bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical properties of p-GaSe single crystals doped with Te
Authors: Evtodiev I. , Leontie L. , Caraman M. , Stamate M. , Arama E.
Published: January 2009

Optical absorption in the region of fundamental absorption edge and photoluminescence (at 78 and 293 K) of p-GaSe crystals doped with Te (0.05, 0.10, and 0.05 at. %) have been studied. At low concentrations (0.05 at. %), Te atoms liquidate structural defects in GaSe single crystals and modify their excitonic absorption and photoluminescence. For increased concentrations of 0.10 and 0.50 at. %, Te creates impurity states responsible for the red shift of the fundamental absorption edge of GaSe and appearance of new photoluminescence bands, B (at 2.000 eV) and C (at 1.700 eV). The activation energies of the thermal quenching of Te-related PL bands B and C was found to be 28 and 32 meV (for T<150 K) and 84 and 62 meV (for T>150 K), respectively.
Theoretical investigation of the direct observation of anharmonic coupling in CDCl3 in the time domain with femtosecond stimulated Raman scattering
Authors: Sun Zhigang , Fu Bina , Zhang Dong H. , Lee Soo-Y.
Published: January 2009

The femtosecond stimulated Raman scattering (FSRS) difference spectra of CDCl3 from the ground potential energy surface, with and without off-resonance impulsive stimulated Raman pumping, taken at various delay times from the impulsive pump by Kukura et al. [Phys. Rev. Lett. 96, 238303 (2006)], showed sidebands of the C–Cl bends with periodic changes in phase as well as having an inversion symmetry to the high and low frequency sides of the Stokes C–D stretch at 2255 cm−1. The semiclassical coupled-wave approach and a one-dimensional (1D) oscillator model for the C–D stretch whose frequency is modulated in time by the C–Cl bends could account for some features of the experimental results. Here, a quantum mechanical investigation is made of the FSRS difference spectra with a modulated 1D oscillator and three-dimensional (3D) harmonic and anharmonic potentials. It is shown that (i) the sidebands are allowed, with or without anharmonic coupling between the C–D stretch and the C–Cl bends, (ii) in the 3D harmonic model the sidebands have mirror symmetry about the Stokes C–D stretch, (iii) in the 3D anharmonic model with appropriate coupling terms between the C–D stretch and the C–Cl bends, the experimental results are well accounted for in both the phase changes in the FSRS difference spectra with time delay as well as the inversion symmetry of the sidebands for the C–Cl bends about the Stokes C–D stretch, (iv) there is a correspondence between the phase changes in the FSRS difference spectra and the wavepacket motion induced by the impulsive pump pulse on the ground potential energy surface as a function of the delay time, and (v) changing the polarization of the impulsive pump pulse, say, directly affects the coordinate dependence of the linear transition dipole moment in the asymmetric mode and hence its phase in the FSRS difference spectra, but not so for the symmetric modes where the displacement of the excited state surface governs the FSRS difference spectra more than the transition dipole moment. This work illustrates the potential of off-resonance FSRS in studying polyatomic molecular dynamics.
A note on optimal transient growth in turbulent channel flows
Authors: Pujals Gregory , García-Villalba Manuel , Cossu Carlo , Depardon Sebastien
Published: January 2009

We compute the optimal transient growth of perturbations sustained by a turbulent channel flow following the same approach recently used by del Álamo and Jiménez [J. Fluid Mech. 559, 205 (2006)]. Contrary to this previous analysis, we use generalized Orr–Sommerfeld and Squire operators consistent with previous investigations of mean flows with variable viscosity. The optimal perturbations are streamwise vortices evolving into streamwise streaks. In accordance with del Álamo and Jiménez, it is found that for very elongated structures and for sufficiently large Reynolds numbers, the optimal energy growth presents a primary peak in the spanwise wavelength, scaling in outer units, and a secondary peak scaling in inner units and corresponding to λz+≈100. Contrary to the previous results, however, it is found that the maximum energy growth associated with the primary peak increases with the Reynolds number. This growth, in a first approximation, scales linearly with an effective Reynolds number based on the centerline velocity, the channel half width and the maximum eddy viscosity associated. The optimal streaks associated with the primary peak have an optimal spacing of λz=4h and scale in outer units in the outer region and in wall units in the near wall region, where they still have up to 50% of their maximum amplitude near y+=10.
Reading molecular messages from high-order harmonic spectra at different orientation angles
Authors: Chen Y. J. , Liu J. , Hu Bambi
Published: January 2009

We investigate the orientation dependence of high-order harmonic generation (HHG) from H2+ with different internuclear distances irradiated by intense laser fields both numerically and analytically. The calculated molecular HHG spectra are found to be sensitive to the molecular axis orientation relative to incident laser field polarization and internuclear separation. In particular, our simulations demonstrate that at certain harmonic orders the envelopes of the HHG spectra taken at different orientation angles intersect. Moreover, the position of intersection is largely independent of the laser intensity while strongly dependent on the internuclear separation. This striking “intersection” phenomenon is identified as arising due to intramolecular two-center interference in the HHG and can be used to probe the molecular instantaneous structure.
Effects of wavy sidewall on vortex breakdown in an enclosed cylindrical chamber with a rotating end wall
Authors: Yu Peng , Meguid Shaker A.
Published: January 2009

The effects of the wavy sidewall on flow behavior in an enclosed cylindrical chamber with a rotating end wall were investigated by a numerical model based on the steady, axisymmetric Navier–Stokes equations. The wavy sidewall influences vortex breakdown by either enhancing or reducing the swirling velocity near the top axis, depending on its orientation, amplitude, and period. When the period is small, the orientation of the wavy sidewall varies the volume of the top region of the chamber, which affects the swirling velocity there, thus influencing the occurrence of vortex breakdown. The volume-variation effect is enhanced with an increase in the amplitude, while reduced with an increase in the period. Moreover, an increase in the amplitude or period increases the length of the wavy sidewall, which enhances the dissipation of the fluid angular momentum along it. Thus, the swirling velocity near the top axis region is decreased and vortex breakdown is delayed. The resultant effect of the wavy sidewall is determined by the competition/cooperation of the volume-variation effect and the dissipation effect. However, if the period is large, the dissipation effect becomes dominant and the orientation of the wavy sidewall becomes unimportant.
Organic photodetector arrays with indium tin oxide electrodes patterned using directly transferred metal masks
Authors: Xu Xin , Mihnev Momchil , Taylor Andre , Forrest Stephen R.
Published: January 2009

We demonstrate the patterning of indium tin oxide (ITO) electrodes with submicron resolution onto both planar and hemispherical plastic surfaces using a process based on the direct transfer of a metal film etch mask via cold welding. Using this process, we fabricate an organic (copper phthalocyanine/C60) photodetector focal plane array on a hemispherical surface in an architecture that mimics the size and form of the human eye. The low absorption of the ITO anodes results in an increase in external quantum efficiency by up to 65% in the visible as compared with that of a previously demonstrated photodetector array with semitransparent Au anodes. The maximum photodetector detectivity is 1.25×1011 cm Hz1/2 W−1.
Electronic properties of hybridized poly (3, 4-ethylenedioxythiophene): Polystyrene sulfonate with surface-capped CdSe nanocrystals
Authors: Wang Seok-Joo , Park Hyung-Ho
Published: February 2009

The chemical state and electronic properties of hybrid material based on poly (3, 4-ethylenedioxythiophene): polystyrene sulfonate (PEDOT:PSS) and pyridine-capped CdSe nanocrystals have been investigated using photoemission spectroscopy, near-edge x-ray absorption fine structure, and ultraviolet photoelectron spectroscopy. With a high dipole moment as well as high physical momentum, CdSe nanocrystals hindered the rearrangement of PEDOT:PSS and induced PSS-rich surface during film formation. Thus, the work function value was decreased by dedoping of PEDOT or charge localization in PEDOT. Through heat treatment, the behavior of π-π∗ transition in C 1s and the work function value was nearly restored, gradually; these mean recovery of electrostatic bonding nature between PEDOT and PSS. However, the ionization potential (IP) was slightly increased by 0.3 eV with CdSe nanocrystal incorporation and interpreted as dielectric property and local electron transfer from highest occupied molecular orbital of PEDOT to valence band of CdSe nanocrystals. Subsequent addition of CdSe nanocrystal and degree of capping with pyridine allows for a well-controlled electronic structure of PEDOT:PSS, work function, and IP.
Computational confirmation of an abnormal Mach reflection wave configuration
Authors: Hu Z. M. , Wang C. , Zhang Y. , Myong R. S.
Published: January 2009

For the Mach reflection (MR) of symmetric shock waves of opposite families, only the wave configuration of an overall Mach reflection (oMR) consisting of two direct Mach reflections (DiMR+DiMR) is theoretically admissible. For asymmetric shock waves, an oMR composed of a DiMR and an inverse Mach reflection (InMR) is possible if the two slip layers assemble a converging-diverging stream tube, while an oMR including two inverse Mach reflections (InMR+InMR) is absolutely impossible. In this paper, an overall Mach reflection configuration with double inverse MR patterns is computationally confirmed using the computational fluid dynamics technique. The aerodynamic mechanism behind such an abnormal wave pattern is illustrated. Classical two- and three-shock theories are also applied for the theoretical analysis.
Effects of organic film morphology on the formation of Rb clusters on surface coatings in alkali metal vapor cells
Authors: Rampulla D. M. , Oncel N. , Abelev E. , Yi Y. W. , Knappe S. , Bernasek S. L.
Published: January 2009

Surface relaxation rates differ for spin-polarized alkali atoms interacting with monolayer or bilayer octadecyltrichlorosilane (OTS) coatings. The morphology and composition of Rb vapor-exposed films of OTS have been studied with atomic force microscopy (AFM) and x-ray photoelectron spectroscopy (XPS). On OTS monolayers, numerous small (<500 nm wide) Rb containing islands nucleate at the boundaries of the ∼1–2 μm wide organic domains. On OTS bilayers, singular large (∼3 μm wide) Rb containing islands were found. Alkali island formation mediated by surface structure could affect the antirelaxation behavior of organic coatings used in atomic magnetometer cells.
Semiclassical on-the-fly computation of the S→S1 absorption spectrum of formaldehyde
Authors: Tatchen Jörg , Pollak Eli
Published: January 2009

The anharmonic S0→S1 vibronic absorption spectrum of the formaldehyde molecule is computed on the fly using semiclassical dynamics. This first example of an on-the-fly semiclassical computation of a vibronic spectrum was achieved using a unit prefactor modified frozen Gaussian semiclassical propagator for the excited state. A sample of 6000 trajectories sufficed for obtaining a converged spectrum, which is in reasonable agreement with experiment. Similar agreement is not obtained when using a harmonic approximation for the spectrum, demonstrating the need for a full anharmonic computation. This first example provides a resolution of ∼100 cm−1. Potential ways of improving the methodology and obtaining higher resolution and accuracy are discussed.
Response to “Comment on ‘New statistical mechanical model for calculating Kirkwood factors in self-associating liquid systems and its application to alkanol+cyclohexane mixtures’ ” [J. Chem. Phys. 127, 047101 (2008)]
Authors: Heintz Andreas
Published: January 2009

A short summary of our theoretical concept for predicting Kirkwood factors in associating liquids system is presented which is based on the so-called extended real associated solution model involving the dipole correlations of chainlike associated alcohol molecules including a cyclic tetramer. Our model is discussed by comparing it with a different, alternative approach developed by Durov et al. Critical agreements and incorrect statements made by Durov have been discussed and tried to clarify.
Laser desorption/ionization time-of-flight mass spectrometry: A predictive tool for the lifetime of organic light emitting devices
Authors: Scholz Sebastian , Meerheim Rico , Lüssem Björn , Leo Karl
Published: January 2009

For improving the lifetime of organic light emitting devices (OLEDs), the analysis of the chemical degradation requires a deep understanding of the involved reaction pathways. We show that the dissociation reactions of phosphorescent emitters and the additional complexations with the used surrounding blocking layers are the dominant intrinsic degradation mechanisms in long living p-i-n type OLEDs. We use the laser desorption/ionization (LDI) time-of-flight mass spectrometry to correlate the laser-induced ion formation with the observed lifetime of the organic devices. The superlinear correlation between the LDI forced reactions and the lifetimes allows the prediction of the lifetime of an OLED with new materials.
A hot-filament discharge with very low electron temperature
Authors: Handley Ward , Robertson Scott
Published: January 2009

Very low electron temperatures have been obtained in a hot-filament discharge device by having a set of conditions designed to minimize heating of the confined electrons. Heating is reduced by having the energy of primaries from the filaments sufficiently large (80 eV) that they do not become confined after ionizing collisions and that they lose little energy through Coulomb collisions. The primaries create secondary electrons at the wall with several eVs of energy which heat the confined electrons through collisions. This heating is minimized by having a liner for the vacuum system coated with colloidal graphite to reduce the emission of secondary electrons and to create a uniform boundary potential. Argon plasmas are created with plasma potentials typically less than 0.2 V. Secondary electrons from the wall are not confined by the plasma potential and have a very low density of order 105 cm−3. The confined electrons have densities of order 108 cm−3 and electron temperatures as low as 0.031 eV (360 K).
Role of tungsten oxide in inverted polymer solar cells
Authors: Tao Chen , Ruan Shengping , Xie Guohua , Kong Xiangzi , Shen Liang , Meng Fanxu , Liu Caixia , Zhang Xindong , Dong Wei , Chen Weiyou
Published: January 2009

Tungsten oxide (WO3) was inserted as an anode interfacial layer between the photoactive layer and top electrode in inverted polymer solar cells (PSCs) with nanocrystalline titanium dioxide as an electron selective layer. The device with WO3 exhibited a remarkable improvement in power conversion efficiency compared with that without WO3, which indicated that WO3 efficiently prevented the recombination of charge carriers at the organic/top electrode interface. The dependence of the device performances on WO3 film thickness and different top metal electrodes was investigated. Transparent inverted PSCs with thermally evaporable Ag/WO3 as a transparent anode were also investigated when introducing a WO3 buffer layer.
High resolution electron microscopy of GaAs capped GaSb nanostructures
Authors: Molina S. I. , Beltrán A. M. , Ben T. , Galindo P. L. , Guerrero E. , Taboada A. G. , Ripalda J. M. , Chisholm M. F.
Published: January 2009

We show in this work that GaAs capping of 2 ML of GaSb grown by molecular beam epitaxy results in the formation of very small (with heights of about 1 nm) GaAsxSb1−x nanostructures surrounded by a GaAs rich layer. This conclusion is obtained by analyzing the morphology of the GaAsxSb1−x nanostructures by high resolution scanning transmission electron microscopy in Z-contrast mode. This result shows that a significant fraction of the Sb atoms must segregate along the growth direction during the GaAs capping process.
Instability of incorporated nitrogen in HfO2 films grown on strained Si0.7Ge0.3 layers
Authors: Chung K. B. , Lucovsky G. , Lee W. J. , Cho M.-H. , Jeon Hyeongtag
Published: January 2009

The interfacial characteristics and thermal stability of nitrided HfO2 films grown on strained Si0.7Ge0.3 layers were investigated by medium energy ion scattering, high-resolution x-ray photoelectron spectroscopy, and near-edge x-ray absorption fine structure. N incorporation of HfO2 films grown on Si0.7Ge0.3 layers was strongly related to the diffusion of Si and Ge from strained Si0.7Ge0.3 layers in the interfacial region between HfO2 films and Si0.7Ge0.3 layers by the annealing treatment in NH3 ambient. The chemical states of SiOxNy and GeOxNy were formed in the interfacial region by N incorporation, and SiOxNy was dominant chemical states rather than that of GeOxNy. However, the incorporated N was not stable, which was mostly diffused out during the postnitridation annealing in a N2 ambient. The instability of incorporated N through the additional annealing treatment extensively caused the change in the structure of HfO2.
Diamagnetic shifts of free excitons in CuInS2 in magnetic fields
Authors: Yakushev M. V. , Martin R. W. , Mudryi A. V.
Published: January 2009

Single crystals of CuInS2 were studied with reflectance (RF) and photoluminescence (PL) at 4.2 K in magnetic fields up to 10 T. The diamagnetic energy shifts observed for the free excitonic lines in both the RF and PL spectra were used to calculate the reduced masses (0.141m0, 0.142m0, and 0.114m0), binding energies (18.46, 18.59, and 14.90 meV), Bohr radii (3.82, 3.79, and 4.73 nm), and hole effective masses (1.20m0, 1.28m0, and 0.40m0) for the ALPB, AUPB, and BC excitons, respectively, using a low-field perturbation approach.
Concurrent magnetic and metal-insulator transitions in Eu1−xSmxB6 single crystals
Authors: Yeo S. , Bunder J. E. , Lin Hsiu-Hau , Jung Myung-Hwa , Lee Sung-Ik
Published: January 2009

The effects of magnetic doping on a EuB6 single crystal were investigated based on magnetic and transport measurements. A modest 5% Sm substitution for Eu changes the magnetic and transport properties dramatically and gives rise to concurrent antiferromagnetic and metal-insulator transitions (MITs) from ferromagnetic MIT for EuB6. Magnetic doping simultaneously changes the itinerant carrier density and the magnetic interactions. We discuss the origin of the concurrent magnetic MIT in Eu1−xSmxB6.
Stacking-fault structure explains unusual elasticity of nanocrystalline diamonds
Authors: Tanei H. , Tanigaki K. , Kusakabe K. , Ogi H. , Nakamura N. , Hirao M.
Published: January 2009

This letter reveals that unusual elasticity of nanocrystalline diamond is consistently explained by stacking fault inside the diamond grains instead of the graphitic plate inclusion, which was only possible mechanism. Ab initio calculation shows that stacking fault introduced in the diamond structure behaves as graphitic sp2 bonds, and the elastic constants calculated from the strain-energy relationship agree with the acoustic measurements.
Near-field plane-wave-like beam emitting antenna fabricated by anisotropic metamaterial
Authors: Ma Y. G. , Wang P. , Chen X. , Ong C. K.
Published: January 2009

In this work, the authors showed that the directivity and efficiency of an electromagnetic (EM) emission could be greatly improved by embedding the source in an anisotropic matrix with one component of the physical parameters near zero. This unique property led us to design a slab-shaped rectangular antenna that could emit a monopolarized planar wave beam into the near field. This greatly reduced the spatial and anechoic requirements needed for polarization-relevant EM characterizations. The practical feasibility of building such a device was numerically discussed by engineering a real anisotropic embedding matrix made of metamaterial.
Erbium-ytterbium codoped waveguide amplifier fabricated with solution-processable complex
Authors: Chen Cong , Zhang Dan , Li Tong , Zhang Daming , Song Limei , Zhen Zhen
Published: January 2009

A solution-processable erbium-ytterbium codoped complex is synthesized. The absorption and photoluminescence spectra of the complex are observed. The full width at half maximum of the emission spectrum is 80 nm around 1530 nm. A structure of embedded waveguide with the complex as core layer is designed. With an input signal power of 0.3 mW, an optical gain of 5.2 dB at a wavelength of 1550 nm is obtained in a 15-mm-long waveguide when the cladding layer is SU-8. When the cladding layer is polymethyl methacrylate, an optical gain of 6.5 dB is obtained in a 12-mm-long waveguide with an input signal power of 1 mW.
Electron-shading effect on the horizontal aligned growth of carbon nanotubes
Authors: Chai Yang , Xiao Zhiyong , Chan Philip C. H.
Published: January 2009

Based on the well-accepted electron-shading theory during plasma processing, we designed microstructures to control the local built-in electric-field on the substrate surface. The distortion magnitude of the electric-field is largest near the sidewalls of the microstructures, creating a horizontal electric-field in this region. We showed that the horizontally aligned carbon nanotubes (CNTs) were grown by making use of this built-in electric-field during the plasma-enhanced chemical vapor deposition process, with a tactical choice of geometries and materials of the microstructures on the substrate. This technique opens up a way to selectively and controllably grow horizontally aligned CNTs on the substrate surface.
Type III restriction enzymes communicate in 1D without looping between their target sites
Authors: Ramanathan Subramanian P. , van Aelst Kara , Sears Alice , Peakman Luke J. , Diffin Fiona M. , Szczelkun Mark D. , Seidel Ralf
Published: January 2009

To cleave DNA, Type III restriction enzymes must communicate the relative orientation of two asymmetric recognition sites over hundreds of base pairs. The basis of this long-distance communication, for which ATP hydrolysis by their helicase domains is required, is poorly understood. Several conflicting DNA-looping mechanisms have been proposed, driven either by active DNA translocation or passive 3D diffusion. Using single-molecule DNA stretching in combination with bulk-solution assays, we provide evidence that looping is both highly unlikely and unnecessary, and that communication is strictly confined to a 1D route. Integrating our results with previous data, a simple communication scheme is concluded based on 1D diffusion along DNA.
Signals in bacterial β-barrel proteins are functional in eukaryotic cells for targeting to and assembly in mitochondria
Authors: Walther Dirk M. , Papic Drazen , Bos Martine P. , Tommassen Jan , Rapaport Doron
Published: January 2009

The outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts harbor β-barrel proteins. The signals that allow precursors of such proteins to be targeted to mitochondria were not characterized so far. To better understand the mechanism by which β-barrel precursor proteins are recognized and sorted within eukaryotic cells, we expressed the bacterial β-barrel proteins PhoE, OmpA, Omp85, and OmpC in
Saccharomyces cerevisiae
and demonstrated that they were imported into mitochondria. A detailed investigation of the import pathway of PhoE revealed that it is shared with mitochondrial β-barrel proteins. PhoE interacts initially with surface import receptors, and its further sorting depends on components of the TOB/SAM complex. The bacterial Omp85 and PhoE integrated into the mitochondrial outer membrane as native-like oligomers. For the latter protein this assembly depended on the C-terminal Phe residue, which is important also for the correct assembly of PhoE into the bacterial outer membrane. Collectively, it appears that mitochondrial β-barrel proteins have not evolved eukaryotic-specific signals to ensure their import into mitochondria. Furthermore, the signal for assembly of β-barrel proteins into the bacterial outer membrane is functional in mitochondria.
Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in
Arabidopsis
Authors: Kurihara Yukio , Matsui Akihiro , Hanada Kousuke , Kawashima Makiko , Ishida Junko , Morosawa Taeko , Tanaka Maho , Kaminuma Eli , Mochizuki Yoshiki , Matsushima Akihiro , Toyoda Tetsuro , Shinozaki Kazuo , Seki Motoaki
Published: January 2009

The nonsense-mediated mRNA decay (NMD) pathway is a well-known eukaryotic surveillance mechanism that eliminates aberrant mRNAs that contain a premature termination codon (PTC). The UP-Frameshift (UPF) proteins, UPF1, UPF2, and UPF3, are essential for normal NMD function. Several NMD substrates have been identified, but detailed information on NMD substrates is lacking. Here, we noticed that, in
Arabidopsis
, most of the mRNA-like nonprotein-coding RNAs (ncRNAs) have the features of an NMD substrate. We examined the expression profiles of 2
Arabidopsis
mutants,
upf1-1
and
upf3-1
, using a whole-genome tiling array. The results showed that expression of not only protein-coding transcripts but also many mRNA-like ncRNAs (mlncRNAs), including natural antisense transcript RNAs (nat-RNAs) transcribed from the opposite strands of the coding strands, were up-regulated in both mutants. The percentage of the up-regulated mlncRNAs to all expressed mlncRNAs was much higher than that of the up-regulated protein-coding transcripts to all expressed protein- coding transcripts. This finding demonstrates that one of the most important roles of NMD is the genome-wide suppression of the aberrant mlncRNAs including nat-RNAs.
The cavity-chaperone Skp protects its substrate from aggregation but allows independent folding of substrate domains
Authors: Walton Troy A. , Sandoval Cristina M. , Fowler C. Andrew , Pardi Arthur , Sousa Marcelo C.
Published: January 2009

Outer membrane proteins (OMPs) of Gram-negative bacteria are synthesized in the cytosol and must cross the periplasm before insertion into the outer membrane. The 17-kDa protein (Skp) is a periplasmic chaperone that assists the folding and insertion of many OMPs, including OmpA, a model OMP with a membrane embedded β-barrel domain and a periplasmic αβ domain. Structurally, Skp belongs to a family of cavity-containing chaperones that bind their substrates in the cavity, protecting them from aggregation. However, some substrates, such as OmpA, exceed the capacity of the chaperone cavity, posing a mechanistic challenge. Here, we provide direct NMR evidence that, while bound to Skp, the β-barrel domain of OmpA is maintained in an unfolded state, whereas the periplasmic domain is folded in its native conformation. Complementary cross-linking and NMR relaxation experiments show that the OmpA β-barrel is bound deep within the Skp cavity, whereas the folded periplasmic domain protrudes outside of the cavity where it tumbles independently from the rest of the complex. This domain-based chaperoning mechanism allows the transport of β-barrels across the periplasm in an unfolded state, which may be important for efficient insertion into the outer membrane.
Ppp1r15 gene knockout reveals an essential role for translation initiation factor 2 alpha (eIF2α) dephosphorylation in mammalian development
Authors: Harding Heather P. , Zhang Yuhong , Scheuner Donalyn , Chen Jane-Jane , Kaufman Randal J. , Ron David
Published: January 2009

Diverse cellular stress responses are linked to phosphorylation of serine 51 on the alpha subunit of translation initiation factor 2. The resultant attenuation of protein synthesis and activation of gene expression figure heavily in the adaptive response to stress, but dephosphorylation of eIF2(αP), which terminates signaling in this pathway, is less well understood. GADD34 and CReP, the products of the related mammalian genes
Ppp1r15a
and
Ppp1r15b
, can recruit phosphatase catalytic subunits of the PPP1 class to eIF2(αP), but the significance of their contribution to its dephosphorylation has not been explored systematically. Here we report that unlike
Ppp1r15a
mutant mice, which are superficially indistinguishable from wild type,
Ppp1r15b
−/−
mouse embryos survive gestation but exhibit severe growth retardation and impaired erythropoiesis, and loss of both
Ppp1r15
genes leads to early embryonic lethality. These loss-of-function phenotypes are rescued by a mutation,

Eif2a
S51A

, that prevents regulated phosphorylation of eIF2α. These findings reveal that the essential process of eIF2(αP) dephosphorylation is the predominant role of PPP1R15 proteins in mammalian development.
Explosive Pleistocene diversification and hemispheric expansion of a “great speciator”
Authors: Moyle Robert G. , Filardi Christopher E. , Smith Catherine E. , Diamond Jared
Published: January 2009

Factors that influence speciation rates among groups of organisms are integral to deciphering macroevolutionary processes; however, they remain poorly understood. Here, we use molecular phylogenetic data and divergence time estimates to reconstruct the pattern and tempo of speciation within a widespread and homogeneous bird family (white-eyes, Zosteropidae) that contains an archetypal “great speciator.” Our analyses show that the majority of this species-rich family constitutes a clade that arose within the last 2 million years, yielding a per-lineage diversification rate among the highest reported for vertebrates (1.95–2.63 species per million years). However, unlike most rapid radiations reported to date, this burst of diversification was not limited in geographic scope, but instead spanned the entire Old World tropics, parts of temperate Asia, and numerous Atlantic, Pacific, and Indian Ocean archipelagos. The tempo and geographic breadth of this rapid radiation defy any single diversification paradigm, but implicate a prominent role for lineage-specific life-history traits (such as rapid evolutionary shifts in dispersal ability) that enabled white-eyes to respond rapidly and persistently to the geographic drivers of diversification.
Odor coding by modules of coherent mitral/tufted cells in the vertebrate olfactory bulb
Authors: Chen Tsai-Wen , Lin Bei-Jung , Schild Detlev
Published: January 2009

Odor representation in the olfactory bulb (OB) undergoes a transformation from a combinatorial glomerular map to a distributed mitral/tufted (M/T) cell code. To understand this transformation, we analyzed the odor representation in large populations of individual M/T cells in the
Xenopus
OB. The spontaneous [Ca
2+
] activities of M/T cells appeared to be irregular, but there were groups of spatially distributed neurons showing synchronized [Ca
2+
] activities. These neurons were always connected to the same glomerulus. Odorants elicited complex spatiotemporal response patterns in M/T cells where nearby neurons generally showed little correlation. But the responses of neurons connected to the same glomerulus were virtually identical, irrespective of whether the responses were excitatory or inhibitory, and independent of the distance between them. Synchronous neurons received correlated EPSCs and were coupled by electrical conductances that could account for the correlated responses. Thus, at the output stage of the OB, odors are represented by modules of distributed and synchronous M/T cells associated with the same glomeruli. This allows for parallel input to higher brain centers.
Tissue plasminogen activator modulates the cellular and behavioral response to cocaine
Authors: Maiya Rajani , Zhou Yan , Norris Erin H. , Kreek Mary Jeanne , Strickland Sidney
Published: January 2009

Cocaine exposure induces long-lasting molecular and structural adaptations in the brain. In this study, we show that tissue plasminogen activator (tPA), an extracellular protease involved in neuronal plasticity, modulates the biochemical and behavioral response to cocaine. When injected in the acute binge paradigm, cocaine enhanced tPA activity in the amygdala, which required activation of corticotropin-releasing factor type-1 (CRF-R1) receptors. Compared with WT mice, tPA−/− mice injected with cocaine displayed attenuated phosphorylation of ERK, cAMP response element binding protein (CREB), and dopamine and cAMP-regulated phosphoprotein 32 kDa (DARPP-32) and blunted induction of immediate early genes (IEGs) c-Fos, Egr-1, and Homer 1a in the amygdala and the nucleus accumbens (NAc). tPA−/− mice also displayed significantly higher basal preprodynorphin (ppDyn) mRNA levels in the NAc in comparison to WT mice, and cocaine decreased ppDyn mRNA levels in tPA−/− mice only. Cocaine-induced locomotor sensitization and conditioned place preference (CPP) were attenuated in tPA−/− mice. Cocaine exposure also had an anxiolytic effect in tPA−/− but not WT mice. These results identify tPA as an important and novel component of the signaling pathway that modulates cocaine-induced changes in neuroadaptation and behavior.
Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays
Authors: Merbl Yifat , Kirschner Marc W.
Published: January 2009

Identification of protein targets of post-translational modification is an important analytical problem in biology. Protein microarrays exposed to cellular extracts could offer a rapid and convenient means of identifying modified proteins, but this kind of biochemical assay, unlike DNA microarrays, depends on a faithful reconstruction of in vivo conditions. Over several years, concentrated cellular extracts have been developed, principally for cell cycle studies that reproduce very complex cellular states. We have used extracts that replicate the mitotic checkpoint and anaphase release to identify differentially regulated poyubiquitination. Protein microarrays were exposed to these complex extracts, and the polyubiquitinated products were detected by specific antibodies. We expected that among the substrates revealed by the microarray should be substrates of the anaphase promoting complex (APC). Among 8,000 proteins on the chip, 10% were polyubiquitinated. Among those, we found 11 known APC substrates (out of 16 present on the chip) to be polyubiquitinated. Interestingly, only 1.5% of the proteins were differentially ubiquitinated on exit from the checkpoint. When we arbitrarily chose 6 proteins thought to be involved in mitosis from the group of differentially modified proteins, all registered as putative substrates of the APC, and among 4 arbitrarily chosen non-mitotic proteins picked from the same list, 2 were ubiquitinated in an APC-dependent manner. The striking yield of potential APC substrates from a simple assay with concentrated cell extracts suggests that combining microarray analysis of the products of post-translational modifications with extracts that preserve the physiological state of the cell can yield information on protein modification under various in vivo conditions.
Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line
Authors: Zhao Qi , Caballero Otavia L. , Levy Samuel , Stevenson Brian J. , Iseli Christian , de Souza Sandro J. , Galante Pedro A. , Busam Dana , Leversha Margaret A. , Chadalavada Kalyani , Rogers Yu-Hui , Venter J. Craig , Simpson Andrew J. G. , Strausberg Robert L.
Published: January 2009

We have identified new genomic alterations in the breast cancer cell line HCC1954, using high-throughput transcriptome sequencing. With 120 Mb of cDNA sequences, we were able to identify genomic rearrangement events leading to fusions or truncations of genes including MRE11 and NSD1, genes already implicated in oncogenesis, and 7 rearrangements involving other additional genes. This approach demonstrates that high-throughput transcriptome sequencing is an effective strategy for the characterization of genomic rearrangements in cancers.
Detergent binding explains anomalous SDS-PAGE migration of membrane proteins
Authors: Rath Arianna , Glibowicka Mira , Nadeau Vincent G. , Chen Gong , Deber Charles M.
Published: January 2009

Migration on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) that does not correlate with formula molecular weights, termed “gel shifting,” appears to be common for membrane proteins but has yet to be conclusively explained. In the present work, we investigate the anomalous gel mobility of helical membrane proteins using a library of wild-type and mutant helix-loop-helix (“hairpin”) sequences derived from transmembrane segments 3 and 4 of the human cystic fibrosis transmembrane conductance regulator (CFTR), including disease-phenotypic residue substitutions. We find that these hairpins migrate at rates of −10% to +30% vs. their actual formula weights on SDS-PAGE and load detergent at ratios ranging from 3.4–10 g SDS/g protein. We additionally demonstrate that mutant gel shifts strongly correlate with changes in hairpin SDS loading capacity (

R
2

= 0.8), and with hairpin helicity (

R
2

= 0.9), indicating that gel shift behavior originates in altered detergent binding. In some cases, this differential solvation by SDS may result from replacing protein-detergent contacts with protein-protein contacts, implying that detergent binding and folding are intimately linked. The CF-phenotypic V232D mutant included in our library may thus disrupt CFTR function via altered protein-lipid interactions. The observed interdependence between hairpin migration, SDS aggregation number, and conformation additionally suggests that detergent binding may provide a rapid and economical screen for identifying membrane proteins with robust tertiary and/or quaternary structures.
Flanker and Simon effects interact at the response selection stage
Authors: Treccani Barbara , Cubelli Roberto , Sala Sergio Della , Umiltà Carlo
Published: January 2009

The present study aimed at investigating the processing stage underlying stimulus–stimulus (S–S) congruency effects by examining the relation of a particular type of congruency effect (i.e., the flanker effect) with a stimulus–response (S–R) spatial correspondence effect (i.e., the Simon effect). Experiment 1 used a unilateral flanker task in which the flanker also acted as a Simon-like accessory stimulus. Results showed a significant S–S Congruency × S–R Correspondence interaction: An advantage for flanker–response spatially corresponding trials was observed in target–flanker congruent conditions, whereas, in incongruent conditions, there was a noncorresponding trials’ advantage. The analysis of the temporal trend of the correspondence effects ruled out a temporal-overlap account for the observed interaction. Moreover, results of Experiment 2, in which the flanker did not belong to the target set, demonstrated that this interaction cannot be attributed to perceptual grouping of the target–flanker pairs and referential coding of the target with respect to the flanker in the congruent and incongruent conditions, respectively. Taken together, these findings are consistent with a response selection account of congruency effects: Both the position and the task-related attribute of the flanker would activate the associated responses. In noncorresponding-congruent trials and corresponding-incongruent trials, this would cause a conflict at the response selection stage.
Impact of ICRH on the measurement of fusion alphas by collective Thomson scattering in ITER
Authors: Salewski M. , Eriksson L.-G. , Bindslev H. , Korsholm S.B. , Leipold F. , Meo F. , Michelsen P.K. , Nielsen S.K.
Published: January 2009

Collective Thomson scattering (CTS) has been proposed for measuring the phase space distributions of confined fast ion populations in ITER plasmas. This study determines the impact of fast ions accelerated by ion cyclotron resonance heating (ICRH) on the ability of CTS to diagnose fusion alphas in ITER. Fast ions with large perpendicular velocities, such as the populations investigated here, can be detected with the ‘enabled’ part of the proposed ITER CTS diagnostic. The investigated ICRH scenarios include pure second harmonic tritium heating and 3He minority heating at a frequency of 50 MHz, corresponding to an off-axis resonance. The sensitivities of the results to the 3He concentration (0.1–4%) and the heating power (20–40 MW) are considered. Fusion born alphas dominate the total CTS signal for large Doppler shifts of the scattered radiation. The tritons generate a negligible fraction of the total fast ion CTS signal in any of these heating scenarios. The minority species 3He, however, contributes more than 10% of the fast ion CTS signal at locations close to the resonance layer for 3He concentrations larger than ∼1%. In this particular region in space for resolution of near perpendicular velocities, it may be difficult to draw conclusions about the physics of alpha particles alone by CTS. With this exception, the CTS diagnostic can reveal the physics of the fusion alphas in ITER even under the presence of fast ions due to ICRH.
New B2SOLPS5.2 transport code for H-mode regimes in tokamaks
Authors: Rozhansky V. , Kaveeva E. , Molchanov P. , Veselova I. , Voskoboynikov S. , Coster D. , Counsell G. , Kirk A. , Lisgo S.
Published: January 2009

A new B2SOLPS5.2 transport code has been developed and implemented for the simulation of H-mode shots. A new equation system is proposed, which is equivalent to the system which was used in B2SOLPS5.0 previously. The main idea is to replace the major part of the large radial ∇B driven convective fluxes by poloidal fluxes with the same divergence both in the particle balance and in the energy balance equations. This is of special importance for the H-mode where the diffusion coefficient is strongly reduced inside the barrier and large radial convective flows are strongly undesirable from the numerical point of view. The H-mode shots of ASDEX-Upgrade and MAST have been simulated with the new version with reasonable time steps and convergence. It is demonstrated that the radial electric field inside the edge transport barrier and in the pedestal region is close to the neoclassical electric field as in previous simulations of Ohmic shots. The toroidal rotation is co-current directed as in L-mode but is significantly larger in absolute value. It is shown that the shear of the poloidal
drift at the inner side of the barrier is close to the value of the shear before the transition, while inside the barrier the value of the shear is significantly bigger. This fact determines self-consistently the width of the edge transport barrier. It is demonstrated that to match the experimental density and temperature radial profiles the drop in the diffusion coefficient within the barrier needs to be significantly larger than the drop in the electron heat conductivity coefficient.

For the H-mode the pedestal region usually corresponds to the collisionless regime, so several corrections were introduced into the transport coefficients to extend the applicability of the code to the plateau and banana regimes in the inner regions of the simulation domain.
NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results
Authors: Lagnel Jacques , Tsigenopoulos Costas S. , Iliopoulos Ioannis
Published: January 2009

Summary: NOBLAST (New Options for BLAST) is an open source program that provides a new user-friendly tabular output format for various NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn, Tblastx, Mega BLAST and Psi BLAST) without any use of a parser and provides E-value correction in case of use of segmented BLAST database. JAMBLAST using the NOBLAST output allows the user to manage, view and filter the BLAST hits using a number of selection criteria.

Availability: A distribution package of NOBLAST and JAMBLAST including detailed installation procedure is freely available from http://sourceforge.net/projects/JAMBLAST/ and http://sourceforge.net/projects/NOBLAST.

Contact:  lagnel@her.hcmr.gr; ioannis@iti.gr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans
Authors: Hillier LaDeana W. , Reinke Valerie , Green Philip , Hirst Martin , Marra Marco A. , Waterston Robert H.
Published: January 2009

Using massively parallel sequencing by synthesis methods, we have surveyed the polyA+ transcripts from four stages of the nematode Caenorhabditis elegans to an unprecedented depth. Using novel statistical approaches, we evaluated the coverage of annotated features of the genome and of candidate processed transcripts, including splice junctions, trans-spliced leader sequences, and polyadenylation tracts. The data provide experimental support for >85% of the annotated protein-coding transcripts in WormBase (WS170) and confirm additional details of processing. For example, the total number of confirmed splice junctions was raised from 70,911 to over 98,000. The data also suggest thousands of modifications to WormBase annotations and identify new spliced junctions and genes not part of any WormBase annotation, including at least 80 putative genes not found in any of three predicted gene sets. The quantitative nature of the data also suggests that mRNA levels may be measured by this approach with unparalleled precision. Although most sequences align with protein-coding genes, a small fraction falls in introns and intergenic regions. One notable region on the X chromosome encodes a noncoding transcript of >10 kb localized to somatic nuclei.
Isolation of DNA, RNA, and Protein from the Moss Physcomitrella patens Gametophytes
Authors: Cove David J. , Perroud Pierre-François , Charron Audra J. , McDaniel Stuart F. , Khandelwal Abha , Quatrano Ralph S.
Published: February 2009

INTRODUCTION

This protocol describes a series of procedures for isolating nucleic acids (DNA and RNA) and proteins from moss (Physcomitrella patens) tissue. This series includes a rapid, small-scale procedure for isolating DNA, which results in genomic DNA that is only suitable for polymerase chain reaction (PCR), as well as a method for obtaining much larger amounts of genomic DNA suitable for Southern analysis. The latter method makes use of the Nucleon PhytoPure Genomic DNA Extraction Kit (GE Healthcare). The RNA extraction procedure uses the Plant RNA Isolation Mini Kit (Agilent) with some modifications. A method for extracting proteins from moss gametophytes is also presented.
A Simple Free-Radical Polymerization Method for the Fabrication of Microscale Acrylonitrile Fibers for Cellular Probing
Authors: Guido Matthew R.
Published: February 2009

INTRODUCTION

This protocol describes a simple method to free-radical-polymerize reagent-grade acrylonitrile and then fabricate microscale fibers with diameter constraints of 1-2 μm and lengths of 10-50 mm. These fibers have stiffness and elastic modulus values with powerful implications for cellular probing and positioning on the microscale, as well as potential applications in the field of cellular mechanics of materials. In the past, creation of polymer fibers of known dimensions was accomplished using complex mechanical devices that introduced the polymer into a heated and pressurized vessel for a specified time period. These devices were either laboratory fabrications or purchased, and each was specific to a given polymer. This protocol is a more rapid procedure requiring only standard laboratory bench equipment. It also provides the time-dependent parameters for control of the fiber properties. The protocol has three modifiable parameters that can alter the material properties of the fibers. Here we present the definitive techniques that remove the need for more complicated machinery.