bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of slow molecular order parameters for Markov model construction
Authors: Pérez-Hernández Guillermo , Paul Fabian , Giorgino Toni , De Fabritiis Gianni , Noé Frank
Published: July 2013

A goal in the kinetic characterization of a macromolecular system is the description of its slow relaxation processes via (i) identification of the structural changes involved in these processes and (ii) estimation of the rates or timescales at which these slow processes occur. Most of the approaches to this task, including Markov models, master-equation models, and kinetic network models, start by discretizing the high-dimensional state space and then characterize relaxation processes in terms of the eigenvectors and eigenvalues of a discrete transition matrix. The practical success of such an approach depends very much on the ability to finely discretize the slow order parameters. How can this task be achieved in a high-dimensional configuration space without relying on subjective guesses of the slow order parameters? In this paper, we use the variational principle of conformation dynamics to derive an optimal way of identifying the “slow subspace” of a large set of prior order parameters – either generic internal coordinates or a user-defined set of parameters. Using a variational formulation of conformational dynamics, it is shown that an existing method—the time-lagged independent component analysis—provides the optional solution to this problem. In addition, optimal indicators—order parameters indicating the progress of the slow transitions and thus may serve as reaction coordinates—are readily identified. We demonstrate that the slow subspace is well suited to construct accurate kinetic models of two sets of molecular dynamics simulations, the 6-residue fluorescent peptide MR121-GSGSW and the 30-residue intrinsically disordered peptide kinase inducible domain (KID). The identified optimal indicators reveal the structural changes associated with the slow processes of the molecular system under analysis.
Going beyond “no-pair relativistic quantum chemistry”
Authors: Liu Wenjian , Lindgren Ingvar
Published: July 2013

The current field of relativistic quantum chemistry (RQC) has been built upon the no-pair and no-retardation approximations. While retardation effects must be treated in a time-dependent manner through quantum electrodynamics (QED) and are hence outside RQC, the no-pair approximation (NPA) has to be removed from RQC for it has some fundamental defects. Both configuration space and Fock space formulations have been proposed in the literature to do this. However, the former is simply wrong, whereas the latter is still incomplete. To resolve the old problems pertinent to the NPA itself and new problems beyond the NPA, we propose here an effective many-body (EMB) QED approach that is in full accordance with standard methodologies of electronic structure. As a first application, the full second order energy E2 of a closed-shell many-electron system subject to the instantaneous Coulomb-Breit interaction is derived, both algebraically and diagrammatically. It is shown that the same E2 can be obtained by means of 3 Goldstone-like diagrams through the standard many-body perturbation theory or 28 Feynman diagrams through the S-matrix technique. The NPA arises naturally by retaining only the terms involving the positive energy states. The potential dependence of the NPA can be removed by adding in the QED one-body counter terms involving the negative energy states, thereby leading to a “potential-independent no-pair approximation” (PI-NPA). The NPA, PI-NPA, EMB-QED, and full QED then span a continuous spectrum of relativistic molecular quantum mechanics.
Phase shift cavity ring down and Fourier transform infrared measurements of C–H vibrational transitions, energy levels, and intensities of (CH3)3Si–C≡C–H
Authors: Barroso Jenny Z. , Perez-Delgado Yasnahir , Manzanares Carlos E.
Published: July 2013

Phase shift cavity ring down and Fourier transform IR techniques have been used to observe the C–H stretch fundamental and overtone absorptions of the acetylenic (Δυ = 1-5) and methyl (Δυ = 1-6) C–H bonds of trimethyl-silyl-acetylene [(CH3)3CSi≡CH] at 295 K. Harmonic frequencies ω(ν1), ωa, and ωs and anharmonicities x(ν1), ωaxa, ωsxs were calculated for the acetylenic, methyl out-of-plane, and methyl in-plane C–H bonds, respectively. The harmonically coupled anharmonic oscillator (HCAO) model was used to determine the overtone energy levels and assign the absorption bands to vibrational transitions of methyl C–H bonds. A hot band, assigned as υν1 + ν24 − ν24 is observed for transitions with Δυ = 1-5 in a region near the acetylenic stretch. The intensity of the hot band is reduced considerably at 240 K. The strength of a Fermi resonance between C–Ha transition (υνa) and the combination band ((υ−1)νa + 2νbend) with (υ = 3-6) was calculated using the experimental perturbed energies and relative intensities. The main bands are separated by computer deconvolution and are integrated at each level to get the experimental band strengths. For methyl absorptions, the dipole moment function is expanded as a function of two C–H stretching coordinates and the intensities are calculated in terms of the HCAO model where only the C–H modes are considered. Acetylenic intensities are derived with a one dimensional dipole moment function. The expansion coefficients are obtained from molecular orbital calculations. The intensities are calculated without using adjustable parameters and they are of the same order of magnitude of the experimental intensities for all C–H transitions.
Dielectric relaxation, lattice dynamics and polarization mechanisms in Bi0.5Na0.5TiO3-based lead-free ceramics
Authors: Viola Giuseppe , Ning Huanpo , Wei Xiaojong , Deluca Marco , Adomkevicius Arturas , Khaliq Jibran , John Reece Michael , Yan Haixue
Published: July 2013

In 0.95[0.94Bi0.5Na0.5TiO3-0.06BaTiO3]-0.05CaTiO3 ceramics, the temperature TS (dielectric permittivity shoulder at about 125 °C) represents a transition between two different thermally activated dielectric relaxation processes. Below TS, the approximately linear decrease of the permittivity with the logarithm of frequency was attributed to the presence of a dominant ferroelectric phase. Above TS, the permittivity shows a more complicated dependence of the frequency and Raman modes indicate a sudden increase in the spatial disorder of the material, which is ascribed to the presence of a nonpolar phase and to a loss of interaction between polar regions. From 30 to 150 °C, an increase in the maximum polarization with increasing temperature was related to three possible mechanisms: polarization extension favoured by the simultaneous presence of polar and non-polar phases; the occurrence of electric field-induced transitions from weakly polar relaxor to ferroelectric polar phase; and the enhanced polarizability of the crystal structure induced by the weakening of the Bi-O bond with increasing temperature. The occurrence of different electric field induced polarization processes with increasing temperature is supported by the presence of additional current peaks in the current-electric field loops.
Optoelectronic analysis of multijunction wire array solar cells
Authors: Turner-Evans Daniel B. , Chen Christopher T. , Emmer Hal , McMahon William E. , Atwater Harry A.
Published: July 2013

Wire arrays have demonstrated promising photovoltaic performance as single junction solar cells and are well suited to defect mitigation in heteroepitaxy. These attributes can combine in tandem wire array solar cells, potentially leading to high efficiencies. Here, we demonstrate initial growths of GaAs on Si0.9Ge0.1 structures and investigate III-V on Si1-xGex device design with an analytical model and optoelectronic simulations. We consider Si0.1Ge0.9 wires coated with a GaAs0.9P0.1 shell in three different geometries: conformal, hemispherical, and spherical. The analytical model indicates that efficiencies approaching 34% are achievable with high quality materials. Full field electromagnetic simulations serve to elucidate the optical loss mechanisms and demonstrate light guiding into the wire core. Simulated current-voltage curves under solar illumination reveal the impact of a varying GaAs0.9P0.1 minority carrier lifetime. Finally, defective regions at the hetero-interface are shown to have a negligible effect on device performance if highly doped so as to serve as a back surface field. Overall, the growths and the model demonstrate the feasibility of the proposed geometries and can be used to guide tandem wire array solar cell designs.
Migration of interfacial oxygen ions modulated resistive switching in oxide-based memory devices
Authors: Chen C. , Gao S. , Zeng F. , Tang G. S. , Li S. Z. , Song C. , Fu H. D. , Pan F.
Published: July 2013

Oxides-based resistive switching memory induced by oxygen ions migration is attractive for future nonvolatile memories. Numerous works had focused their attentions on the sandwiched oxide materials for depressing the characteristic variations, but the comprehensive studies of the dependence of electrodes on the migration behavior of oxygen ions are overshadowed. Here, we investigated the interaction of various metals (Ni, Co, Al, Ti, Zr, and Hf) with oxygen atoms at the metal/Ta2O5 interface under electric stress and explored the effect of top electrode on the characteristic variations of Ta2O5-based memory device. It is demonstrated that chemically inert electrodes (Ni and Co) lead to the scattering switching characteristics and destructive gas bubbles, while the highly chemically active metals (Hf and Zr) formed a thick and dense interfacial intermediate oxide layer at the metal/Ta2O5 interface, which also degraded the resistive switching behavior. The relatively chemically active metals (Al and Ti) can absorb oxygen ions from the Ta2O5 film and avoid forming the problematic interfacial layer, which is benefit to the formation of oxygen vacancies composed conduction filaments in Ta2O5 film thus exhibit the minimum variations of switching characteristics. The clarification of oxygen ions migration behavior at the interface can lead further optimization of resistive switching performance in Ta2O5-based memory device and guide the rule of electrode selection for other oxide-based resistive switching memories.
Electromagnetic Casimir effect on the boundary of a
D
-dimensional cavity and the high temperature asymptotics
Authors: Teo L. P.
Published: July 2013

We consider the finite temperature Casimir stress acting on the boundary of a D ⩾ 3 dimensional cavity due to the vacuum fluctuations of electromagnetic fields. Both perfectly conducting and infinitely permeable boundary conditions are considered, and it is proved that they correspond mathematically to the relative and absolute boundary conditions. The divergence terms of the Casimir free energy are related to the heat kernel coefficients of the Laplace operator. It is shown that the Casimir stress is free of divergence if and only if D is exactly three. The high temperature asymptotics of the regularized Casimir free energy are also found to depend on the heat kernel coefficients. When D > 3, renormalization is required to remove terms of order higher than or equal to T2.
Time-resolved temperature study in a high-power impulse magnetron sputtering discharge
Authors: Britun Nikolay , Palmucci Maria , Konstantinidis Stephanos , Gaillard Mireille , Snyders Rony
Published: July 2013

The gas heating dynamics is studied in a high-power impulse magnetron sputtering discharge operating in Ar-N2 gas mixtures. The time-resolved rotational temperature analysis based on the spectral transition between the B2Σu+-X2Σg+ energy levels in molecular nitrogen ion (N2+ First Negative Band) is undertaken for this purpose. The rotational temperature in the discharge is found to increase linearly during the plasma pulse being roughly independent on the nitrogen content in the examined range. Such a temperature increase is attributed to the bulk gas heating which is the result of collisions with the sputtered species. Two sputtered materials, Ti and W, are examined during the study. In the case of W sputtering, the gas heating is found to be more pronounced than in the Ti case, which is explained by more efficient energy exchange between the sputtered W atoms and the bulk gas atoms during the plasma on-time. The obtained temperature data are compared to the laser-induced fluorescence study of Ar metastable atoms performed recently in the same discharge in our group. The particularities related to gas thermalization as well as to validity of the utilized approach for characterization of the pulsed sputtering discharges are discussed.
Sensitivity enhancement in optical micro-tube resonator sensors via mode coupling
Authors: Ling Tao , Guo L. Jay
Published: July 2013

A liquid filled, silica micro-tube with a low refractive index material inner-coating has been proposed and theoretically studied as a coupled micro-resonator sensor to greatly enhance biochemical sensor sensitivity. Its unique coupling phenomenon has been analyzed and utilized to boost the device's refractive index sensitivity to 967 nm/Refractive Index Unit (RIU). Through optimization of the coupling strength between the two micro-resonators, further improvement in refractive index sensitivity up to 1100 nm/RIU has been predicted. This mode coupling strategy allows us to design robust, thick-walled micro-tube sensors with ultra-high sensitivity which is useful in practical biochemical sensing applications.
LiRE2Si3 (RE = Nd, Sm, and Eu) as potential photovoltaic materials
Authors: Feng J. , Xiao B. , Pan W. , Jiang Y. H. , Zhou R.
Published: July 2013

The equilibrium lattice properties, electronic and optical properties of LiRE2Si3 (RE = Nd, Sm, and Eu) compounds have been investigated. LiRE2Si3 compounds show strong absorption in the entire range of solar spectrum. The conversion efficiencies are 52.4, 70.2, and 63.9% for LiNd2Si3, LiSm2Si3, and LiEu2Si3, respectively. The efficiencies of LiSm2Si3 and LiEu2Si3 are about twice of GaAs (34%), and they are three times higher than Si (20%). The presence of 4f shell and the unoccupied π* states enhance the electron transportation invoked by photon adsorption. The LiRE2Si3 compounds are the excellent candidates of photovoltaic materials so far.
Cascaded integrated waveguide linear microcavity filters
Authors: Pruessner Marcel W. , Stievater Todd H. , Goetz Peter G. , Rabinovich William S. , Urick Vincent J.
Published: July 2013

We experimentally demonstrate cascaded Fabry-Perot microcavity filters fabricated on silicon-on-insulator substrates. The cavities are formed by etching three sets of quarter-wavelength trenches along a rib waveguide, each set forming a Bragg reflector. Various configurations are examined with a view towards maximizing the filter extinction and minimizing the linewidth. We investigate the origin of spurious cavity modes and show how these are minimized. The effect of mode-splitting due to inter-cavity coupling is suppressed by increasing the reflectivity of the center mirror. Experimental results compare well with transfer matrix predictions.
Trapping and identifying single-nanoparticles using a low-aspect-ratio nanopore
Authors: Tsutsui Makusu , Maeda Yoichi , He Yuhui , Hongo Sadato , Ryuzaki Sou , Kawano Satoyuki , Kawai Tomoji , Taniguchi Masateru
Published: July 2013

Manipulation of particles and molecules in fluid is a fundamental technology in biosensors. Here, we report electrical trapping and identification of single-nanoparticles using a low-aspect-ratio nanopore. Particle trapping and detrapping are implemented through a control of the cross-membrane electrophoretic voltage. This electrical method is found to enable placing an individual nanoparticle in vicinity of a lithographically-defined nanopore by virtue of the balance between the two counteracting factors, electrostatic and electroosmotic forces. We also demonstrate identification of trapped nanoparticles by the ionic current through the particle-pore gap space. This technique may find applications in electrode-embedded nanopore sensors.
Excellent dielectric properties of polymer composites based on core-shell structured carbon/silica nanohybrid
Authors: Lei Tuo , Xue Qingzhong , Chu Liangyong , Han Zhide , Sun Jin , Xia Fujun , Zhang Zhongyang , Guo Qikai
Published: July 2013

Polymer based composites with high dielectric constant and low dielectric loss were fabricated by dispersing core-shell structured carbon/silica nanohybrid (CS) into a poly (vinylidene fluoride) (PVDF) matrix. Due to the high conductive carbon core, nonconductive silica shell and the good dispersion of the CS fillers in PVDF, the CS/PVDF composites exhibited better dielectric properties than most nano-carbon materials/polymer composites. These experimental results can be understood by the percolation theory and microcapacitor model. Our strategy provides a pathway to achieve nano-carbon materials/polymer composites with good dielectric performances.
Improved superconducting qubit coherence using titanium nitride
Authors: Chang Josephine B. , Vissers Michael R. , Córcoles Antonio D. , Sandberg Martin , Gao Jiansong , Abraham David W. , Chow Jerry M. , Gambetta Jay M. , Beth Rothwell Mary , Keefe George A. , Steffen Matthias , Pappas David P.
Published: July 2013

We demonstrate enhanced relaxation and dephasing times of transmon qubits, up to ∼60 μs, by fabricating the interdigitated shunting capacitors using titanium nitride (TiN). Compared to qubits made with lift-off aluminum deposited simultaneously with the Josephson junction, this represents as much as a six-fold improvement and provides evidence that surface losses from two-level system (TLS) defects residing at or near interfaces contribute to decoherence. Concurrently, we observe an anomalous temperature dependent frequency shift of TiN resonators, which is inconsistent with the predicted TLS model.
Tunable mechanical properties of diamond superlattices generated by interlayer bonding in twisted bilayer graphene
Authors: Machado Alyne S. , Maroudas Dimitrios , Muniz Andre R.
Published: July 2013

Using molecular-dynamics simulations of tensile deformation and shear loading tests, we determine the mechanical properties of superlattices of diamond-like nanocrystals embedded in twisted bilayer graphene (TBG) generated by covalent interlayer bonding through patterned hydrogenation. We find that the mechanical properties of these superstructures can be precisely tuned by controlling the fraction of sp3-hybridized C-C bonds in the material, fsp3, through the extent of chemical functionalization. The Young modulus and ultimate tensile strength weaken compared with pristine TBG with increasing fsp3, but they remain superior to those of most conventional materials. The interlayer shear modulus increases monotonically with fsp3.
Living the difference: alternative functional designs in five perennial herbs coexisting in a coastal dune environment
Authors: Bermúdez Raimundo , Retuerto Rubén
Published: July 2013

Ecological theory suggests that in harsh environments major abiotic stress factors may act as environmental filters, thereby reducing the range of possible plant strategies through environmental trait selection. This would lead to functional similarity of species coexisting in hostile environments. To test this prediction, we evaluated six functional leaf traits at three different times of year in five species coexisting in a coastal dune ecosystem. The functional traits examined were associated with water status and light interception and use – two of the most limiting factors that lead to stress in dune systems. Species differed in traits associated with light absorption, namely chlorophyll content, the vigour index NDVI, and the proportion of the light absorbed that is used in photochemistry (as expressed by the effective and maximum quantum yield of PSII and the photochemical reflectance index). For most of the traits, the relative performance of species depended significantly on time. This research revealed a significant divergence in functional traits of coexisting species, which does not conform to findings in other harsh environments where species tend to functional convergence. The data provide experimental support for the hypothesis that there is no single combination of traits for a given environment, but that alternative functional designs of similar fitness may evolve in the same environment as a result of complex interactions and trade-offs among traits. This suggests that factors claimed to promote divergence, such as limiting similarity and disturbance processes, may play an important role in structuring the dune community under study. The high variability in functional traits suggests a significant degree of functional diversity and highlights the importance of preserving the species composition of threatened coastal dune habitats in order to preserve distinctive functional processes that may be unique to the systems.
Variation in carbon isotope discrimination and its relationship with harvest index in the reference collection of chickpea germplasm
Authors: Krishnamurthy Lakshmanan , Kashiwagi Junichi , Tobita Satoshi , Ito Osamu , Upadhyaya Hari D. , Gowda Cholenahalli L. L. , Gaur Pooran M. , Sheshshayee Madavalam S. , Singh Sube , Vadez Vincent , Varshney Rajeev K.
Published: July 2013

Terminal drought is a major constraint to chickpea productivity. Carbon isotope discrimination (Δ13C), an integrator of plant behaviour influencing transpiration efficiency (TE), is an important component of yield under drought. The variation in Δ13C and its association with yield was assessed in the reference collection of chickpea germplasm. Drought stress reduced shoot biomass by 36–39% and grain yield by 23%. Mean Δ13C was low and the range of genetic variation was high under drought stress. Largely, high Δ13C accessions were early in flowering (40–50 days), moderate in shoot biomass, high in seed yields and high in harvest index (HI). Δ13C was positively correlated with seed yield in both the years under drought stress, only in 2008–09 under optimal irrigation. This positive association was very close with HI. Among the yield components, Δ13C was closely associated with pod numbers per unit area and seed size under drought stress. Path coefficients showed no direct association of Δ13C with grain yield but an indirect negative association through shoot biomass at maturity and a close positive association through HI. The closest association of HI or shoot biomass was seen in the maturity group of accessions that experienced the optimum terminal drought stress.
Combustibility of a mixture of live and dead fuel components
Authors: Viegas D. X. , Soares J. , Almeida M.
Published: July 2013

The problem of predicting the rate of spread of a linear fire front in a fuel bed composed of one live and one dead fuel component in no-slope and no-wind conditions is addressed. Two linear models based on the mass fraction of each fuel component are proposed to predict the rate of spread of a fire front as a function of the mass fraction of the dead or dry fuel component. Experimental results obtained with two different mixtures show that for each fuel mixture there is a threshold value of mass concentration of the dead fuel below which the fire front does not spread. The rate of spread results compare favourably with the proposed models. A composite fuel moisture content of the fuel bed is shown to be a good descriptor of the rate of spread of the mixture. An exponential model using composite fuel moisture content of the fuel bed is proposed to estimate the rate of spread of the mixture and a comparison is made with the concept of fuel curing that is used to characterise live fuels.
Quorum sensing allows T cells to discriminate between self and nonself
Authors: Butler Thomas Charles , Kardar Mehran , Chakraborty Arup K.
Published: July 2013

T cells orchestrate pathogen-specific adaptive immune responses by identifying peptides derived from pathogenic proteins that are displayed on the surface of infected cells. Host cells also display peptide fragments from the host’s own proteins. Incorrectly identifying peptides derived from the body’s own proteome as pathogenic can result in autoimmune disease. To minimize autoreactivity, immature T cells that respond to self-peptides are deleted in the thymus by a process called negative selection. However, negative selection is imperfect, and autoreactive T cells exist in healthy individuals. To understand how autoimmunity is yet avoided, without loss of responsiveness to pathogens, we have developed a model of T-cell training and response. Our model shows that T cells reliably respond to infection and avoid autoimmunity because collective decisions made by the T-cell population, rather than the responses of individual T cells, determine biological outcomes. The theory is qualitatively consistent with experimental data and yields a criterion for thymic selection to be adequate for suppressing autoimmunity.
Natural killer cells in HIV controller patients express an activated effector phenotype and do not up-regulate NKp44 on IL-2 stimulation
Authors: Marras Francesco , Nicco Elena , Bozzano Federica , Di Biagio Antonio , Dentone Chiara , Pontali Emanuele , Boni Silvia , Setti Maurizio , Orofino Giancarlo , Mantia Eugenio , Bartolacci Valentina , Bisio Francesca , Riva Agostino , Biassoni Roberto , Moretta Lorenzo , De Maria Andrea
Published: July 2013

Control of HIV replication in elite controller (EC) and long-term nonprogressor (LTNP) patients has been associated with efficient CD8
+
cytotoxic T-lymphocyte function. However, innate immunity may play a role in HIV control. We studied the expression of natural cytotoxicity receptors (NKp46, NKp30, and NKp44) and their induction over a short time frame (2–4 d) on activation of natural killer (NK) cells in 31 HIV controller patients (15 ECs, 16 LTNPs). In EC/LTNP, induction of NKp46 expression was normal but short (2 d), and NKp30 was induced to lower levels vs. healthy donors. Notably, in antiretroviral-treated aviremic progressor patients (TAPPs), no induction of NKp46 or NKp30 expression occurred. More importantly, EC/LTNP failed to induce expression of NKp44, a receptor efficiently induced in activated NK cells in TAPPs. The specific lack of NKp44 expression resulted in sharply decreased capability of killing target cells by NKp44, whereas TAPPs had conserved NKp44-mediated lysis. Importantly, conserved NK cell responses, accompanied by a selective defect in the NKp44-activating pathway, may result in lack of killing of uninfected CD4
+
NKp44Ligand
+
cells when induced by HIVgp41 peptide-S3, representing a relevant mechanism of CD4
+
depletion. In addition, peripheral NK cells from EC/LTNP had increased NKG2D expression, significant HLA-DR up-regulation, and a mature (NKG2A−CD57
+
killer cell Ig-like receptor
+
CD85j
+
) phenotype, with cytolytic function also against immature dendritic cells. Thus, NK cells in EC/LTNP can maintain substantially unchanged functional capabilities, whereas the lack of NKp44 induction may be related to CD4 maintenance, representing a hallmark of these patients.
Family-based training program improves brain function, cognition, and behavior in lower socioeconomic status preschoolers
Authors: Neville Helen J. , Stevens Courtney , Pakulak Eric , Bell Theodore A. , Fanning Jessica , Klein Scott , Isbell Elif
Published: July 2013

Using information from research on the neuroplasticity of selective attention and on the central role of successful parenting in child development, we developed and rigorously assessed a family-based training program designed to improve brain systems for selective attention in preschool children. One hundred forty-one lower socioeconomic status preschoolers enrolled in a Head Start program were randomly assigned to the training program, Head Start alone, or an active control group. Electrophysiological measures of children’s brain functions supporting selective attention, standardized measures of cognition, and parent-reported child behaviors all favored children in the treatment program relative to both control groups. Positive changes were also observed in the parents themselves. Effect sizes ranged from one-quarter to half of a standard deviation. These results lend impetus to the further development and broader implementation of evidence-based education programs that target at-risk families.
Genome-wide association study identifies vitamin B
5
biosynthesis as a host specificity factor in
Campylobacter
Authors: Sheppard Samuel K. , Didelot Xavier , Meric Guillaume , Torralbo Alicia , Jolley Keith A. , Kelly David J. , Bentley Stephen D. , Maiden Martin C. J. , Parkhill Julian , Falush Daniel
Published: July 2013

Genome-wide association studies have the potential to identify causal genetic factors underlying important phenotypes but have rarely been performed in bacteria. We present an association mapping method that takes into account the clonal population structure of bacteria and is applicable to both core and accessory genome variation.
Campylobacter
is a common cause of human gastroenteritis as a consequence of its proliferation in multiple farm animal species and its transmission via contaminated meat and poultry. We applied our association mapping method to identify the factors responsible for adaptation to cattle and chickens among 192
Campylobacter
isolates from these and other host sources. Phylogenetic analysis implied frequent host switching but also showed that some lineages were strongly associated with particular hosts. A seven-gene region with a host association signal was found. Genes in this region were almost universally present in cattle but were frequently absent in isolates from chickens and wild birds. Three of the seven genes encoded vitamin B
5
biosynthesis. We found that isolates from cattle were better able to grow in vitamin B
5
-depleted media and propose that this difference may be an adaptation to host diet.
Size distribution dynamics reveal particle-phase chemistry in organic aerosol formation
Authors: Shiraiwa Manabu , Yee Lindsay D. , Schilling Katherine A. , Loza Christine L. , Craven Jill S. , Zuend Andreas , Ziemann Paul J. , Seinfeld John H.
Published: July 2013

Organic aerosols are ubiquitous in the atmosphere and play a central role in climate, air quality, and public health. The aerosol size distribution is key in determining its optical properties and cloud condensation nucleus activity. The dominant portion of organic aerosol is formed through gas-phase oxidation of volatile organic compounds, so-called secondary organic aerosols (SOAs). Typical experimental measurements of SOA formation include total SOA mass and atomic oxygen-to-carbon ratio. These measurements, alone, are generally insufficient to reveal the extent to which condensed-phase reactions occur in conjunction with the multigeneration gas-phase photooxidation. Combining laboratory chamber experiments and kinetic gas-particle modeling for the dodecane SOA system, here we show that the presence of particle-phase chemistry is reflected in the evolution of the SOA size distribution as well as its mass concentration. Particle-phase reactions are predicted to occur mainly at the particle surface, and the reaction products contribute more than half of the SOA mass. Chamber photooxidation with a midexperiment aldehyde injection confirms that heterogeneous reaction of aldehydes with organic hydroperoxides forming peroxyhemiacetals can lead to a large increase in SOA mass. Although experiments need to be conducted with other SOA precursor hydrocarbons, current results demonstrate coupling between particle-phase chemistry and size distribution dynamics in the formation of SOAs, thereby opening up an avenue for analysis of the SOA formation process.
Transgene- and locus-dependent imprinting reveals allele-specific chromosome conformations
Authors: Lonfat Nicolas , Montavon Thomas , Jebb David , Tschopp Patrick , Nguyen Huynh Thi Hanh , Zakany Jozsef , Duboule Denis
Published: July 2013

When positioned into the
integrin α-6
gene, an
Hoxd9lacZ
reporter transgene displayed parental imprinting in mouse embryos. While the expression from the paternal allele was comparable with patterns seen for the same transgene when present at the neighboring
HoxD
locus, almost no signal was scored at this integration site when the transgene was inherited from the mother, although the
Itga6
locus itself is not imprinted. The transgene exhibited maternal allele-specific DNA hypermethylation acquired during oogenesis, and its expression silencing was reversible on passage through the male germ line. Histone modifications also corresponded to profiles described at known imprinted loci. Chromosome conformation analyses revealed distinct chromatin microarchitectures, with a more compact structure characterizing the maternally inherited repressed allele. Such genetic analyses of well-characterized transgene insertions associated with a de novo-induced parental imprint may help us understand the molecular determinants of imprinting.
Aryl hydrocarbon receptor-mediated induction of the microRNA-132/212 cluster promotes interleukin-17–producing T-helper cell differentiation
Authors: Nakahama Taisuke , Hanieh Hamza , Nguyen Nam Trung , Chinen Ichino , Ripley Barry , Millrine David , Lee Soyoung , Nyati Kishan Kumar , Dubey Praveen Kumar , Chowdhury Kamal , Kawahara Yukio , Kishimoto Tadamitsu
Published: July 2013

Aryl hydrocarbon receptor (AHR) plays critical roles in various autoimmune diseases such as multiple sclerosis by controlling interleukin-17 (IL-17)–producing T-helper (T
H
17) and regulatory T cells. Although various transcription factors and cytokines have been identified as key participants in T
H
17 generation, the role of microRNAs in this process is poorly understood. In this study, we found that expression of the microRNA (miR)-132/212 cluster is up-regulated by AHR activation under T
H
17-inducing, but not regulatory T-inducing conditions. Deficiency of the miR-132/212 cluster prevented the enhancement of T
H
17 differentiation by AHR activation. We also identified B-cell lymphoma 6, a negative regulator of T
H
17 differentiation, as a potential target of the miR-212. Finally, we investigated the roles of the miR-132/212 cluster in experimental autoimmune encephalomyelitis, a murine model of multiple sclerosis. Mice deficient in the miR-132/212 cluster exhibited significantly higher resistance to the development of experimental autoimmune encephalomyelitis and lower frequencies of both T
H
1 and T
H
17 cells in draining lymph nodes. Our findings reveal a unique mechanism of AHR-dependent T
H
17 differentiation that depends on the miR-132/212 cluster.
Probing the depths of cellular senescence
Authors: Baker Darren J. , Sedivy John M.
Published: July 2013

Cellular senescence is a state of irreversible cell cycle arrest that has been documented to both suppress cancer and promote aging. Although not well understood, extensive nuclear changes, including the remodeling of chromatin, take place as cells become senescent. In this issue, Ivanov et al. (2013. J. Cell Biol. http://dx.doi.org/jcb.201212110) report that chromatin fragments are released from the nuclei of senescent cells and are subsequently targeted for processing through the autophagy/lysosomal pathway.
Differential Epitope Tagging of Actin in TransformedDrosophilaProduces Distinct Effects on Myofibril Assembly and Function of the Indirect Flight Muscle
Authors: Brault Véronique , Sauder Ursula , Reedy Mary C. , Aebi Ueli , Schoenenberger Cora-Ann
Published: July 2013

We have tested the impact of tags on the structure and function of indirect flight muscle (IFM)-specific Act88F actin by transforming mutant Drosophila melanogaster, which do not express endogenous actin in their IFMs, with tagged Act88F constructs. Epitope tagging is often the method of choice to monitor the fate of a protein when a specific antibody is not available. Studies addressing the functional significance of the closely related actin isoforms rely almost exclusively on tagged exogenous actin, because only few antibodies exist that can discriminate between isoforms. Thereby it is widely presumed that the tag does not significantly interfere with protein function. However, in most studies the tagged actin is expressed in a background of endogenous actin and, as a rule, represents only a minor fraction of the total actin. The Act88F gene encodes the only Drosophila actin isoform exclusively expressed in the highly ordered IFM. Null mutations in this gene do not affect viability, but phenotypic effects in transformants can be directly attributed to the transgene. Transgenic flies that express Act88F with either a 6x histidine tag or an 11-residue peptide derived from vesicular stomatitis virus G protein at the C terminus were flightless. Overall, the ultrastructure of the IFM resembled that of the Act88F null mutant, and only low amounts of C-terminally tagged actins were found. In contrast, expression of N-terminally tagged Act88F at amounts comparable with that of wild-type flies yielded fairly normal-looking myofibrils and partially reconstituted flight ability in the transformants. Our findings suggest that the N terminus of actin is less sensitive to modifications than the C terminus, because it can be tagged and still polymerize into functional thin filaments.
Association of Nonribosomal Nucleolar Proteins in Ribonucleoprotein Complexes during Interphase and Mitosis
Authors: Piñol-Roma Serafı́n
Published: July 2013

rRNA precursors are bound throughout their length by specific proteins, as the pre-rRNAs emerge from the transcription machinery. The association of pre-rRNA with proteins as ribonucleoprotein (RNP) complexes persists during maturation of 18S, 5.8S, and 28S rRNA, and through assembly of ribosomal subunits in the nucleolus. Preribosomal RNP complexes contain, in addition to ribosomal proteins, an unknown number of nonribosomal nucleolar proteins, as well as small nucleolar RNA-ribonucleoproteins (sno-RNPs). This report describes the use of a specific, rapid, and mild immunopurification approach to isolate and analyze human RNP complexes that contain nonribosomal nucleolar proteins, as well as ribosomal proteins and rRNA. Complexes immunopurified with antibodies to nucleolin—a major nucleolar RNA-binding protein—contain several distinct specific polypeptides that include, in addition to nucleolin, the previously identified nucleolar proteins B23 and fibrillarin, proteins with electrophoretic mobilities characteristic of ribosomal proteins including ribosomal protein S6, and a number of additional unidentified proteins. The physical association of these proteins with one another is mediated largely by RNA, in that the complexes dissociate upon digestion with RNase. Complexes isolated from M-phase cells are similar in protein composition to those isolated from interphase cell nuclear extracts. Therefore, the predominant proteins that associate with nucleolin in interphase remain in RNP complexes during mitosis, despite the cessation of rRNA synthesis and processing in M-phase. In addition, precursor rRNA, as well as processed 18S and 28S rRNA and candidate rRNA processing intermediates, is found associated with the immunopurified complexes. The characteristics of the rRNP complexes described here, therefore, indicate that they represent bona fide precursors of mature cytoplasmic ribosomal subunits.
Cytoskeletal Reorganization Induced by Engagement of the NG2 Proteoglycan Leads to Cell Spreading and Migration
Authors: Fang Xuexun , Burg Michael A. , Barritt Diana , Dahlin-Huppe Kimberlee , Nishiyama Akiko , Stallcup William B.
Published: July 2013

Cells expressing the NG2 proteoglycan can attach, spread, and migrate on surfaces coated with NG2 mAbs, demonstrating that engagement of NG2 can trigger the cytoskeletal rearrangements necessary for changes in cell morphology and motility. Engagement of different epitopes of the proteoglycan results in distinct forms of actin reorganization. On mAb D120, the cells contain radial actin spikes characteristic of filopodial extension, whereas on mAb N143, the cells contain cortical actin bundles characteristic of lamellipodia. Cells that express NG2 variants lacking the transmembrane and cytoplasmic domains are unable to spread or migrate on NG2 mAb-coated surfaces, indicating that these portions of the molecule are essential for NG2-mediated signal transduction. Cells expressing an NG2 variant lacking the C-terminal half of the cytoplasmic domain can still spread normally on mAbs D120 and N143, suggesting that the membrane-proximal cytoplasmic segment is responsible for this process. In contrast, this variant migrates poorly on mAb D120 and exhibits abnormal arrays of radial actin filaments decorated with fascin during spreading on this mAb. The C-terminal portion of the NG2 cytoplasmic domain, therefore, may be involved in regulating molecular events that are crucial for cell motility.
Association of the Cell Cycle Transcription Factor Mbp1 with the Skn7 Response Regulator in Budding Yeast
Authors: Bouquin Nicolas , Johnson Anthony L. , Morgan Brian A. , Johnston Leland H.
Published: July 2013

We previously isolated the SKN7 gene in a screen designed to isolate new components of the G1-S cell cycle transcription machinery in budding yeast. We have now found that Skn7 associates with Mbp1, the DNA-binding component of the G1-S transcription factor DSC1/MBF. SKN7 and MBP1 show several genetic interactions. Skn7 overexpression is lethal and is suppressed by a mutation in MBP1. Similarly, high overexpression of Mbp1 is lethal and can be suppressed by skn7 mutations.SKN7 is also required for MBP1 function in a mutant compromised for G1-specific transcription. Gel-retardation assays indicate that Skn7 is not an integral part of MBF. However, a physical interaction between Skn7 and Mbp1 was detected using two-hybrid assays and GST pulldowns. Thus, Skn7 and Mbp1 seem to form a transcription factor independent of MBF. Genetic data suggest that this new transcription factor could be involved in the bud-emergence process.
Coilin Shuttles between the Nucleus and Cytoplasm InXenopusOocytes
Authors: Bellini Michel , Gall Joseph G.
Published: July 2013

Coiled bodies are discrete nuclear organelles often identified by the marker protein p80-coilin. Because coilin is not detected in the cytoplasm by immunofluorescence and Western blotting, it has been considered an exclusively nuclear protein. In theXenopus germinal vesicle (GV), most coilin actually resides in the nucleoplasm, although it is highly concentrated in 50–100 coiled bodies. When affinity-purified anti-coilin antibodies were injected into the cytoplasm of oocytes, they could be detected in coiled bodies within 2–3 h. Coiled bodies were intensely labeled after 18 h, whereas other nuclear organelles remained negative. Because the nuclear envelope does not allow passive diffusion of immunoglobulins, this observation suggests that anti-coilin antibodies are imported into the nucleus as an antigen–antibody complex with coilin. Newly synthesized coilin is not required, because cycloheximide had no effect on nuclear import and subsequent targeting of the antibodies. Additional experiments with myc-tagged coilin and myc-tagged pyruvate kinase confirmed that coilin is a shuttling protein. The shuttling of Nopp140, NO38/B23, and nucleolin was easily demonstrated by the targeting of their respective antibodies to the nucleoli, whereas anti-SC35 did not enter the germinal vesicle. We suggest that coilin, perhaps in association with Nopp140, may function as part of a transport system between the cytoplasm and the coiled bodies.
Polarized Sphingolipid Transport from the Subapical Compartment: Evidence for Distinct Sphingolipid Domains
Authors: van IJzendoorn Sven C. D. , Hoekstra Dick
Published: July 2013

In polarized HepG2 cells, the sphingolipids glucosylceramide and sphingomyelin (SM), transported along the reverse transcytotic pathway, are sorted in subapical compartments (SACs), and subsequently targeted to either apical or basolateral plasma membrane domains, respectively. In the present study, evidence is provided that demonstrates that these sphingolipids constitute separate membrane domains at the luminal side of the SAC membrane. Furthermore, as revealed by the use of various modulators of membrane trafficking, such as calmodulin antagonists and dibutyryl-cAMP, it is shown that the fate of these separate sphingolipid domains is regulated by different signals, including those that govern cell polarity development. Thus under conditions that stimulate apical plasma membrane biogenesis, SM is rerouted from a SAC-to-basolateral to a SAC-to-apical pathway. The latter pathway represents the final leg in the transcytotic pathway, followed by the transcytotic pIgR–dIgA protein complex. Interestingly, this pathway is clearly different from the apical recycling pathway followed by glucosylceramide, further indicating that randomization of these pathways, which are both bound for the apical membrane, does not occur. The consequence of the potential coexistence of separate sphingolipid domains within the same compartment in terms of “raft” formation and apical targeting is discussed.
Chimeric Cytokine Receptor Can Transduce Expansion Signals in Interleukin 6 Receptor α (IL-6Rα)-, IL-11Rα-, and gp130-low to -negative Primitive Hematopoietic Progenitors
Authors: Takagi Mineo , Nakamura Takanori , Sawada Toshie , Kaneko Azusa , Nozaki-Ukai Manabu , Nakahata Tatsutoshi , Yokota Takashi , Heike Toshio
Published: July 2013

We generated transgenic mice expressing chimeric receptors, which comprise extracellular domains of the human granulocyte–macrophage colony-stimulating factor (hGM-CSF) receptor and transmembrane and cytoplasmic domains of the mouse leukemia inhibitory factor receptor. In suspension cultures of lineage-negative (Lin−), 5-fluorouracil-resistant bone marrow cells of the transgenic mice, a combination of hGM-CSF and stem cell factor (SCF) induced exponential expansions of mixed colony-forming unit. The combination of hGM-CSF and SCF was effective on enriched, Lin−Sca-1+c-kit+progenitors and increased either mixed colony-forming unit or cobblestone area–forming cells. In case of stimulation with hGM-CSF and SCF, interleukin-6 (IL-6) and SCF, or IL-11 and SCF, the most efficient expansion was achieved with hGM-CSF and SCF. When Lin−Sca-1+c-kit+CD34−further enriched progenitors were clone sorted and individually incubated in the presence of SCF, hGM-CSF stimulated a larger number of cells than did IL-6, IL-6 and soluble IL-6 receptor (IL-6R), or IL-11. These data suggest the presence of IL-6Rα-, IL-11Rα-, and gp130-low to -negative primitive hematopoietic progenitors. Such primitive progenitors are equipped with signal transduction molecules and can expand when these chimeric receptors are genetically introduced into the cells and stimulated with hGM-CSF in the presence of SCF.