potential hazards to these highly-mobile populations increasingly requires a detailed understanding of their seasonal distributions and habitats. Pursuant to the urgent need for this knowledge for the U.S. Atlantic and Gulf of Mexico, we integrated 23 years of aerial and shipboard cetacean surveys, linked them to environmental covariates obtained from remote sensing and ocean models, and built habitat-based density models for 26 species and 3 multi-species guilds using distance sampling methodology. In the Atlantic, for 11 well-known species, model predictions resembled seasonal movement patterns previously suggested in the literature. For these we produced monthly mean density maps. For lesser-known taxa, and in the Gulf of Mexico, where seasonal movements were less well described, we produced year-round mean density maps. The results revealed high regional differences in small delphinoid densities, confirmed the importance of the continental slope to large delphinoids and of canyons and seamounts to beaked and sperm whales, and quantified seasonal shifts in the densities of migratory baleen whales. The density maps, freely available online, are the first for these regions to be published in the peer-reviewed literature.
Anderson Localization in Degenerate Spin-Orbit Coupled Fermi Gas with Disorder
Authors: Liu Sheng , Zhou Xiang-Fa , Guo Guang-Can , Zhang Yong-Sheng 
Published: March 2016

AbstractCompetition between superconductivity and disorder plays an essential role in understanding the metal-insulator transition. Based on the Bogoliubov-de Gennes framework, we studied an 2D s-wave fermionic optical lattice system with both spin- orbit coupling and disorder are presented. We find that, with the increase of the strength of disorder, the mean superconducting order parameter will vanish while the energy gap will persist, which indicates that the system undergoes a transition from a superconducting state to a gapped insulating state. This can be confirmed by calculating the inverse participation ratio. We also find that, if the strength of disorder is small, the superconducting order parameter and the energy gap will decrease if we increase the strength of spin-orbit coupling and Zeeman field. In the large disorder limits, the increase of the strength of spin- orbit coupling will increase the mean superconducting order parameter. This phenomenon shows that the system is more insensitive to disorder if the spin-orbit coupling is presented. Numerical computing also shows that the whole system breaks up into several superconducting islands instead of being superconductive.
Skyrmion Creation and Manipulation by Nano-Second Current Pulses
Authors: Yuan H. Y. , Wang X. R. 
Published: March 2016

AbstractEasy creation and manipulation of skyrmions is important in skyrmion based devices for data storage and information processing. We show that a nano-second current pulse alone is capable of creating/deleting and manipulating skyrmions in a spin valve with a perpendicularly magnetized free layer and broken chiral symmetry. Interestingly, for an in-plane magnetized fixed layer, the free layer changes from a single domain at zero current to a Neel wall at an intermediate current density. Reverse the current polarity, the Neel wall changes to its image inversion. A properly designed nano-second current pulse, that tends to convert one type of Neel walls to its image inversion, ends up to create a stable skyrmion without assistance of external fields. For a perpendicularly magnetized fixed layer, the skyrmion size can be effectively tuned by a current density.
Direct formation of peritectic phase but no primary phase appearance within Ni83.25Zr16.75 peritectic alloy during free fall
Authors: Lü P. , Wang H. P. 
Published: March 2016

AbstractNi83.25Zr16.75 peritectic alloy was containerlessly solidified in a drop tube. When the droplet diameter exceeds a critical value (Dcrit), Ni7Zr2 phase primarily solidifies, followed by the peritectic reaction of Ni7Zr2 + L → Ni5Zr. Once the droplet diameter is smaller than the critical value (Dcrit), peritectic phase Ni5Zr directly solidifies from the undercooled melt by completely suppressing the nucleation and growth of Ni7Zr2 phase, which is ascribed to high undercooling and cooling rate. Additionally, peritectic phase Ni5Zr grows equiaxially in the sample solidified in a DSC at a cooling rate of 0.167 K/s.
Membrane-proximal TRAIL species are incapable of inducing short circuit apoptosis signaling: Implications for drug development and basic cytokine biology
Authors: Tatzel Katharina , Kuroki Lindsay , Dmitriev Igor , Kashentseva Elena , Curiel David T. , Goedegebuure S. Peter , Powell Matthew A. , Mutch David G. , Hawkins William G. , Spitzer Dirk 
Published: March 2016

AbstractTRAIL continues to garner substantial interest as a recombinant cancer therapeutic while the native cytokine itself serves important tumor surveillance functions when expressed in membrane-anchored form on activated immune effector cells. We have recently developed the genetically stabilized TRAIL platform TR3 in efforts to improve the limitations associated with currently available drug variants. While in the process of characterizing mesothelin-targeted TR3 variants using a single chain antibody (scFv) delivery format (SS-TR3), we discovered that the membrane-tethered cytokine had a substantially increased activity profile compared to non-targeted TR3. However, cell death proceeded exclusively via a bystander mechanism and protected the mesothelin-positive targets from apoptosis rather than leading to their elimination. Incorporation of a spacer-into the mesothelin surface antigen or the cancer drug itself-converted SS-TR3 into a cis-acting phenotype. Further experiments with membrane-anchored TR3 variants and the native cytokine confirmed our hypothesis that membrane-proximal TRAIL species lack the capacity to physically engage their cognate receptors coexpressed on the same cell membrane. Our findings not only provide an explanation for the “peaceful” coexistence of ligand and receptor of a representative member of the TNF superfamily but give us vital clues for the design of activity-enhanced TR3-based cancer therapeutics.
Microwave Assisted Synthesis of Porous NiCo2O4 Microspheres: Application as High Performance Asymmetric and Symmetric Supercapacitors with Large Areal Capacitance
Authors: Khalid Syed , Cao Chuanbao , Wang Lin , Zhu Youqi 
Published: March 2016

AbstractLarge areal capacitance is essentially required to integrate the energy storage devices at the microscale electronic appliances. Energy storage devices based on metal oxides are mostly fabricated with low mass loading per unit area which demonstrated low areal capacitance. It is still a challenge to fabricate supercapacitor devices of porous metal oxides with large areal capacitance. Herein we report microwave method followed by a pyrolysis of the as-prepared precursor is used to synthesize porous nickel cobaltite microspheres. Porous NiCo2O4 microspheres are capable to deliver large areal capacitance due to their high specific surface area and small crystallite size. The facile strategy is successfully demonstrated to fabricate aqueous-based asymmetric & symmetric supercapacitor devices of porous NiCo2O4 microspheres with high mass loading of electroactive materials. The asymmetric & symmetric devices exhibit maximum areal capacitance and energy density of 380 mF cm−2 & 19.1 Wh Kg−1 and 194 mF cm−2 & 4.5 Wh Kg−1 (based on total mass loading of 6.25 & 6.0 mg) respectively at current density of 1 mA cm−2. The successful fabrication of symmetric device also indicates that NiCo2O4 can also be used as the negative electrode material for futuristic asymmetric devices.
LncRNA DQ786243 contributes to proliferation and metastasis of colorectal cancer both in vitro and in vivo
Authors: Sun Longci , Xue Hanbing , Jiang Chunhui , Zhou Hong , Gu Lei , Liu Ye , Xu Chunjie , Xu Qing 
Published: March 2016

Accumulating evidence demonstrates that long non-coding RNAs (LncRNAs) play important roles in regulating gene expression and are involved in various cancers, including colorectal cancer (CRC). However, LncRNA profiles in CRC remain largely unknown. The present study aims to find the key LncRNA associated with CRC and to study its biological functions in CRC progression. We focused on LncRNA DQ786243, one of LncRNAs which promoted development of CRC from the Gene Expression Omnibus (GEO) and validated using quantitative real-time PCR among about 20 paired CRC tissues. The effects of LncRNA DQ786243 were assessed by silencing the LncRNA in vitro and in vivo. Results showed that the expression level LncRNA DQ786243 was significantly higher in CRC tissues and cell lines. We also found LncRNA DQ786243 knockdown by RNA interference with siRNA significantly arrested the cell cycle in the G2/M-phase, promoted apoptosis and weaken the abilities of cell proliferation and invasion in vitro. Further investigation into the mechanisms responsible for the growth inhibitory effects by DQ786243 silencing revealed that its knockdown resulted in the induction of cell cycle arrest and apoptosis through certain cell cycle-related and apoptosis-related proteins. Finally, xenograft experiments confirmed that the growth of xenograft tumours formed by CRC cells was suppressed after silencing LncRNA DQ786243 expression. In conclusion, the present study suggests that LncRNA DQ786243 is an oncogene that promotes tumour progression and leads us to propose that LncRNAs may serve as key regulatory hubs in CRC progression.
Amplified spontaneous emission pulses for high‐power supercontinuum generation
Authors: Liu Huan Huan , Chow Kin Kee 
Published: March 2016

The authors demonstrate an incoherent light source based on a reflective semiconductor optical amplifier as pump for high‐power supercontinuum generation for the first time. The obtained power level is about 160 mW and 20 dB spectral bandwidth is around 170 nm.