bluuebunny/crossref_metadata_2025_split huggingface dataset:
A chimeric haemagglutinin-based influenza split virion vaccine adjuvanted with AS03 induces protective stalk-reactive antibodies in mice
Authors: Nachbagauer Raffael , Kinzler David , Choi Angela , Hirsh Ariana , Beaulieu Edith , Lecrenier Nicolas , Innis Bruce L , Palese Peter , Mallett Corey P , Krammer Florian 
Published: September 2016

AbstractSeasonal influenza virus vaccines are generally effective at preventing disease, but need to be well matched to circulating virus strains for maximum benefit. Influenza viruses constantly undergo antigenic changes because of their high mutation rate in the immunodominant haemagglutinin (HA) head domain, which necessitates annual re-formulation and re-vaccination for continuing protection. In case of pandemic influenza virus outbreaks, new vaccines need to be produced and quickly distributed. Novel influenza virus vaccines that redirect the immune response towards more conserved epitopes located in the HA stalk domain may remove the need for annual vaccine re-formulation and could also protect against emergent pandemic strains to which the human population is immunologically naive. One approach to create such universal influenza virus vaccines is the use of constructs expressing chimeric HAs. By sequential immunization with vaccine strains expressing the same conserved HA stalk domain and exotic HA heads to which the host is naive, antibodies against the stalk can be boosted to high titres. Here we tested a monovalent chimeric HA-based prototype universal influenza virus split virion vaccine candidate with and without AS03 adjuvant in primed mice. We found that the chimeric HA-based vaccination regimen induced higher stalk antibody titres than the seasonal vaccine. The stalk antibody responses were long lasting, cross-reactive to distantly related HAs and provided protection in vivo in a serum transfer challenge model. The results of this study are promising and support further development of a universal influenza vaccine candidate built on the chimeric HA technology platform.
Analysis of Sogatella furcifera proteome that interact with P10 protein of Southern rice black-streaked dwarf virus
Authors: Than Win , Qin Faliang , Liu Wenwen , Wang Xifeng 
Published: September 2016

AbstractSouthern rice black-streaked dwarf virus (SRBSDV) is transmitted efficiently only by white-backed planthopper (WBPH, Sogatella furcifera) in a persistent propagative manner. Here we used a yeast two-hybrid system to investigate the interactions between the SRBSDV- P10 and the cDNA library of WBPH. Of 130 proteins identified as putative interactors, 28 were further tested in a retransformation analysis and β-galactosidase assay to confirm the interaction. The full-length gene sequences of 5 candidate proteins: vesicle-associated membrane protein 7 (VAMP7), vesicle transport V-SNARE protein (Vti1A), growth hormone-inducible transmembrane protein (Ghitm), nascent polypeptide-associated complex subunit alpha, and ATP synthase lipid-binding protein) were amplified by 5′ rapid amplification of cDNA ends (RACE) and used in a GST fusion protein pull-down assay. Three of these proteins interacted with SRBSDV-P10 in vitro experiment GST pull-down assay. In a gene expression analysis of 3 different growth stages and 6 different tissue organs of S. furcifera, the mRNA level of VAMP7 was high in adult males and gut. Vti1A was abundant in adult female, and malpighian tubule, gut and ovary. Ghitm was predominantly found in adult male and the malpighian tubule. These research findings are greatly helpful to understand the interaction between SRBSDV and insect vector.
Violation of the transit-time limit toward generation of ultrashort electron bunches with controlled velocity chirp
Authors: Jeon Seok-Gy , Shin Dongwon , Hur Min Sup 
Published: September 2016

AbstractVarious methods to generate ultrashort electron bunches for the ultrafast science evolved from the simple configuration of two-plate vacuum diodes to advanced technologies such as nanotips or photocathodes excited by femtosecond lasers. In a diode either in vacuum or of solid-state, the transit-time limit originating from finite electron mobility has caused spatiotemporal bunch-collapse in ultrafast regime. Here, we show for the first time that abrupt exclusion of transit-phase is a more fundamental origin of the bunch-collapse than the transit-time limit. We found that by significantly extending the cathode-anode gap distance, thereby violating the transit-time limit, the conventional transit-time-related upper frequency barrier in diodes can be removed. Furthermore, we reveal how to control the velocity chirp of bunches leading to ballistic bunch-compression. Demonstration of 0.707 THz-, 46.4 femtosecond-bunches from a 50 μm-wide diode in three-dimensional particle-in-cell simulations shows a way toward simple and compact sources of ultrafast electron bunches for diverse ultrafast sciences.
Microstructure, local dynamics, and flow behavior of colloidal suspensions with weak attractive interactions
Authors: Weis Clara , Oelschlaeger Claude , Dijkstra Dick , Ranft Meik , Willenbacher Norbert 
Published: September 2016

AbstractWe present a comprehensive micro- and macrorheological study of the effect of weak depletion attraction (Ψdep ≈ 1–10 kBT) on dense colloidal suspensions stabilized by short-range repulsive interactions. We used aqueous polymer dispersions as model system and demonstrated the unique capabilities of multiple particle tracking (MPT) to disclose structural changes in such technically important systems exhibiting many characteristic features of hard sphere systems. Below the hard sphere freezing point ϕc, viscosity increases monotonically with increasing Ψdep due to the transition from a fluid to a fluid/crystalline and finally to a gel state. Above ϕc, increasing attraction strength first results in a viscosity reduction corresponding to the formation of large, permeable crystals and then in a viscosity increase when a network of dense, small crystals forms. The fraction of the fluid and crystal phase, particle concentration in each phase as well as the modulus of the micro-crystals are obtained, the latter decreases with Ψdep. Above the colloidal glass transition strong heterogeneities and different local particle mobility in the repulsive and attractive arrested states are found. Particles are trapped in the cage of neighboring particles rather than in an attractive potential well. The intermediate ergodic state exhibits uniform tracer diffusivity.
Generation of biallelic knock-out sheep via gene-editing and somatic cell nuclear transfer
Authors: Li Honghui , Wang Gui , Hao Zhiqiang , Zhang Guozhong , Qing Yubo , Liu Shuanghui , Qing Lili , Pan Weirong , Chen Lei , Liu Guichun , Zhao Ruoping , Jia Baoyu , Zeng Luyao , Guo Jianxiong , Zhao Lixiao , Zhao Heng , Lv Chaoxiang , Xu Kaixiang , Cheng Wenmin , Li Hushan , Zhao Hong-Ye , Wang Wen , Wei Hong-Jiang 
Published: September 2016

AbstractTransgenic sheep can be used to achieve genetic improvements in breeds and as an important large-animal model for biomedical research. In this study, we generated a TALEN plasmid specific for ovine MSTN and transfected it into fetal fibroblast cells of STH sheep. MSTN biallelic-KO somatic cells were selected as nuclear donor cells for SCNT. In total, cloned embryos were transferred into 37 recipient gilts, 28 (75.7%) becoming pregnant and 15 delivering, resulting in 23 lambs, 12 of which were alive. Mutations in the lambs were verified via sequencing and T7EI assay and the gene mutation site was consistent with that in the donor cells. Off-target analysis was performed and no off-target mutations were detected. MSTN KO affected the mRNA expression of MSTN relative genes. The growth curve for the resulting sheep suggested that MSTN KO caused a remarkable increase in body weight compared with those of wild-type sheep. Histological analyses revealed that MSTN KO resulted in muscle fiber hypertrophy. These findings demonstrate the successful generation of MSTN biallelic-KO STH sheep via gene editing in somatic cells using TALEN technology and SCNT. These MSTN mutant sheep developed and grew normally and exhibited increased body weight and muscle growth.
Theory of tailorable optical response of two-dimensional arrays of plasmonic nanoparticles at dielectric interfaces
Authors: Sikdar Debabrata , Kornyshev Alexei A. 
Published: September 2016

AbstractTwo-dimensional arrays of plasmonic nanoparticles at interfaces are promising candidates for novel optical metamaterials. Such systems materialise from ‘top–down’ patterning or ‘bottom–up’ self-assembly of nanoparticles at liquid/liquid or liquid/solid interfaces. Here, we present a comprehensive analysis of an extended effective quasi-static four-layer-stack model for the description of plasmon-resonance-enhanced optical responses of such systems. We investigate in detail the effects of the size of nanoparticles, average interparticle separation, dielectric constants of the media constituting the interface and the nanoparticle position relative to the interface. Interesting interplays of these different factors are explored first for normally incident light. For off-normal incidence, the strong effects of the polarisation of light are found at large incident angles, which allows to dynamically tune the reflectance spectra. All the predictions of the theory are tested against full-wave simulations, proving this simplistic model to be adequate within the quasi-static limit. The model takes seconds to calculate the system’s optical response and makes it easy to unravel the effect of each system parameter. This helps rapid rationalization of experimental data and understanding of the optical signals from these novel ‘metamaterials’, optimised for light reflection or harvesting.
Dopaminergic Receptors on CD4+ T Naive and Memory Lymphocytes Correlate with Motor Impairment in Patients with Parkinson’s Disease
Authors: Kustrimovic Natasa , Rasini Emanuela , Legnaro Massimiliano , Bombelli Raffaella , Aleksic Iva , Blandini Fabio , Comi Cristoforo , Mauri Marco , Minafra Brigida , Riboldazzi Giulio , Sanchez-Guajardo Vanesa , Marino Franca , Cosentino Marco 
Published: September 2016

AbstractParkinson’s disease (PD) is characterized by loss of dopaminergic neurons in substantia nigra pars compacta, α-synuclein (α-syn)-rich intraneuronal inclusions (Lewy bodies), and microglial activation. Emerging evidence suggests that CD4+ T lymphocytes contribute to neuroinflammation in PD. Since the mainstay of PD treatment is dopaminergic substitution therapy and dopamine is an established transmitter connecting nervous and immune systems, we examined CD4+ T naive and memory lymphocytes in PD patients and in healthy subjects (HS), with specific regard to dopaminergic receptor (DR) expression. In addition, the in vitro effects of α-syn were assessed on CD4+ T naive and memory cells. Results showed extensive association between DR expression in T lymphocytes and motor dysfunction, as assessed by UPDRS Part III score. In total and CD4+ T naive cells expression of D1-like DR decrease, while in T memory cells D2-like DR increase with increasing score. In vitro, α-syn increased CD4+ T memory cells, possibly to a different extent in PD patients and in HS, and affected DR expression with cell subset-specific patterns. The present results support the involvement of peripheral adaptive immunity in PD, and may contribute to develop novel immunotherapies for PD, as well as to better use of current dopaminergic antiparkinson drugs.
Identification of miRNAs and their targets in wild tomato at moderately and acutely elevated temperatures by high-throughput sequencing and degradome analysis
Authors: Zhou Rong , Wang Qian , Jiang Fangling , Cao Xue , Sun Mintao , Liu Min , Wu Zhen 
Published: September 2016

AbstractMicroRNAs (miRNAs) are 19–24 nucleotide (nt) noncoding RNAs that play important roles in abiotic stress responses in plants. High temperatures have been the subject of considerable attention due to their negative effects on plant growth and development. Heat-responsive miRNAs have been identified in some plants. However, there have been no reports on the global identification of miRNAs and their targets in tomato at high temperatures, especially at different elevated temperatures. Here, three small-RNA libraries and three degradome libraries were constructed from the leaves of the heat-tolerant tomato at normal, moderately and acutely elevated temperatures (26/18 °C, 33/33 °C and 40/40 °C, respectively). Following high-throughput sequencing, 662 conserved and 97 novel miRNAs were identified in total with 469 conserved and 91 novel miRNAs shared in the three small-RNA libraries. Of these miRNAs, 96 and 150 miRNAs were responsive to the moderately and acutely elevated temperature, respectively. Following degradome sequencing, 349 sequences were identified as targets of 138 conserved miRNAs, and 13 sequences were identified as targets of eight novel miRNAs. The expression levels of seven miRNAs and six target genes obtained by quantitative real-time PCR (qRT-PCR) were largely consistent with the sequencing results. This study enriches the number of heat-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in tomatoes at elevated temperatures.
Preferential uptake of antioxidant carbon nanoparticles by T lymphocytes for immunomodulation
Authors: Huq Redwan , Samuel Errol L. G. , Sikkema William K. A. , Nilewski Lizanne G. , Lee Thomas , Tanner Mark R. , Khan Fatima S. , Porter Paul C. , Tajhya Rajeev B. , Patel Rutvik S. , Inoue Taeko , Pautler Robia G. , Corry David B. , Tour James M. , Beeton Christine 
Published: September 2016

AbstractAutoimmune diseases mediated by a type of white blood cell—T lymphocytes—are currently treated using mainly broad-spectrum immunosuppressants that can lead to adverse side effects. Antioxidants represent an alternative approach for therapy of autoimmune disorders; however, dietary antioxidants are insufficient to play this role. Antioxidant carbon nanoparticles scavenge reactive oxygen species (ROS) with higher efficacy than dietary and endogenous antioxidants. Furthermore, the affinity of carbon nanoparticles for specific cell types represents an emerging tactic for cell-targeted therapy. Here, we report that nontoxic poly(ethylene glycol)-functionalized hydrophilic carbon clusters (PEG-HCCs), known scavengers of the ROS superoxide (O2•−) and hydroxyl radical, are preferentially internalized by T lymphocytes over other splenic immune cells. We use this selectivity to inhibit T cell activation without affecting major functions of macrophages, antigen-presenting cells that are crucial for T cell activation. We also demonstrate the in vivo effectiveness of PEG-HCCs in reducing T lymphocyte-mediated inflammation in delayed-type hypersensitivity and in experimental autoimmune encephalomyelitis, an animal model of multiple sclerosis. Our results suggest the preferential targeting of PEG-HCCs to T lymphocytes as a novel approach for T lymphocyte immunomodulation in autoimmune diseases without affecting other immune cells.
Dynamics of single photon transport in a one-dimensional waveguide two-point coupled with a Jaynes-Cummings system
Authors: Wang Yuwen , Zhang Yongyou , Zhang Qingyun , Zou Bingsuo , Schwingenschlogl Udo 
Published: September 2016

AbstractWe study the dynamics of an ultrafast single photon pulse in a one-dimensional waveguide two-point coupled with a Jaynes-Cummings system. We find that for any single photon input the transmissivity depends periodically on the separation between the two coupling points. For a pulse containing many plane wave components it is almost impossible to suppress transmission, especially when the width of the pulse is less than 20 times the period. In contrast to plane wave input, the waveform of the pulse can be modified by controlling the coupling between the waveguide and Jaynes-Cummings system. Tailoring of the waveform is important for single photon manipulation in quantum informatics.
Metabolic and Dynamic Profiling for Risk Assessment of Fluopyram, a Typical Phenylamide Fungicide Widely Applied in Vegetable Ecosystem
Authors: Wei Peng , Liu Yanan , Li Wenzhuo , Qian Yuan , Nie Yanxia , Kim Dongyeop , Wang Mengcen 
Published: September 2016

AbstractFluopyram, a typical phenylamide fungicide, was widely applied to protect fruit vegetables from fungal pathogens-responsible yield loss. Highly linked to the ecological and dietary risks, its residual and metabolic profiles in the fruit vegetable ecosystem still remained obscure. Here, an approach using modified QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) extraction combined with GC-MS/MS analysis was developed to investigate fluopyram fate in the typical fruit vegetables including tomato, cucumber, pepper under the greenhouse environment. Fluopyram dissipated in accordance with the first-order rate dynamics equation with the maximum half-life of 5.7 d. Cleveage of fluopyram into 2-trifluoromethyl benzamide and subsequent formation of 3-chloro-5-(trifluoromethyl) pyridine-2-acetic acid and 3-chloro-5-(trifluoromethyl) picolinic acid was elucidated to be its ubiquitous metabolic pathway. Moreover, the incurrence of fluopyram at the pre-harvest interval (PHI) of 7–21 d was between 0.0108 and 0.1603 mg/kg, and the Hazard Quotients (HQs) were calculated to be less than 1, indicating temporary safety on consumption of the fruit vegetables incurred with fluopyram, irrespective of the uncertain toxicity of the metabolites. Taken together, our findings reveal the residual essential of fluopyram in the typical agricultural ecosystem, and would advance the further insight into ecological risk posed by this fungicide associated with its metabolites.
Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica
Authors: Park Ae Kyung , Kim Il-Sup , Do Hackwon , Jeon Byung Wook , Lee Chang Woo , Roh Soo Jung , Shin Seung Chul , Park Hyun , Kim Young-Saeng , Kim Yul-Ho , Yoon Ho-Sung , Lee Jun Hyuck , Kim Han-Woo 
Published: September 2016

AbstractAscorbic acid (AsA) maintains redox homeostasis by scavenging reactive oxygen species from prokaryotes to eukaryotes, especially plants. The enzyme monodehydroascorbate reductase (MDHAR) regenerates AsA by catalysing the reduction of monodehydroascorbate, using NADH or NADPH as an electron donor. The detailed recycling mechanism of MDHAR remains unclear due to lack of structural information. Here, we present the crystal structures of MDHAR in the presence of cofactors, nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), and complexed with AsA as well as its analogue, isoascorbic acid (ISD). The overall structure of MDHAR is similar to other iron-sulphur protein reductases, except for a unique long loop of 63–80 residues, which seems to be essential in forming the active site pocket. From the structural analysis and structure-guided point mutations, we found that the Arg320 residue plays a major substrate binding role, and the Tyr349 residue mediates electron transfer from NAD(P)H to bound substrate via FAD. The enzymatic activity of MDHAR favours NADH as an electron donor over NADPH. Our results show, for the first time, structural insights into this preference. The MDHAR-ISD complex structure revealed an alternative binding conformation of ISD, compared with the MDHAR-AsA complex. This implies a broad substrate (antioxidant) specificity and resulting greater protective ability of MDHAR.
Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone
Authors: Louca Stilianos , Hawley Alyse K. , Katsev Sergei , Torres-Beltran Monica , Bhatia Maya P. , Kheirandish Sam , Michiels Céline C. , Capelle David , Lavik Gaute , Doebeli Michael , Crowe Sean A. , Hallam Steven J. 
Published: September 2016

Significance
Modern molecular sequencing is beginning to provide great insight into microbial community structure and function at ecosystem scales. However, the quantitative integration of multiomic sequence information (DNA, mRNA, and protein) and geochemical processes has so far been elusive. Here, we develop a biogeochemical model that integrates geochemistry and multiomic sequence information to explain key metabolic processes in the oxygen-starved waters of Saanich Inlet, a model ecosystem for studying microbial community responses to oxygen minimum zone expansion. Our model largely explains DNA, mRNA, and protein distributions and sheds light on the metabolic networks coupling carbon, sulfur, and nitrogen transformations across a redox gradient. Our approach is extensible to other biogeochemical models incorporating feedbacks of global change on ecosystem functions.
Lateral association and elongation of vimentin intermediate filament proteins: A time-resolved light-scattering study
Authors: Lopez Carlos G. , Saldanha Oliva , Huber Klaus , Köster Sarah 
Published: September 2016

Significance
The hierarchical assembly pathway of the cytoskeletal protein vimentin may be responsible for the astonishing mechanical properties of the emerging filaments, such as high flexibility and extensibility, and thus play a key role in cellular mechanics. A two-step assembly mechanism, involving a lateral and a subsequent elongational step, has been established; however, the elongational step could not be followed in solution. Here, we show direct in situ observation and modeling of the elongation reaction of the filaments on the relevant length and time scales, using time-resolved, multiangle static and dynamic light scattering. We thus achieve sufficient spatio-temporal resolution without the need of labeling, staining, or adsorption to substrates.
How curvature-generating proteins build scaffolds on membrane nanotubes
Authors: Simunovic Mijo , Evergren Emma , Golushko Ivan , Prévost Coline , Renard Henri-François , Johannes Ludger , McMahon Harvey T. , Lorman Vladimir , Voth Gregory A. , Bassereau Patricia 
Published: September 2016

Significance
Lipid membranes are dynamic assemblies, changing shape on nano- to micron-sized scales. Some proteins can sculpt membranes by organizing into a molecular scaffold, dictating the membrane’s shape and properties. We combine microscopy, mathematical modeling, and simulations to explore how Bin/Amphiphysin/Rvs proteins assemble to form scaffolds on nanotubes. We show that the way protein locally deforms the membrane affects where it will nucleate before making a scaffold. In this process, the protein’s amphipathic helices—which shallowly insert into the membrane—seem dispensable. Surprisingly, the scaffold forms at low protein density on the nanotube. We simulate a structure of protein scaffolds at molecular resolution, shedding light on how these proteins may sculpt the membrane to facilitate important dynamic events in cells.