bluuebunny/crossref_metadata_2025 huggingface dataset:
Introduction
Authors: Neilson D , Das MP
Published: June 2013

The subjects for this workshop were nanostructures and quasi-two-dimensional systems. Artificial nanostructures have structure on the scale of nanometres (1O~9 m). The nanometre represents a limit on the miniaturisation of artificial structures since atomic diameters are of this scale. Two-dimensional systems are atomically thin layers, usually of electrons embedded in a semiconductor substrate. These fascinating systems owe their existence to the rapid advances within the last ten years in electronic device miniaturisation and manufacture. Spectacular as the technological advances have been, the focus of the workshop was not on these achievements themselves, but on the opportunities the technology provides to think up and build artificial systems having exotic physical properties that give us insight into structure on a quantum scale. Since the atomic scale is determined by the dictates of quantum mechanics it is not surprising that artificial structures on this scale should have properties which are dominated by quantum mechanical effects and strong correlations, and that these often generate novel ground states.
Plasmons on Wide Epitaxially-grown Quantum Wells
Authors: F Dobson John
Published: June 2013

Quantum wells can now be grown by molecular beam epitaxy in the Gal~xAlxAs system with almost any desired electron confinement potential V (z) in the growth or z direction. The wells can be filled by remote doping, giving finely controllable high-mobility electron gases with a dimensionality between two and three. Grating coupler techniques permit observation at finite surface wavenumber of the infrared plasmon modes of these structures. This provides in principle a window onto fundamental and applicable many-electron physics. Of special interest are the 'pseudo-jellium' properties of parabolic and parabolic~linear wells, which are discussed in detail here. A theorem applicable to more general wells is also introduced.
Optical Oscillator Strengths from 'Electron-impact Photoionisation' in the RCX Potential
Authors: Padma R , Deshmukh PC
Published: June 2013

Electron-impact collisions excite optically allowed as well as optically forbidden transitions. In this paper we report details of optical oscillator strengths calculated using the RCS potential. The oscillator strengths have been calculated using the small-momentum-transfer limit (K -+ 0) of the electron-impact generalised oscillator strength. Results for the Cooperminimum trajectories for some high-Z (82-90) atoms and for Kr 3p ionisation are reported. These have been found to be in fair agreement with results of previous calculations in which more involved techniques were used. The present results offer further support to the utility of the RCS potential in atomic physics by providing first estimates of some important atomic properties, using a relativistic atomic potential which is computationally not very demanding
Electronic Structure and Spin Fluctuations in the fcc Fe?Pd System
Authors: Mohn P , Supanetz E , Schwarz K
Published: June 2013

The electronic structure of the fcc Fe~Pd alloy system is investigated by band structure calculations employing the augmented spherical wave (ASW) method. The three compositions Fe3Pd, FePd and FePd3 are studied assuming the ordered CU3Au and the CuAu structure respectively. The total energy is computed as a function of volume and magnetic moment E(V, lvJ) by performing fixed spin moment (FSM) calculations for all three systems. The energy surface of Fe3Pd shows two minima, a ground state with an average magnetic moment of 2� Olj1.B/atom and a metastable minimum with a very small moment. The intermetallic compound FePd shows the usual behaviour of a strong itinerant ferromagnet with an average magnetic moment of 1� 56j1.B, where iron carries about 2� 8j1.B as for the high-spin state of pure fcc Fe. In FePd3 the iron states form rather localised bands and the magnetic moment rises to 3�2j1.B. Inclusion of spin fluctuations allows treatment of the finite-temperature behaviour of such systems. The magnetic contribution to the thermal expansion coefficient at room temperature for Fe3Pd is Qm::::; -18xlO~6 K~l, which largely compensates the positive phonon (Griineisen) part of Q.
A Heuristic Account of the Electron?Phonon Coupling Mechanism in the Formation of Pre-martensite Tweed Structures
Authors: Norman Peter
Published: June 2013

Electron-phonon coupling has been proposed by a number of researchers as the probable mechanism involved in martensitic transformations of many metals and alloys. This paper provides a plausible account of the way in which Kohn anomalies may give rise to tweed microstructure in pre-martensitic phases of fcc and bcc crystals.
Inequalities for Isothermal Linear Response
Authors: Stewart AM
Published: June 2013

The inequality that Brown, Hornreich and Shtrikman (1968) reported for the magneto-electric susceptibility is shown to be valid quite generally for all isothermal linear response coefficients. Certain difficulties in the derivation are removed.
Recollections of John G Bolton at Dover Heights and Caltech
Authors: J Stanley Gordon
Published: June 2013

Personal recollections are presented by the author of the commencement of galactic and extragalactic radio astronomy at Dover Heights and the design and construction of the California Institute of Technology's Owens Valley Interferometer.
Some Memories of the Dover Heights Field Station, 1946?1954
Authors: Slee Bruce
Published: June 2013

The author describes the first eight years of his astronomical career. His collaboration with John Bolton, Gordon Stanley, Kevin West fold and Dick McGee at the Dover Heights field station resulted in the detection and optical identification of the first radio sources outside the solar system. The first radio spectra, angular sizes and source variability measurements were made during this interval.
Some Memories of John Bolton from Caltech and Early Years at Parkes
Authors: Roberts JA
Published: June 2013

John Bolton had such an influence on radio astronomy that a major review of his contributions should be prepared by an historian of science. Here just some events from his last few years at the California Institute of Technology and from the first few years of the Parkes Telescope are recalled.
Accurate Optical Positions for Radio Source Identifications
Authors: W Hunstead Richard
Published: June 2013

The optical identification of strong radio sources was a key step in establishing a grid of southern hemisphere calibrators, both for Parkes and for Molonglo. However, the measurement of precise positions for these optical counterparts presented some special astrometric problems and led to some novel solutions. This paper summarises the progress of optical position measurement from a radio astronomer's viewpoint and examines the role of the COSMOS database against this background. The source 0007-44, from the first Parkes catalogue, is used as a case study to illustrate the present-day approach to optical identifications.
Estimation of Magnetic Field Strength from Enhanced Solar Radio Emission
Authors: Sarma SBSS
Published: June 2013

The manifestation of solar activity on radio noise records at 28.6 MHz is discussed with special emphasis on Type-I noise storms and the associated coronal magnetic fields above the active regions in time. Magnetic fields are estimated, assuming that the Type-I radio emission at decametre wavelengths is due to shock waves, by making use of the observed shock velocity. The results are comparable with the existing estimates.
Solar Flare Surges in relation to Active Prominences and Sunspots
Authors: Das TK , Chatterjee TN , Sen AK
Published: June 2013

A study has been made of flare surges (FS) after correlating them with prominences and sunspots. Results obtained are: (i) the duration of the 88% events lies between 0-40 min; (ii) in most cases the distance between FS and filaments ranges from 0�03 R0 to 0�12R0 whereas' that between FS and sunspots ranges from 0�05R0 to 0�25R0; (iii) there are several active regions which can produce sympathetic FS; and (iv) the number of FS from a particular sunspot group is proportional to the number of X-ray flares from the same active region.
Basic and Applied Research at NTT and Postgraduate Education
Authors: Kimura Tatsuya
Published: June 2013

Several current research topics, which are studied at NTT Basic Research Laboratories, are reviewed in the fields of semiconductor physics, quantum optics and biophysics. These topics include the surface structure transition of GaAs, InAs and Si, electron transport in low-dimensional structure, microcavity quantum-wire semiconductor lasers, quantum nondemolition measurement of fibre solitons, and artificial network development of cultivated neural cells.
Modeling and Measurement of Submicron Particles in RF Plasmas in Ar
Authors: Hosokauia Y , Kitajima T , Makabe T
Published: June 2013

The work is focused on the growth and transport of submicron particles in nonreactive radiofrequency plasma in Ar at 13�56 MHz, studied by numerical modeling using the relaxation continuum model, and by experiment using spatiotemporally resolved optical emission spectroscopy with Mie scattering. The particle growth/decay under conditions of the initially injected (CF2)n, and the related spatiotemporal change of the rf plasma structure, are discussed in terms of their numerical and experimental results. The results give suggestions with respect to the influence of particles in a dusty rf plasma system, such as dry etching and sputtering.
Analysis of the Coulomb-solidification Process in Particle Plasmas
Authors: Tachibana K , Hayashi Y
Published: June 2013

The Coulomb-solidification process is analysed using Mie-scattering ellipsometry with the assistance of photography and scanning electron microscopy. Spherical monodisperse carbon particles are observed to grow in a methane plasma. The Coulomb-coupling parameter at the liquid-to-solid phase transition is evaluated to be around 200, which is close to the value predicted by a Monte Carlo simulation. The growth of monodisperse particles of pss: size having the same charge favours the formation of a Coulomb solid.
Newtonian Quantum Gravity
Authors: Jones KRW
Published: June 2013

We develop a nonlinear quantum theory of Newtonian gravity consistent with an objective interpretation of the wavefunction. Inspired by the ideas of Schrodinger, and Bell, we seek a dimensional reduction procedure to map complex wavefunctions in configuration space onto a family of observable fields in space-time. Consideration of quasi-classical conservation laws selects the reduced one-body quantities as the basis for an explicit quasi-classical coarse-graining. These we interpret as describing the objective reality of the laboratory. Thereafter, we examine what may stand in the role of the usual Copenhagen observer to localise this quantity against macroscopic dispersion. Only a tiny change is needed, via a generically attractive self-potential. A nonlinear treatment of gravitational self-energy is thus advanced. This term sets a scale for all wavepackets. The Newtonian cosmology is thus closed, without need of an external observer. Finally, the concept of quantisation is re-interpreted as a nonlinear eigenvalue problem. To illustrate, we exhibit an elementary family of gravitationally self-bound solitary waves. Contrasting this theory with its canonically quantised analogue, we find that the given interpretation is empirically distinguishable, in principle. This result encourages deeper study of nonlinear field theories as a testable alternative to canonically quantised gravity.
Summation of the Dominating Diagrams in Many-body Perturbation Theory
Authors: Dzuba VA , Flambaum VV , King WA
Published: June 2013

In this paper we present a description of an approach within many-body perturbation theory, which takes into account the infinite series of diagrams that describe screening and the interaction between the excited-core electron and the hole. We also present an extension to this theory that allows us to describe the interaction of a positron with an atom. To do this the infinite series of diagrams that describes virtual positronium formation is taken into account. Some results of these calculations are presented.
Electronic Structure Information from Electron Impact Ionisation Experiments
Authors: Coplan MA , Doering JP , Madison DH , Moore JH , Pinkás AA
Published: June 2013

Electron impact ionisation with full determination of the kinematics (measurement of energies and momenta of the incident, scattered and ejected electrons) has proven to be useful for investigating both the electronic structure of atoms and molecules and the mechanism of ionisation. These experiments are, by definition, coincidence experiments since it is necessary to be sure that all the detected electrons originate from the same collision. For single-electron ionisation, (e, 2e), the emphasis has been on momentum densities and spectroscopic factors–see for example Coplan et al. (1994), McCarthy and Weigold (1976, 1988, 1991) and Leung (1991). For double ionisation, (e,3e), data are just beginning to emerge, with early results on the Auger process and direct double ionisation (Duguet and Lahmam-Bennani 1992). Both (e, 2e) and (e, 3e) experiments are technically challenging because the signals are small and there is usually a large background. In the last few years, electrostatic spectrographs and position sensitive detectors have improved the resolution and precision of (e, 2e) measurements and have made (e,3e) measurements a practical reality.
Laser Focusing of Atoms for Nanostructure Fabrication
Authors: McClelland JJ , Gupta R , Jabbour ZJ , Celotta RJ
Published: June 2013

Laser focusing of atoms has emerged as a viable form of nanofabrication. Structures are formed by focusing chromium atoms as they deposit onto a surface. The focusing occurs in a standing-wave laser field in one or two dimensions, resulting in arrays spaced at exactly half the laser wavelength (λ/2 = 212�78 nm). Atomic force, scanning electron, and transmission electron microscopies are used to view the fabricated structures. Improvements in the technique, including narrowing of the linewidth and extension to two dimensions are discussed. Theoretical predictions for the shape of the deposited structures are also discussed.
Brans - Dicke Cosmology with Causal Viscous Fluid
Authors: Banerjee N , Beesham A
Published: June 2013

Exact solutions for the spatially flat (k = 0) Robertson–Walker cosmological model in Brans–Dicke scalar tensor theory have been obtained in the presence of a causal viscous fluid. It is found that if the scale factor is a power function of the scalar field, then solutions can be obtained in the full causal theory but not in the truncated theory of non-equilibrium thermodynamics.
Forward-walking Green's Function Monte Carlo Method for Correlation Functions
Authors: Samaras M. , Hamer C. J.
Published: June 2013

The forward-walking Green's Function Monte Carlo method is used to
compute expectation values for the transverse Ising model in (1 +
1)D, and the results are compared with exact values. The
magnetisation Mz and the
correlation function p z
(n) are computed. The algorithm reproduces the exact
results, and convergence for the correlation functions seems almost as rapid
as for local observables such as the magnetisation. The results are found to
be sensitive to the trial wavefunction, however, especially at the critical
point.
Spin-wave Gap Critical Index for the Quantum Two-layer Heisenberg Antiferromagnet at T = 0
Authors: Shevchenko P. V. , Sushkov O. P.
Published: June 2013

The two-layer Heisenberg antiferromagnet exhibits a zero temperature quantum
phase transition from a disordered dimer phase to a collinear Neel phase, with
long range order in the ground state. The spin-wave gap vanishes as Δ
∝ (J ⊥ – J ⊥
c) ν approaching the transition point. To account
for strong correlations, the S = 1 elementary
excitations triplets are described as a dilute Bose gas with infinite on-site
repulsion. We apply the Brueckner diagram approach which gives the critical
index ν ≈ 0 . 5. We demonstrate also that the linearised in
density Brueckner equations give the mean field result ν = 1.
Finally, an expansion of the Brueckner equations in powers of the density,
combined with the scaling hypothesis, gives ν ≈ 0 . 67. This value
agrees reasonably with that of the nonlinear O(3) σ model. Our approach
demonstrates that for other quantum spin models the critical index can be
different from that in the nonlinear σ model. We discuss the conditions
for this to occur.
Time-dependent Approach to Positron - Hydrogen Scattering
Authors: Wang J. B. , Riste N. , Midgley S. , Stelbovics A. T. , Williams J. F.
Published: June 2013

This paper examines the positron–hydrogen scattering process by
numerically solving the time-dependent Schrödinger equation in the s-wave
model. The overall behaviour of the system wavefunction as it propagates
through the collision region is studied above the positronium formation
threshold and is found to match expectations qualitatively.
Monte Carlo Transport Simulation Techniques for Stellarator Fusion Experiments
Authors: Dettrick S. A. , Gardner H. J. , Painter S. L.
Published: June 2013

We describe an implementation of a particle orbit-following simulation
approach to the Monte Carlo calculation of neoclassical transport coecients
which has been developed for application to the H-1NF Heliac. We compare and
contrast some Monte Carlo transport coecient estimators that can be used in
such computer codes, from both physical and computational perspectives, and we
make recommendations for their use. Transport coecient calculations are
performed for the H-1NF in conditions that will be available after the full
National Facility upgrade.
Towards a Direct Numerical Solution of Schrödinger’s Equation for (e, 2e) Reactions
Authors: Jones S. , Stelbovics A. T.
Published: June 2013

The finite-difference method for electron{hydrogen scattering is
presented in a simple, easily understood form for a model collision problem in
which all angular momentum is neglected. The model Schrödinger equation
is integrated outwards from the atomic centre on a grid of fixed spacing
h. The number of difference equations is reduced each
step outwards using an algorithm due to Poet, resulting in a propagating
solution of the partial-differential equation. By imposing correct asymptotic
boundary conditions on this general, propagating solution, the particular
solution that physically corresponds to scattering is obtained along with the
scattering amplitudes. Previous works using finite differences (and finite
elements) have extracted scattering amplitudes only for low-level transitions
(elastic scattering and n = 2 excitation). If we
are to eventually extract ionisation amplitudes, however, the numerical method
must remain stable for higher-level transitions. Here we report converged
cross sections for transitions up to n = 8, as a
first step towards obtaining ionisation (e;
2e) results.
Spin-polarised Electron Studies of Low-dimensional Magnetic Systems
Authors: Donath Markus
Published: June 2013

Spin-polarised electrons provide unique experimental access to magnetic
properties of surfaces and layered structures. The combined use of different
techniques allows us to develop a microscopic picture of the physics
underlying the macroscopic magnetic properties, e.g. magnetic phase
transitions, magnetic coupling phenomena, exceptional surface magnetic
properties. In this paper, two techniques are described together with the kind
of questions addressed by them. Spin-resolved appearance potential
spectroscopy gives local magnetic information about multi-component systems by
probing the spin-dependent local density of unoccupied states. Spin-resolved
inverse photo-emission measures specific electron states above the Fermi
level. In particular, two-dimensional states serve as magnetic sensors at
surfaces. Examples from surfaces as well as thin-film structures of band and
local-moment ferromagnets are presented.
Excitation of Heavy Metal Clusters by Strong fs Laser Pulses
Authors: Teuber S. , Döppner T. , Schumacher M. , Tiggesbäumker J. , Meiwes-Broer K. H.
Published: June 2013

The excitation of neutral platinum and lead clusters by intense femtosecond
laser pulses is studied by time-of-flight spectroscopy. Clusters are
completely destroyed when interacting in the high intensity region of the
laser focus. Moreover, highly charged atomic ions with up to 20 charges are
detected under special pulse conditions. The atomic ion distribution shows a
pronounced dependence on the chosen pulse width, suggesting that multi-plasmon
excitations are responsible for the high charge states measured. The Coulomb
explosion of a metal sphere is simulated under tunneling ionisation
conditions. The calculated optical response of such a cluster within the
framework of the random phase approximation agrees well with the experimental
observations.
Continuous Localisation - Delocalisation Transition at Intermediate Electron Densities
Authors: Neilson D. , Thakur J. S.
Published: June 2013

We find in 2D electron layers in quantum transistors that the interplay
between the electron correlations and their interactions with defects in the
semiconductor substrate generates a continuous
localisation–delocalisation transition for intermediate electron
densities (5 ≲ rs ≲ 9).
We distinguish this transition from the discontinuous metal–insulator
transition which is observed at lower electron densities
(rs ≳ 10). The approach we
use is based on the behaviour of electrons at low densities. We take into
account the interactions between electrons and also their interactions with
disorder. We determine a zero temperature phase diagram of localised and
delocalised states as a function of electron and impurity densities. The phase
boundary of the continuous transition is determined by the localisation length
of the electrons.
Hydrogels that mimic developmentally relevant matrix and N-cadherin interactions enhance MSC chondrogenesis
Authors: Bian Liming , Guvendiren Murat , Mauck Robert L. , Burdick Jason A.
Published: June 2013

Methacrylated hyaluronic acid (HA) hydrogels provide a backbone polymer with which mesenchymal stem cells (MSCs) can interact through several cell surface receptors that are expressed by MSCs, including CD44 and CD168. Previous studies showed that this 3D hydrogel environment supports the chondrogenesis of MSCs, and here we demonstrate through functional blockade that these specific cell–material interactions play a role in this process. Beyond matrix interactions, cadherin molecules, a family of transmembrane glycoproteins, play a critical role in tissue development during embryogenesis, and N-cadherin is a key factor in mediating cell–cell interactions during mesenchymal condensation and chondrogenesis. In this study, we functionalized HA hydrogels with N-cadherin mimetic peptides and evaluated their role in regulating chondrogenesis and cartilage matrix deposition by encapsulated MSCs. Our results show that conjugation of cadherin peptides onto HA hydrogels promotes both early chondrogenesis of MSCs and cartilage-specific matrix production with culture, compared with unmodified controls or those with inclusion of a scrambled peptide domain. This enhanced chondrogenesis was abolished via treatment with N-cadherin–specific antibodies, confirming the contribution of these N-cadherin peptides to chondrogenesis. Subcutaneous implantation of MSC-seeded constructs also showed superior neocartilage formation in implants functionalized with N-cadherin mimetic peptides compared with controls. This study demonstrates the inherent biologic activity of HA-based hydrogels, as well as the promise of biofunctionalizing HA hydrogels to emulate the complexity of the natural cell microenvironment during embryogenesis, particularly in stem cell-based cartilage regeneration.
Influence of sulfate reduction rates on the Phanerozoic sulfur isotope record
Authors: Leavitt William D. , Halevy Itay , Bradley Alexander S. , Johnston David T.
Published: June 2013

Phanerozoic levels of atmospheric oxygen relate to the burial histories of organic carbon and pyrite sulfur. The sulfur cycle remains poorly constrained, however, leading to concomitant uncertainties in O
2
budgets. Here we present experiments linking the magnitude of fractionations of the multiple sulfur isotopes to the rate of microbial sulfate reduction. The data demonstrate that such fractionations are controlled by the availability of electron donor (organic matter), rather than by the concentration of electron acceptor (sulfate), an environmental constraint that varies among sedimentary burial environments. By coupling these results with a sediment biogeochemical model of pyrite burial, we find a strong relationship between observed sulfur isotope fractionations over the last 200 Ma and the areal extent of shallow seafloor environments. We interpret this as a global dependency of the rate of microbial sulfate reduction on the availability of organic-rich sea-floor settings. However, fractionation during the early/mid-Paleozoic fails to correlate with shelf area. We suggest that this decoupling reflects a shallower paleoredox boundary, primarily confined to the water column in the early Phanerozoic. The transition between these two states begins during the Carboniferous and concludes approximately around the Triassic–Jurassic boundary, indicating a prolonged response to a Carboniferous rise in O
2
. Together, these results lay the foundation for decoupling changes in sulfate reduction rates from the global average record of pyrite burial, highlighting how the local nature of sedimentary processes affects global records. This distinction greatly refines our understanding of the S cycle and its relationship to the history of atmospheric oxygen.
Iron traps terrestrially derived dissolved organic matter at redox interfaces
Authors: Riedel Thomas , Zak Dominik , Biester Harald , Dittmar Thorsten
Published: June 2013

Reactive iron and organic carbon are intimately associated in soils and sediments. However, to date, the organic compounds involved are uncharacterized on the molecular level. At redox interfaces in peatlands, where the biogeochemical cycles of iron and dissolved organic matter (DOM) are coupled, this issue can readily be studied. We found that precipitation of iron hydroxides at the oxic surface layer of two rewetted fens removed a large fraction of DOM via coagulation. On aeration of anoxic fen pore waters, >90% of dissolved iron and 27 ± 7% (mean ± SD) of dissolved organic carbon were rapidly (within 24 h) removed. Using ultra-high-resolution MS, we show that vascular plant-derived aromatic and pyrogenic compounds were preferentially retained, whereas the majority of carboxyl-rich aliphatic acids remained in solution. We propose that redox interfaces, which are ubiquitous in marine and terrestrial settings, are selective yet intermediate barriers that limit the flux of land-derived DOM to oceanic waters.
Marital satisfaction and break-ups differ across on-line and off-line meeting venues
Authors: Cacioppo John T. , Cacioppo Stephanie , Gonzaga Gian C. , Ogburn Elizabeth L. , VanderWeele Tyler J.
Published: June 2013

Marital discord is costly to children, families, and communities. The advent of the Internet, social networking, and on-line dating has affected how people meet future spouses, but little is known about the prevalence or outcomes of these marriages or the demographics of those involved. We addressed these questions in a nationally representative sample of 19,131 respondents who married between 2005 and 2012. Results indicate that more than one-third of marriages in America now begin on-line. In addition, marriages that began on-line, when compared with those that began through traditional off-line venues, were slightly less likely to result in a marital break-up (separation or divorce) and were associated with slightly higher marital satisfaction among those respondents who remained married. Demographic differences were identified between respondents who met their spouse through on-line vs. traditional off-line venues, but the findings for marital break-up and marital satisfaction remained significant after statistically controlling for these differences. These data suggest that the Internet may be altering the dynamics and outcomes of marriage itself.
Peripheral elevation of TNF-α leads to early synaptic abnormalities in the mouse somatosensory cortex in experimental autoimmune encephalomyelitis
Authors: Yang Guang , Parkhurst Christopher N. , Hayes Scott , Gan Wen-Biao
Published: June 2013

Sensory abnormalities such as numbness and paresthesias are often the earliest symptoms in neuroinflammatory diseases including multiple sclerosis. The increased production of various cytokines occurs in the early stages of neuroinflammation and could have detrimental effects on the central nervous system, thereby contributing to sensory and cognitive deficits. However, it remains unknown whether and when elevation of cytokines causes changes in brain structure and function under inflammatory conditions. To address this question, we used a mouse model for experimental autoimmune encephalomyelitis (EAE) to examine the effect of inflammation and cytokine elevation on synaptic connections in the primary somatosensory cortex. Using in vivo two-photon microscopy, we found that the elimination and formation rates of dendritic spines and axonal boutons increased within 7 d of EAE induction—several days before the onset of paralysis—and continued to rise during the course of the disease. This synaptic instability occurred before T-cell infiltration and microglial activation in the central nervous system and was in conjunction with peripheral, but not central, production of TNF-α. Peripheral administration of a soluble TNF inhibitor prevented abnormal turnover of dendritic spines and axonal boutons in presymptomatic EAE mice. These findings indicate that peripheral production of TNF-α is a key mediator of synaptic instability in the primary somatosensory cortex and may contribute to sensory and cognitive deficits seen in autoimmune diseases.
Arabidopsis
μ-adaptin subunit AP1M of adaptor protein complex 1 mediates late secretory and vacuolar traffic and is required for growth
Authors: Park Misoon , Song Kyungyoung , Reichardt Ilka , Kim Hyeran , Mayer Ulrike , Stierhof York-Dieter , Hwang Inhwan , Jürgens Gerd
Published: June 2013

Adaptor protein (AP) complexes are the predominant coat proteins of membrane vesicles in post-Golgi trafficking of mammalian cells. Each AP complex contains a specific medium subunit, μ-adaptin, that selects cargo proteins bearing sequence-specific sorting motifs. Much less is known about the AP complexes and their μ subunits in plants. Because of uncertain homology, the μ-adaptins of
Arabidopsis
have been designated muA through muD [Happel et al. (2004)
Plant J
37(5):678–693]. Furthermore, only muD has been assigned to a specific AP complex, AP-3, involved in Golgi-vacuolar trafficking [Niihama et al. (2009)
Plant Cell Physiol
50(12):2057–2068, Zwiewka et al. (2011)
Cell Res
21(12):1711–1722, and Wolfenstetter et al. (2012)
Plant Cell
24(1):215–232]. In contrast, the μ subunit of neither the post-Golgi trafficking AP-1 complex nor the endocytic AP-2 complex has been identified. Here, we report the functional analysis of redundant AP-1 μ-adaptins AP1M1 (also known as muB1) and AP1M2 (also known as muB2). Coimmunoprecipitation revealed that both AP1M2 and its less strongly expressed isoform AP1M1 are complexed with the large subunit γ-adaptin of AP-1. In addition, AP1M2 was localized at or near the
trans
-Golgi network. Knockout mutations of AP1M2 impaired pollen function and arrested plant growth whereas the
ap1m1 ap1m2
double mutant was nearly pollen-lethal. At the cellular level, the absence of AP1M2 entailed inhibition of multiple trafficking pathways from the
trans
-Golgi network to the vacuole and to the plasma membrane in interphase and to the plane of cell division in cytokinesis. Thus, AP-1 is crucial in post-Golgi trafficking in plant cells and required for cell division and plant growth.
Kinetics of gene derepression by ERK signaling
Authors: Lim Bomyi , Samper Núria , Lu Hang , Rushlow Christine , Jiménez Gerardo , Shvartsman Stanislav Y.
Published: June 2013

ERK controls gene expression in development, but mechanisms that link ERK activation to changes in transcription are not well understood. We used high-resolution analysis of signaling dynamics to study transcriptional interpretation of ERK signaling during
Drosophila
embryogenesis, at a stage when ERK induces transcription of
intermediate neuroblasts defective
(
ind
), a gene essential for patterning of the nerve cord. ERK induces
ind
by antagonizing its repression by Capicua (Cic), a transcription factor that acts as a sensor of receptor tyrosine kinases in animal development and human diseases. A recent study established that active ERK reduces the nuclear levels of Cic, but it remained unclear whether this is required for the induction of Cic target genes. We provide evidence that Cic binding sites within the regulatory DNA of
ind
control the spatial extent and the timing of
ind
expression. At the same time, we demonstrate that ERK induces
ind
before Cic levels in the nucleus are reduced. Based on this, we propose that ERK-dependent relief of gene repression by Cic is a two-step process, in which fast reduction of repressor activity is followed by slower changes in nuclear localization and overall protein levels. This may be a common feature of systems in which ERK induces genes by relief of transcriptional repression.
Neisseria gonorrhoeae-derived heptose elicits an innate immune response and drives HIV-1 expression
Authors: Malott Rebecca J. , Keller Bernd O. , Gaudet Ryan G. , McCaw Shannon E. , Lai Christine C. L. , Dobson-Belaire Wendy N. , Hobbs J. Leigh , St. Michael Frank , Cox Andrew D. , Moraes Trevor F. , Gray-Owen Scott D.
Published: June 2013

Clinical and epidemiological synergy exists between the globally important sexually transmitted infections, gonorrhea and HIV.Neisseria gonorrhoeae,which causes gonorrhea, is particularly adept at driving HIV-1 expression, but the molecular determinants of this relationship remain undefined.N. gonorrhoeaeliberates a soluble factor that potently induces expression from the HIV-1 LTR in coinfected cluster of differentiation 4-positive (CD4+) T lymphocytes, but this factor is not a previously described innate effector. A genome-wide mutagenesis approach was undertaken to reveal which component(s) ofN. gonorrhoeaeinduce HIV-1 expression in CD4+T lymphocytes. A mutation in the ADP-heptose biosynthesis gene,hldA,rendered the bacteria unable to induce HIV-1 expression. ThehldAmutant has a truncated lipooligosaccharide structure, contains lipid A in its outer membrane, and remains bioactive in a TLR4 reporter-based assay but did not induce HIV-1 expression. Mass spectrometry analysis of extensively fractionatedN. gonorrhoeae-derived supernatants revealed that the LTR-inducing fraction contained a compound having a mass consistent with heptose-monophosphate (HMP). Heptose is a carbohydrate common in microbes but is absent from the mammalian glycome. Although ADP-heptose biosynthesis is common among Gram-negative bacteria, and heptose is a core component of most lipopolysaccharides,N. gonorrhoeaeis peculiar in that it effectively liberates HMP during growth. ThisN. gonorrhoeae-derived HMP activates CD4+T cells to invoke an NF-κB–dependent transcriptional response that drives HIV-1 expression and viral production. Our study thereby shows that heptose is a microbial-specific product that is sensed as an innate immune agonist and unveils the molecular link betweenN. gonorrhoeaeand HIV-1.
Evidence for reactive reduced phosphorus species in the early Archean ocean
Authors: Pasek Matthew A. , Harnmeijer Jelte P. , Buick Roger , Gull Maheen , Atlas Zachary
Published: June 2013

It has been hypothesized that before the emergence of modern DNA–RNA–protein life, biology evolved from an “RNA world.” However, synthesizing RNA and other organophosphates under plausible early Earth conditions has proved difficult, with the incorporation of phosphorus (P) causing a particular problem because phosphate, where most environmental P resides, is relatively insoluble and unreactive. Recently, it has been proposed that during the Hadean–Archean heavy bombardment by extraterrestrial impactors, meteorites would have provided reactive P in the form of the iron–nickel phosphide mineral schreibersite. This reacts in water, releasing soluble and reactive reduced P species, such as phosphite, that could then be readily incorporated into prebiotic molecules. Here, we report the occurrence of phosphite in early Archean marine carbonates at levels indicating that this was an abundant dissolved species in the ocean before 3.5 Ga. Additionally, we show that schreibersite readily reacts with an aqueous solution of glycerol to generate phosphite and the membrane biomolecule glycerol–phosphate under mild thermal conditions, with this synthesis using a mineral source of P. Phosphite derived from schreibersite was, hence, a plausible reagent in the prebiotic synthesis of phosphorylated biomolecules and was also present on the early Earth in quantities large enough to have affected the redox state of P in the ocean. Phosphorylated biomolecules like RNA may, thus, have first formed from the reaction of reduced P species with the prebiotic organic milieu on the early Earth.
Structure and function of an insect α-carboxylesterase (αEsterase7) associated with insecticide resistance
Authors: Jackson Colin J. , Liu Jian-Wei , Carr Paul D. , Younus Faisal , Coppin Chris , Meirelles Tamara , Lethier Mathilde , Pandey Gunjan , Ollis David L. , Russell Robyn J. , Weik Martin , Oakeshott John G.
Published: June 2013

Insect carboxylesterases from the αEsterasegene cluster, such as αE7 (also known as E3) from the Australian sheep blowflyLucilia cuprina(LcαE7), play an important physiological role in lipid metabolism and are implicated in the detoxification of organophosphate (OP) insecticides. Despite the importance of OPs to agriculture and the spread of insect-borne diseases, the molecular basis for the ability of α-carboxylesterases to confer OP resistance to insects is poorly understood. In this work, we used laboratory evolution to increase the thermal stability ofLcαE7, allowing its overexpression inEscherichia coliand structure determination. The crystal structure reveals a canonical α/β-hydrolase fold that is very similar to the primary target of OPs (acetylcholinesterase) and a unique N-terminal α-helix that serves as a membrane anchor. Soaking ofLcαE7 crystals in OPs led to the capture of a crystallographic snapshot ofLcαE7 in its phosphorylated state, which allowed comparison with acetylcholinesterase and rationalization of its ability to protect insects against the effects of OPs. Finally, inspection of the active site ofLcαE7 reveals an asymmetric and hydrophobic substrate binding cavity that is well-suited to fatty acid methyl esters, which are hydrolyzed by the enzyme with specificity constants (∼106M−1s−1) indicative of a natural substrate.
Genome-wide RNAi screen reveals a role for the ESCRT complex in rotavirus cell entry
Authors: Silva-Ayala Daniela , López Tomás , Gutiérrez Michelle , Perrimon Norbert , López Susana , Arias Carlos F.
Published: June 2013

Rotavirus (RV) is the major cause of childhood gastroenteritis worldwide. This study presents a functional genome-scale analysis of cellular proteins and pathways relevant for RV infection using RNAi. Among the 522 proteins selected in the screen for their ability to affect viral infectivity, an enriched group that participates in endocytic processes was identified. Within these proteins, subunits of the vacuolar ATPase, small GTPases, actinin 4, and, of special interest, components of the endosomal sorting complex required for transport (ESCRT) machinery were found. Here we provide evidence for a role of the ESCRT complex in the entry of simian and human RV strains in both monkey and human epithelial cells. In addition, the ESCRT-associated ATPase VPS4A and phospholipid lysobisphosphatidic acid, both crucial for the formation of intralumenal vesicles in multivesicular bodies, were also found to be required for cell entry. Interestingly, it seems that regardless of the molecules that rhesus RV and human RV strains use for cell-surface attachment and the distinct endocytic pathway used, all these viruses converge in early endosomes and use multivesicular bodies for cell entry. Furthermore, the small GTPases RHOA and CDC42, which regulate different types of clathrin-independent endocytosis, as well as early endosomal antigen 1 (EEA1), were found to be involved in this process. This work reports the direct involvement of the ESCRT machinery in the life cycle of a nonenveloped virus and highlights the complex mechanism that these viruses use to enter cells. It also illustrates the efficiency of high-throughput RNAi screenings as genetic tools for comprehensively studying the interaction between viruses and their host cells.
Gene flow from North Africa contributes to differential human genetic diversity in southern Europe
Authors: Botigué Laura R. , Henn Brenna M. , Gravel Simon , Maples Brian K. , Gignoux Christopher R. , Corona Erik , Atzmon Gil , Burns Edward , Ostrer Harry , Flores Carlos , Bertranpetit Jaume , Comas David , Bustamante Carlos D.
Published: June 2013

Human genetic diversity in southern Europe is higher than in other regions of the continent. This difference has been attributed to postglacial expansions, the demic diffusion of agriculture from the Near East, and gene flow from Africa. Using SNP data from 2,099 individuals in 43 populations, we show that estimates of recent shared ancestry between Europe and Africa are substantially increased when gene flow from North Africans, rather than Sub-Saharan Africans, is considered. The gradient of North African ancestry accounts for previous observations of low levels of sharing with Sub-Saharan Africa and is independent of recent gene flow from the Near East. The source of genetic diversity in southern Europe has important biomedical implications; we find that most disease risk alleles from genome-wide association studies follow expected patterns of divergence between Europe and North Africa, with the principal exception of multiple sclerosis.
Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans
Authors: Liu C. Tony , Hanoian Philip , French Jarrod B. , Pringle Thomas H. , Hammes-Schiffer Sharon , Benkovic Stephen J.
Published: June 2013

With the rapidly growing wealth of genomic data, experimental inquiries on the functional significance of important divergence sites in protein evolution are becoming more accessible. Here we trace the evolution of dihydrofolate reductase (DHFR) and identify multiple key divergence sites among 233 species between humans and bacteria. We connect these sites, experimentally and computationally, to changes in the enzyme’s binding properties and catalytic efficiency. One of the identified evolutionarily important sites is the N23PP modification (∼mid-Devonian, 415–385 Mya), which alters the conformational states of the active site loop in
Escherichia coli
dihydrofolate reductase and negatively impacts catalysis. This enzyme activity was restored with the inclusion of an evolutionarily significant lid domain (G51PEKN in
E. coli
enzyme; ∼2.4 Gya). Guided by this evolutionary genomic analysis, we generated a human-like
E. coli
dihydrofolate reductase variant through three simple mutations despite only 26% sequence identity between native human and
E. coli
DHFRs. Molecular dynamics simulations indicate that the overall conformational motions of the protein within a common scaffold are retained throughout evolution, although subtle changes to the equilibrium conformational sampling altered the free energy barrier of the enzymatic reaction in some cases. The data presented here provide a glimpse into the evolutionary trajectory of functional DHFR through its protein sequence space that lead to the diverged binding and catalytic properties of the
E. coli
and human enzymes.
Negative expansions of interatomic distances in metallic melts
Authors: Lou Hongbo , Wang Xiaodong , Cao Qingping , Zhang Dongxian , Zhang Jing , Hu Tiandou , Mao Ho-kwang , Jiang Jian-Zhong
Published: June 2013

When a material is heated, generally, it dilates. Here, we find a general trend that the average distance between a center atom and atoms in the first nearest-neighbor shell contracts for several metallic melts upon heating. Using synchrotron X-ray diffraction technique and molecular dynamics simulations, we elucidate that this anomaly is caused by the redistribution of polyhedral clusters affected by temperature. In metallic melts, the high-coordinated polyhedra are inclined to evolve into low-coordinated ones with increasing temperature. As the coordination number decreases, the average atomic distance between a center atom and atoms in the first shell of polyhedral clusters is reduced. This phenomenon is a ubiquitous feature for metallic melts consisting of various-sized polyhedra. This finding sheds light on the understanding of atomic structures and thermal behavior of disordered materials and will trigger more experimental and theoretical studies of liquids, amorphous alloys, glasses, and casting temperature effect on solidification process of crystalline materials.
The DMAP interaction domain of UDP-GlcNAc:lysosomal enzyme
N
-acetylglucosamine-1-phosphotransferase is a substrate recognition module
Authors: Qian Yi , Flanagan-Steet Heather , van Meel Eline , Steet Richard , Kornfeld Stuart A.
Published: June 2013

UDP-GlcNAc:lysosomal enzyme
N
-acetylglucosamine-1-phosphotransferase (GlcNAc-1-phosphotransferase) is an α
2
β
2
γ
2
heterohexamer that mediates the initial step in the formation of the mannose 6-phosphate recognition signal on lysosomal acid hydrolases. We previously reported that the specificity of the reaction is determined by the ability of the α/β subunits to recognize a conformation-dependent protein determinant present on the acid hydrolases. We now present evidence that the DNA methyltransferase-associated protein (DMAP) interaction domain of the α subunit functions in this recognition process. First, GST-DMAP pulled down several acid hydrolases, but not nonlysosomal glycoproteins. Second, recombinant GlcNAc-1-phosphotransferase containing a missense mutation in the DMAP interaction domain (Lys732Asn) identified in a patient with mucolipidosis II exhibited full activity toward the simple sugar α-methyl
d
-mannoside but impaired phosphorylation of acid hydrolases. Finally, unlike the WT enzyme, expression of the K732N mutant in a zebrafish model of mucolipidosis II failed to correct the phenotypic abnormalities. These results indicate that the DMAP interaction domain of the α subunit functions in the selective recognition of acid hydrolase substrates and provides an explanation for the impaired phosphorylation of acid hydrolases in a patient with mucolipidosis II.