bluuebunny/crossref_metadata_2025 huggingface dataset:
Gyrokinetic calculations of diffusive and convective transport of α particles with a slowing-down distribution function
Authors: Angioni C. , Peeters A. G.
Published: May 2008

Quasilinear gyrokinetic calculations of the transport of fast α particles with a slowing-down equilibrium distribution function in the trace limit are presented. Diffusive and convective contributions to the total flux are separated and their dependence on the ratio of the fast particle energy to the background plasma temperature is investigated. The results are compared with those obtained in the case an equivalent Maxwellian distribution function is assumed for the fast particles. On the basis of the gyrokinetic results, simple models for α particle transport are proposed for transport modeling purposes.
Long global gyrokinetic simulations: Source terms and particle noise control
Authors: McMillan B. F. , Jolliet S. , Tran T. M. , Villard L. , Bottino A. , Angelino P.
Published: May 2008

In global gyrokinetic simulations it takes a long time for the turbulence to reach a quasisteady state, and quantitative predictions about the quasisteady state turbulence have been difficult to obtain computationally. In particular, global particle-in-cell gyrokinetic simulations have been inefficient for long simulations due to the accumulation of noise. It is demonstrated that a simple Krook operator can effectively control noise; it also introduces an unphysical dissipation, which damps the zonal flows and can significantly affect simulation results even when the relaxation time is very long. However, it is possible to project out the effects of the Krook operator on the zonal flows. This permits noise accumulation to be controlled while preserving the physics of interest; simulations are then run to determine the level of quasisteady state transport and the variation across the ensemble of turbulent dynamics. Convergence is demonstrated both in the number of computational particles and the unphysical relaxation time.
Discontinuously propagating waves in the bathoferroin-catalyzed Belousov–Zhabotinsky reaction incorporated into a microemulsion
Authors: Cherkashin Alexander A. , Vanag Vladimir K. , Epstein Irving R.
Published: May 2008

Three new types of discontinuously propagating waves are reported in the bathoferroin-catalyzed Belousov–Zhabotinsky (BZ) reaction dispersed in water-in-oil Aerosol OT microemulsion. Jumping waves (JWs) are typically observed at or above room temperature and develop from the familiar trigger waves. Bubble waves (BWs) typically emerge from trigger or JWs at similar temperatures, while rotating waves (RWs) evolve from JW at higher temperatures (>40°C). All these waves propagate discontinuously in a saltatory fashion. Other characteristic features include a discontinuous front for BW consisting of small concentric waves (bubbles) and lateral rotation of annular RWs. All three types of waves, as well as segmented but continuously propagating waves, can coexist. A simple model that is able to describe both jumping and segmented waves is described.
The theoretical prediction of infrared spectra of trans- and cis-hydroxycarbene calculated using full dimensional ab initio potential energy and dipole moment surfaces
Authors: Koziol Lucas , Wang Yimin , Braams Bastiaan J. , Bowman Joel M. , Krylov Anna I.
Published: May 2008

Accurate infrared spectra of the two hydroxycarbene isomers are computed by diagonalizing the Watson Hamiltonian including up to four mode couplings using full dimensional potential energy and dipole moment surfaces calculated at the CCSD(T)/cc-pVTZ (frozen core) and CCSD∕6-311G** (all electrons correlated) levels, respectively. Anharmonic corrections are found to be very important for these elusive higher-energy isomers of formaldehyde. Both the energy levels and intensities of stretching fundamentals and all overtone transitions are strongly affected by anharmonic couplings between the modes. The results for trans-HCOH∕HCOD are in excellent agreement with the recently reported IR spectra, which validates our predictions for the cis-isomers.
Low-threshold and broadly tunable lasers of Yb3+-doped yttrium lanthanum oxide ceramic
Authors: Hao Qiang , Li Wenxue , Zeng Heping , Yang Qiuhong , Dou Chuanguo , Zhou Hongxu , Lu Wei
Published: May 2008

We experimentally demonstrated diode-pumped continuous wave and tunable laser operation of Yb3+-doped yttrium lanthanum oxide transparent ceramic [Yb:(Y1−xLax)2O3,x=0.1], which was fabricated with nanopowders and sintered in H2 atmosphere. As low as 400mW pumping threshold and a slope efficiency of 52% were realized at 1080nm under a high-brightness 976nm diode pump with a fiber core of 50μm and a numerical aperture of 0.22. A maximum output power of 2.1W was obtained when the non-lasing absorbed pump power was 19.5W at 976nm with diode laser of 400μm fiber core. A smooth tunable curve from 1018to1086nm was achieved at 940nm diode pump. Broadband lasing spectra up to 30nm were observed in the tunable laser experiment.
Hard x-rays nanoscale fluorescence imaging of Earth and Planetary science samples
Authors: Bleuet Pierre , Simionovici Alexandre , Lemelle Laurence , Ferroir Tristan , Cloetens Peter , Tucoulou Rémi , Susini Jean
Published: May 2008

A hard x-ray nanoprobe has been implemented at the synchrotron in Grenoble, France, allowing nondestructive trace element imaging of thick samples. Its advantages are nanometer spatial resolution on samples of several tens of micrometer, very high flux, and achromaticity. Nanometer imaging of a cometary grain from the NASA Stardust mission shows the sensitivity and resolution gains obtained while radically changing our understanding of the composition of heterogeneous samples. The probe opens unique possibilities in the study of minute, fragile samples fundamental to the earth and planetary sciences, which until now were out of the reach of direct analytical methods.
Polarizability of a pair of touching dielectric spheres
Authors: Pitkonen Mikko
Published: May 2008

The electrostatic problem of two touching dielectric spheres in a uniform field is analyzed as an eigenfunction expansion in the tangent sphere frame. The spectrum of eigenfunctions is continuous; therefore, the scattered potential is expressed as a weighted integral of those eigenfunctions. It is shown that the weighting function satisfies a second-order ordinary differential equation, which contains only elementary functions. In particular, the longitudinal and transverse polarizabilities of the tangent sphere are being considered. We are also dealing with the plasmonic resonances (electrostatic resonances) that appear at the negative values of the permittivity ε. Some years ago Paley, Radchik, and Smith [A. V. Paley, A. V. Radchik, and G. B. Smith, J. Appl. Phys. 73, 3446 (1993)] claimed to have found an exact solution for the problem of two touching dielectric spheres in a uniform field. In light of the present study, it seems that their result is incorrect.
Dynamic shear strength of S2 glass fiber reinforced polymer composites under shock compression
Authors: Yuan Fuping , Tsai Liren , Prakash Vikas , Dandekar Dattatraya P. , Rajendran A. M.
Published: May 2008

In the present paper, a series of plate impact shock-reshock and shock-release experiments were conducted to study the critical shear strength of a S2 glass fiber reinforced polymer (GRP) composite under shock compression levels ranging from 0.8 to 1.8 GPa. The GRP was fabricated at ARL, Aberdeen, using S2 glass woven roving in a Cycom 4102 polyester resin matrix. The experiments were conducted by using an 82.5 mm bore single-stage gas gun at Case Western Reserve University. In order to conduct shock-reshock and shock-release experiments a dual flyer plate assembly was utilized. The shock-reshock experiments were conducted by using a projectile faced with GRP and backed with a relatively high shock impedance Al 6061-T6 plate; while for the shock-release experiments the GRP was backed by a relatively lower impedance polymethyl methacrylate backup flyer plate. A multibeam velocity interferometer was used to measure the particle velocity profile at the rear surface of the target plate. By using self-consistent technique procedure described by Asay and Chabbildas [Shock Waves and High-Strain-Rate Phenomena, in Metals, edited by M. M. Myers and L. E. Murr (Plenum, New York, 1981), pp. 417–431], the critical shear strength of the GRP (2τc) was determined for impact stresses in the range of 0.8 to 1.8 GPa. The results show that the critical shear strength of the GRP is increased from 0.108 GPa to 0.682 GPa when the impact stress is increased from 0.8 to 1.8 GPa. The increase in critical shear strength may be attributed to rate-dependence and/or pressure dependent yield behavior of the GRP.
Coexistence of layered and cubic rocksalt structures with a common oxygen sublattice in Li1.2Mn0.4Fe0.4O2 particles: A transmission electron microscopy study
Authors: Kikkawa Jun , Akita Tomoki , Tabuchi Mitsuharu , Shikano Masahiro , Tatsumi Kuniaki , Kohyama Masanori
Published: May 2008

Local crystal structures associated with nanoscale variations of the concentration ratio of Fe ions to Mn ions in each single Li1.2Mn0.4Fe0.4O2 particle have been studied by nanobeam electron diffraction, high-resolution transmission electron microscopy, and electron energy-loss spectroscopy combined with scanning transmission electron microscopy. We have found the direct evidence that the Li1.2Mn0.4Fe0.4O2 particle is comprised of Mn-rich nanodomains with the layered rocksalt structure and Fe-rich nanodomains with the cubic rocksalt structure featured by the cation short-range order, within a common oxygen lattice framework of the cubic close-packed structure. Possible oxygen-centered octahedra in the present material are suggested. We discuss both origin and stability of the chemical-nanodomain structure.
Determining the optimal contact length for a metal/multiwalled carbon nanotube interconnect
Authors: Lan Chun , Zakharov Dmitri N. , Reifenberger Ronald G.
Published: May 2008

A focused ion beam (FIB) is used to sequentially reduce the contact length of an evaporated metal film to a multiwalled carbon nanotube (MWCNT). By using this FIB contact cutback technique, the contact resistance between an individual MWCNT and evaporated thin films of Au, Au∕Ti, and Ag are accurately determined. The data permit a rational way to specify the minimum contact length of a metallic thin film to a MWCNT.
Effect of photon irradiation on structural, dielectric, and insulating properties of Ba0.60Sr0.40TiO3 thin films
Authors: Podpirka Adrian , Cole M. W. , Ramanathan Shriram
Published: May 2008

The effect of ultraviolet (UV) photon assisted annealing on the structural, dielectric, and insulating properties of barium strontium titanate (BST) thin films was investigated. Isothermal-temporal annealing experiments revealed that the films annealed utilizing UV assist possessed enhanced crystallization and lattice parameters closer to bulk values with respect to conventional thermal annealed films. The leakage current density and dielectric loss of the films was significantly reduced by employing UV-assisted annealing without degradation of film tunability. Mitigation of oxygen vacancies, associated with the UV-assisted annealing, is deemed responsible for the improvement of the dielectric and electrical properties of the BST thin films.
One-step grown aligned bulk carbon nanotubes by chloride mediated chemical vapor deposition
Authors: Inoue Yoku , Kakihata Kazuyuki , Hirono Yusaku , Horie Toshinori , Ishida Akihiro , Mimura Hidenori
Published: May 2008

We found the easy and efficient synthesis method of the vertically aligned ultralong multiwalled nanotubes using iron chloride powder. The 2.1-mm-long bulk nanotubes can be grown by conventional thermal chemical vapor deposition on bare quartz surface with the single gas flow of acetylene for 20min. In addition to the high growth rate, the bulk of carbon nanotubes is easily spun into the yarn by pulling it out, and the present method also provides the coating ability with nanotubes as a new functionality of this nanomaterial.
Single spin Toffoli–Fredkin logic gate
Authors: Trivedi Amit Ranjan , Bandyopadhyay S.
Published: May 2008

The Toffoli–Fredkin (TF) gate is a universal reversible logic gate capable of performing logic operations without dissipating energy. Here, we show that a linear array of three quantum dots, each hosting a single electron, can realize the TF gate, if we encode logic bits in the spin polarization of the electrons and allow nearest neighbor exchange coupling. The dynamics of the TF gate is realized by selectively driving spin resonances in the coupled spin system with an ac magnetic field. The conditions for gate operation are established, and an estimate of the switching speed and gate error are provided.
Polarization-dependent optical characteristics of violet InGaN laser diodes
Authors: Yen Sheng-Horng , Kuo Yen-Kuang
Published: May 2008

The polarization-dependent optical characteristics of violet InGaN laser diodes, such as band diagrams, emission wavelength, and threshold current, under different operation temperatures have been investigated numerically. Specifically, the normal and reversed polarizations are presented when the laser diodes with wurtzite structure are grown along Ga-face and N-face orientations, respectively. The simulation results show that the lowest threshold current is obtained for the double-quantum-well laser diode with normal polarization, while it is obtained for the single-quantum-well laser diode with reversed polarization. The main physical explanation for the phenomenon is due to effectively reduced electron leakage current, increased hole current density, and reduced Shockley–Read–Hall recombination rate within the active region as the idea of reversed polarization is considered.
Laser-guidance based detection of cells with single-gene modification
Authors: Ma Zhen , Burg Karen J. L. , Wei Yanzhang , Yuan X.-C. , Peng Xiang , Gao Bruce Z.
Published: May 2008

An optical method with single-gene sensitivity for cell detection based on laser guidance was explored. Guided by the optical force from a weakly focused laser beam, a cell will move along the laser axis. Cells with different properties experience different optical forces and thus guidance speeds. The guidance speeds of the TC-1 cell and its genetically modified counterpart with only one gene change, L-10 cell, were studied under the same conditions. The results demonstrated that this laser guidance-based speed-measurement method can precisely distinguish cells that differ by only one gene.
GPX5, the selenium-independent glutathione peroxidase-encoding single copy gene is differentially expressed in mouse epididymis
Authors: Zhang Ting , Chabory Eléonore , Britan Aurore , Grignard Elise , Pitiot Olivier , Saez Fabrice , Cadet Rémi , Henry-Berger Joelle , Vernet Patrick , Drevet Joël R.
Published: May 2008

Using various molecular approaches, including reverse transcription–polymerase chain reaction (RT–PCR), rapid amplification of cDNA ends–PCR, sequencing, northern and western blotting, we found that the mouse GPX5 gene gives rise to at least three different transcripts that are not expressed at the same levels in the mouse epididymis. In addition to the major GPX5 transcript, we show that minor GPX5 transcripts exist, arising either from precocious termination of transcription or an alternative splicing event within intron 4 of the 5 exon-encoding GPX5 single copy gene. Furthermore, we demonstrate that variants of the GPX5 protein that are correlated with the shorter GPX5 transcripts can be detected in caput epididymidis protein extracts and that the various GPX5 isoforms are subject to differential post-transcriptional maturation processes in the mouse epididymis that essentially involve the addition of O-glycosyl extensions. Using a sensitive poly-A+ mRNA tissue blot, as well as RT–PCR and northern assays, we further show that in addition to being expressed in the epididymis, the GPX5 gene is also expressed, albeit at lower levels, in other tissues of the male genital tract, including the testis and prostate. Finally, we present evidence suggesting that the GPX5 gene is expressed in a temporally regulated manner during mouse embryonic development.
Spatial scaling of functional gene diversity across various microbial taxa
Authors: Zhou Jizhong , Kang Sanghoon , Schadt Christopher W. , Garten Charles T.
Published: May 2008

Understanding the spatial patterns of organisms and the underlying mechanisms shaping biotic communities is a central goal in community ecology. One of the most well documented spatial patterns in plant and animal communities is the positive-power law relationship between species (or taxa) richness and area. Such taxa–area relationships (TARs) are one of the principal generalizations in ecology, and are fundamental to our understanding of the distribution of global biodiversity. However, TARs remain elusive in microbial communities, especially in soil habitats, because of inadequate sampling methodologies. Here, we describe TARs as gene–area relationships (GARs), at a whole-community level, across various microbial functional and phylogenetic groups in a forest soil, using a comprehensive functional gene array with >24,000 probes. Our analysis indicated that the forest soil microbial community exhibited a relatively flat gene–area relationship (slope
z
= 0.0624), but the
z
values varied considerably across different functional and phylogenetic groups (
z
= 0.0475–0.0959). However, the
z
values are several times lower than those commonly observed in plants and animals. These results suggest that the turnover in space of microorganisms may be, in general, lower than that of plants and animals.
Involvement of estrogen-related receptors in transcriptional response to hypoxia and growth of solid tumors
Authors: Ao Ada , Wang Heiman , Kamarajugadda Sushama , Lu Jianrong
Published: May 2008

The development of intratumoral hypoxia is a universal hallmark of rapidly growing solid tumors. Adaptation to the hypoxic environment, which is critical for tumor cell survival and growth, is mediated primarily through a hypoxia-inducible factor (HIF)-dependent transcriptional program. HIF activates genes that facilitate crucial adaptive mechanisms including increased glucose uptake and glycolysis and tumor angiogenesis, making it an important therapeutic target. However, the HIF-dependent transcriptional mechanism remains incompletely understood, and targeting HIF is a difficult endeavor. Here, we show that the orphan nuclear receptor estrogen-related receptors (ERRs) physically interact with HIF and stimulate HIF-induced transcription. Importantly, ERRs appear to be essential for HIF's function. Transcriptional activation of hypoxic genes in cells cultured under hypoxia is largely blocked by suppression of ERRs through expression of a dominant negative form of ERR or treatment with a pharmacological ERR inhibitor, diethylstilbestrol. Systematic administration of diethylstilbestrol severely diminished growth and angiogenesis of tumor xenografts
in vivo
. Because nuclear receptors are outstanding targets for drug discovery, the findings not only may offer mechanistic insights into HIF-mediated transcription but also may open new avenues for targeting the HIF pathway for cancer therapy.
T cell receptor signaling controls Foxp3 expression via PI3K, Akt, and mTOR
Authors: Sauer Stephan , Bruno Ludovica , Hertweck Arnulf , Finlay David , Leleu Marion , Spivakov Mikhail , Knight Zachary A. , Cobb Bradley S. , Cantrell Doreen , O'Connor Eric , Shokat Kevan M. , Fisher Amanda G. , Merkenschlager Matthias
Published: May 2008

Regulatory T (Treg) cells safeguard against autoimmunity and immune pathology. Because determinants of the Treg cell fate are not completely understood, we have delineated signaling events that control thede novoexpression of Foxp3 in naive peripheral CD4 T cells and in thymocytes. We report that premature termination of TCR signaling and inibition of phosphatidyl inositol 3-kinase (PI3K) p110α, p110δ, protein kinase B (Akt), or mammalian target of rapamycin (mTOR) conferred Foxp3 expression and Treg-like gene expression profiles. Conversely, continued TCR signaling and constitutive PI3K/Akt/mTOR activity antagonised Foxp3 induction. At the chromatin level, di- and trimethylation of lysine 4 of histone H3 (H3K4me2 and -3) near theFoxp3transcription start site (TSS) and within the 5′ untranslated region (UTR) preceded active Foxp3 expression and, like Foxp3 inducibility, was lost upon continued TCR stimulation. These data demonstrate that the PI3K/Akt/mTOR signaling network regulates Foxp3 expression.
High-fat diets cause insulin resistance despite an increase in muscle mitochondria
Authors: Hancock Chad R. , Han Dong-Ho , Chen May , Terada Shin , Yasuda Toshihiro , Wright David C. , Holloszy John O.
Published: May 2008

It has been hypothesized that insulin resistance is mediated by a deficiency of mitochondria in skeletal muscle. In keeping with this hypothesis, high-fat diets that cause insulin resistance have been reported to result in a decrease in muscle mitochondria. In contrast, we found that feeding rats high-fat diets that cause muscle insulin resistance results in a concomitant gradual increase in muscle mitochondria. This adaptation appears to be mediated by activation of peroxisome proliferator-activated receptor (PPAR)δ by fatty acids, which results in a gradual, posttranscriptionally regulated increase in PPAR γ coactivator 1α (PGC-1α) protein expression. Similarly, overexpression of PPARδ results in a large increase in PGC-1α protein in the absence of any increase in PGC-1α mRNA. We interpret our findings as evidence that raising free fatty acids results in an increase in mitochondria by activating PPARδ, which mediates a posttranscriptional increase in PGC-1α. Our findings argue against the concept that insulin resistance is mediated by a deficiency of muscle mitochondria.
Surface Expression of Epithelial Na Channel Protein in Rat Kidney
Authors: Frindt Gustavo , Ergonul Zuhal , Palmer Lawrence G.
Published: May 2008

Expression of epithelial Na channel (ENaC) protein in the apical membrane of rat kidney tubules was assessed by biotinylation of the extracellular surfaces of renal cells and by membrane fractionation. Rat kidneys were perfused in situ with solutions containing NHS-biotin, a cell-impermeant biotin derivative that attaches covalently to free amino groups on lysines. Membranes were solubilized and labeled proteins were isolated using neutravidin beads, and surface β and γENaC subunits were assayed by immunoblot. Surface αENaC was assessed by membrane fractionation. Most of the γENaC at the surface was smaller in molecular mass than the full-length subunit, consistent with cleavage of this subunit in the extracellular moiety close to the first transmembrane domains. Insensitivity of the channels to trypsin, measured in principal cells of the cortical collecting duct by whole-cell patch-clamp recording, corroborated this finding. ENaC subunits could be detected at the surface under all physiological conditions. However increasing the levels of aldosterone in the animals by feeding a low-Na diet or infusing them directly with hormone via osmotic minipumps for 1 wk before surface labeling increased the expression of the subunits at the surface by two- to fivefold. Salt repletion of Na-deprived animals for 5 h decreased surface expression. Changes in the surface density of ENaC subunits contribute significantly to the regulation of Na transport in renal cells by mineralocorticoid hormone, but do not fully account for increased channel activity.
Genotypic Evolution of Acinetobacter baumannii Strains in an Outbreak Associated With War Trauma
Authors: Wortmann Glenn , Weintrob Amy , Barber Melissa , Scott Paul , Zoll Scott T. , Eshoo Mark W. , Sampath Rangarajan , Ecker David J. , Massire Christian
Published: May 2008

The Walter Reed Army Medical Center has experienced an influx of traumatically injured patients either infected or colonized with Acinetobacter baumannii. Using multilocus polymerase chain reaction (PCR) and mass spectrometry to genotype isolates, we found an atypical and evolving strain distribution, distinct from those found at nonmilitary hospitals in the United States.
Ubc4/5 and c-Cbl Continue to Ubiquitinate EGF Receptor after Internalization to Facilitate Polyubiquitination and Degradation
Authors: Umebayashi Kyohei , Stenmark Harald , Yoshimori Tamotsu
Published: May 2008

c-Cbl is the E3 ubiquitin ligase that ubiquitinates the epidermal growth factor (EGF) receptor (EGFR). On the basis of localization, knockdown, and in vitro activity analyses, we have identified the E2 ubiquitin-conjugating enzyme that cooperates with c-Cbl as Ubc4/5. Upon EGF stimulation, both Ubc4/5 and c-Cbl were relocated to the plasma membrane and then to Hrs-positive endosomes, strongly suggesting that EGFR continues to be ubiquitinated after internalization. Our time-course experiment showed that EGFR undergoes polyubiquitination, which seemed to be facilitated during the transport to Hrs-positive endosomes. Use of a conjugation-defective ubiquitin mutant suggested that receptor polyubiquitination is required for efficient interaction with Hrs and subsequent sorting to lysosomes. Abrupt inhibition of the EGFR kinase activity resulted in dissociation of c-Cbl from EGFR. Concomitantly, EGFR was rapidly deubiquitinated and its degradation was delayed. We propose that sustained tyrosine phosphorylation of EGFR facilitates its polyubiquitination in endosomes and counteracts rapid deubiquitination, thereby ensuring Hrs-dependent lysosomal sorting.
Fas Splicing Regulation during Early Apoptosis Is Linked to Caspase-mediated Cleavage of U2AF65
Authors: Izquierdo José M.
Published: May 2008

U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor 65 kDa (U2AF65) is an essential splicing factor in the recognition of the pre-mRNA 3′ splice sites during the assembly of the splicing commitment complex. We report here that U2AF65 is proteolyzed during apoptosis. This cleavage is group I or III caspase dependent in a noncanonical single site localized around the aspartic acid128residue and leads to the separation of the N- and C-terminal parts of U2AF65. The U2AF65 N-terminal fragment mainly accumulates in the nucleus within nuclear bodies (nucleoli-like pattern) and to a much lesser extent in the cytoplasm, whereas the C-terminal fragment is found in the cytoplasm, even in localization studies on apoptosis induction. From a functional viewpoint, the N-terminal fragment promotes Fas exon 6 skipping from a reporter minigene, by acting as a dominant-negative version of U2AF65, whereas the C-terminal fragment has no significant effect. The dominant-negative behavior of the U2AF65 N-terminal fragment can be reverted by U2AF35 overexpression. Interestingly, U2AF65 proteolysis in Jurkat cells on induction of early apoptosis correlates with the down-regulation of endogenous Fas exon 6 inclusion. Thus, these results support a functional link among apoptosis induction, U2AF65 cleavage, and the regulation of Fas alternative splicing.
The Yeast GID Complex, a Novel Ubiquitin Ligase (E3) Involved in the Regulation of Carbohydrate Metabolism
Authors: Santt Olivier , Pfirrmann Thorsten , Braun Bernhard , Juretschke Jeannette , Kimmig Philipp , Scheel Hartmut , Hofmann Kay , Thumm Michael , Wolf Dieter H.
Published: May 2008

Glucose-dependent regulation of carbon metabolism is a subject of intensive studies. We have previously shown that the switch from gluconeogenesis to glycolysis is associated with ubiquitin-proteasome linked elimination of the key enzyme fructose-1,6-bisphosphatase. Seven glucose induced degradation deficient (Gid)-proteins found previously in a genomic screen were shown to form a complex that binds FBPase. One of the subunits, Gid2/Rmd5, contains a degenerated RING finger domain. In an in vitro assay, heterologous expression of GST-Gid2 leads to polyubiquitination of proteins. In addition, we show that a mutation in the degenerated RING domain of Gid2/Rmd5 abolishes fructose-1,6-bisphosphatase polyubiquitination and elimination in vivo. Six Gid proteins are present in gluconeogenic cells. A seventh protein, Gid4/Vid24, occurs upon glucose addition to gluconeogenic cells and is afterwards eliminated. Forcing abnormal expression of Gid4/Vid24 in gluconeogenic cells leads to fructose-1,6-bisphosphatase degradation. This suggests that Gid4/Vid24 initiates fructose-1,6-bisphosphatase polyubiquitination by the Gid complex and its subsequent elimination by the proteasome. We also show that an additional gluconeogenic enzyme, phosphoenolpyruvate carboxykinase, is subject to Gid complex-dependent degradation. Our study uncovers a new type of ubiquitin ligase complex composed of novel subunits involved in carbohydrate metabolism and identifies Gid4/Vid24 as a major regulator of this E3.
InteroPORC: automated inference of highly conserved protein interaction networks
Authors: Michaut Magali , Kerrien Samuel , Montecchi-Palazzi Luisa , Chauvat Franck , Cassier-Chauvat Corinne , Aude Jean-Christophe , Legrain Pierre , Hermjakob Henning
Published: May 2008

Motivation: Protein–protein interaction networks provide insights into the relationships between the proteins of an organism thereby contributing to a better understanding of cellular processes. Nevertheless, large-scale interaction networks are available for only a few model organisms. Thus, interologs are useful for a systematic transfer of protein interaction networks between organisms. However, no standard tool is available so far for that purpose.

Results: In this study, we present an automated prediction tool developed for all sequenced genomes available in Integr8. We also have developed a second method to predict protein–protein interactions in the widely used cyanobacterium Synechocystis. Using these methods, we have constructed a new network of 8783 inferred interactions for Synechocystis.

Availability: InteroPORC is open-source, downloadable and usable through a web interface at http://biodev.extra.cea.fr/interoporc/

Contact:  michaut.bioinfo@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Prevalence and Predictors of Mental Health Distress Post-Katrina: Findings From the Gulf Coast Child and Family Health Study
Authors: Abramson David , Stehling-Ariza Tasha , Garfield Richard , Redlener Irwin
Published: May 2008

Background:Catastrophic disasters often are associated with massive structural, economic, and population devastation; less understood are the long-term mental health consequences. This study measures the prevalence and predictors of mental health distress and disability of hurricane survivors over an extended period of recovery in a postdisaster setting.

Methods:A representative sample of 1077 displaced or greatly affected households was drawn in 2006 using a stratified cluster sampling of federally subsidized emergency housing settings in Louisiana and Mississippi, and of Mississippi census tracts designated as having experienced major damage from Hurricane Katrina in 2005. Two rounds of data collection were conducted: a baseline face-to-face interview at 6 to 12 months post-Katrina, and a telephone follow-up at 20 to 23 months after the disaster. Mental health disability was measured using the Medical Outcome Study Short Form 12, version 2 mental component summary score. Bivariate and multivariate analyses were conducted examining socioeconomic, demographic, situational, and attitudinal factors associated with mental health distress and disability.

Results:More than half of the cohort at both baseline and follow-up reported significant mental health distress. Self-reported poor health and safety concerns were persistently associated with poorer mental health. Nearly 2 years after the disaster, the greatest predictors of poor mental health included situational characteristics such as greater numbers of children in a household and attitudinal characteristics such as fatalistic sentiments and poor self-efficacy. Informal social support networks were associated significantly with better mental health status. Housing and economic circumstances were not independently associated with poorer mental health.

Conclusions:Mental health distress and disability are pervasive issues among the US Gulf Coast adults and children who experienced long-term displacement or other serious effects as a result of Hurricanes Katrina and Rita. As time progresses postdisaster, social and psychological factors may play greater roles in accelerating or impeding recovery among affected populations. Efforts to expand disaster recovery and preparedness policies to include long-term social re-engagement efforts postdisaster should be considered as a means of reducing mental health sequelae. (Disaster Med Public Health Preparedness. 2008;2:77–86)
Fluttering wing feathers produce the flight sounds of male streamertail hummingbirds
Authors: Clark Christopher James
Published: May 2008

Sounds produced continuously during flight potentially play important roles in avian communication, but the mechanisms underlying these sounds have received little attention. Adult male Red-billed Streamertail hummingbirds (Trochilus polytmus) bear elongated tail streamers and produce a distinctive ‘whirring’ flight sound, whereas subadult males and females do not. The production of this sound, which is a pulsed tone with a mean frequency of 858 Hz, has been attributed to these distinctive tail streamers. However, tail-less streamertails can still produce the flight sound. Three lines of evidence implicate the wings instead. First, it is pulsed in synchrony with the 29 Hz wingbeat frequency. Second, a high-speed video showed that primary feather eight (P8) bends during each downstroke, creating a gap between P8 and primary feather nine (P9). Manipulating either P8 or P9 reduced the production of the flight sound. Third, laboratory experiments indicated that both P8 and P9 can produce tones over a range of 700–900 Hz. The wings therefore produce the distinctive flight sound, enabled via subtle morphological changes to the structure of P8 and P9.
Boolean network models of cellular regulation: prospects and limitations
Authors: Bornholdt Stefan
Published: May 2008

Computer models are valuable tools towards an understanding of the cell's biochemical regulatory machinery. Possible levels of description of such models range from modelling the underlying biochemical details to top-down approaches, using tools from the theory of complex networks. The latter, coarse-grained approach is taken where regulatory circuits are classified in graph-theoretical terms, with the elements of the regulatory networks being reduced to simply nodes and links, in order to obtain architectural information about the network. Further, considering dynamics on networks at such an abstract level seems rather unlikely to match dynamical regulatory activity of biological cells. Therefore, it came as a surprise when recently examples of discrete dynamical network models based on very simplistic dynamical elements emerged which in fact do match sequences of regulatory patterns of their biological counterparts. Here I will review such discrete dynamical network models, or Boolean networks, of biological regulatory networks. Further, we will take a look at such models extended with stochastic noise, which allow studying the role of network topology in providing robustness against noise. In the end, we will discuss the interesting question of why at all such simple models can describe aspects of biology despite their simplicity. Finally, prospects of Boolean models in exploratory dynamical models for biological circuits and their mutants will be discussed.
A common tendency for phylogenetic overdispersion in mammalian assemblages
Authors: Cooper Natalie , Rodríguez Jesús , Purvis Andy
Published: May 2008

Competition has long been proposed as an important force in structuring mammalian communities. Although early work recognized that competition has a phylogenetic dimension, only with recent increases in the availability of phylogenies have true phylogenetic investigations of mammalian community structure become possible. We test whether the phylogenetic structure of 142 assemblages from three mammalian clades (New World monkeys, North American ground squirrels and Australasian possums) shows the imprint of competition. The full set of assemblages display a highly significant tendency for members to be more distantly related than expected by chance (phylogenetic overdispersion). The overdispersion is also significant within two of the clades (monkeys and squirrels) separately. This is the first demonstration of widespread overdispersion in mammal assemblages and implies an important role for either competition between close relatives where traits are conserved, habitat filtering where distant relatives share convergent traits, or both.
Lifelong commitment to the wrong partner: hybridization in ants
Authors: Feldhaar Heike , Foitzik Susanne , Heinze Jürgen
Published: May 2008

The extraordinary lifelong partner commitment in social insects is expected to increase choosiness in both sexes and therefore to be associated with particularly low hybridization frequencies. Yet, more and more studies reveal that in many ant taxa hybrids are surprisingly common, with up to half of all female sexuals receiving sperm from allospecific males in extreme cases. In a few ant species, hybridization has led to the evolution of reproductively isolated new lineages with a bizarre system of genetic caste differentiation: colonies produce hybrid workers and pure-lineage female sexuals. This requires that colonies either contain multiple queens or that queens mate multiple times. In most other cases, hybridization appears to be an evolutionary dead end and fertile hybrid queens are rarely found. In such cases, haplodiploid sex determination appears to decrease the costs of mating with an allospecific male. As long as hybrid workers are viable, a cross-mated queen can partially rescue its fitness by producing males from unfertilized eggs. Mating with an allospecific partner may thus be an option for queens when conspecific mates are not available. The morphological similarity of most ant males, perhaps resulting from the lack of sexual conflict, may similarly contribute to the commonness of hybridization.
Daphniahybridization along ecological gradients in pelagic environments: the potential for the presence of hybrid zones in plankton
Authors: Petrusek Adam , Seda Jaromír , Macháček Jiří , Ruthová Štěpánka , Šmilauer Petr
Published: May 2008

The relative homogeneity of pelagic environments has been regarded as the reason for the absence of hybrid zones for hybridizing planktonicDaphnia(Crustacea: Cladocera); occasional dominance of interspecific hybrids over parental species was explained by their temporal superiority in fluctuating environments. However, water bodies with spatially varying environmental conditions might facilitate the formation of hybrid zones in plankton. We studied the distribution of species and hybrids of theDaphnia longispinacomplex in 11 canyon-shaped reservoirs, localities characterized by horizontal environmental gradients (particularly of food supply and size-selective predation); we also analysed patterns of carapace size and fecundity among coexisting taxa. Spatial distribution of taxa agreed with their ecological characteristics; those showing different affinities along longitudinal reservoir profiles differed in size according to the presumed fish predation gradient. Only hybrids ofDaphnia galeatawithDaphnia cucullataandD. longispina(=hyalina) were recorded. The latter two species preferred opposite ends of gradients, such spatial segregation probably explaining the absence of their hybrids. Distributional patterns were relatively stable in two consecutive summers, apart from a substantial decline ofD. galeata×cucullatain the second year. The observed pattern of a hybrid-dominated zone in intermediate conditions suggests that localDaphniahybrid zones may indeed form within reservoirs.
Bayesian inference of species hybrids using multilocus dominant genetic markers
Authors: Anderson Eric C
Published: May 2008

Neutral genetic markers are useful for identifying species hybrids in natural populations, especially when used in conjunction with statistical methods like the one implemented in the softwareNewHybrids. Here, a short description of the extension ofNewHybridsto dominant markers is given. Subsequently, an extensive series of simulations of amplified fragment length polymorphism (AFLP) data is performed to evaluate the prospects for hybrid identification with (possibly non-diagnostic) dominant markers. Distinguishing between F1's and F2's is shown to be difficult, possibly requiring upwards of 100 AFLP markers to be done accurately. Discriminating between pure-bred and non-pure (hybrid) individuals, however, is shown to be much easier, requiring perhaps as few as 10 dominant markers, even from relatively weakly diverged species.
Female mating preference functions predict sexual selection against hybrids between sibling species of cichlid fish
Authors: van der Sluijs Inke , Van Dooren Tom J.M , Hofker Kees D , van Alphen Jacques J.M , Stelkens Rike B , Seehausen Ole
Published: May 2008

The evolutionary outcome of interspecific hybridization, i.e. collapse of species into a hybrid swarm, persistence or even divergence with reinforcement, depends on the balance between gene flow and selection against hybrids. If female mating preferences are open-ended but sign-inversed between species, they can theoretically be a source of such selection. Cichlid fish in African lakes have sustained high rates of speciation despite evidence for widespread hybridization, and sexual selection by female choice has been proposed as important in the origin and maintenance of species boundaries. However, it had never been tested whether hybridizing species have open-ended preference rules. Here we report the first experimental test usingPundamilia pundamilia,Pundamilia nyerereiand their hybrids in three-way choice experiments. Hybrid males are phenotypically intermediate. Wild-caught females of both species have strong preferences for conspecific over heterospecific males. Their responses to F1hybrid males are intermediate, but more similar to responses to conspecifics in one species and more similar to responses to heterospecifics in the other. We suggest that their mate choice mechanism may predispose haplochromine cichlids to maintain and perhaps undergo phenotypic diversification despite hybridization, and that species differences in female preference functions may predict the potential for adaptive trait transfer between hybridizing species.
The ubiquitous mountain hare mitochondria: multiple introgressive hybridization in hares, genusLepus
Authors: Alves Paulo C , Melo-Ferreira José , Freitas Hélder , Boursot Pierre
Published: May 2008

Climatic oscillations during the glaciations forced dramatic changes in species distributions, such that some presently temperate regions were alternately occupied by temperate and arctic species. These species could have met and hybridized during climatic transitions. This phenomenon happened for three hare species present in Iberia (Lepus granatensis,Lepus europaeusandLepus castroviejoi), which display high frequencies of mitochondrial DNA (mtDNA) fromLepus timidus, an arctic/boreal species presently extinct in Iberia. Here, we extend our previous geographical survey to determine whether the distribution of this mtDNA lineage extends beyond the northern half of the Iberian Peninsula, where it is found at high frequencies. We also review the taxonomy, distribution and molecular phylogeny of the genusLepus. The phylogenetic inference reveals the presence ofL. timidus-like mtDNA in several other hare species in Asia and North America, suggesting that the mitochondrial introgression observed in Iberia might be generalized. Comparison with the available nuclear gene phylogenies suggests that introgression could have happened repeatedly, possibly during different climatic transitions. We discuss demographic and adaptive scenarios that could account for the repetition in time and space of this spectacular phenomenon and suggest ways to improve our understanding of its determinants and consequences. Such high levels of introgressive hybridization should discourage attempts to revise hare taxonomy based solely on mtDNA.
Evidence for recovery of fear following immediate extinction in rats and humans
Authors: Schiller Daniela , Cain Christopher K. , Curley Nina G. , Schwartz Jennifer S. , Stern Sarah A. , LeDoux Joseph E. , Phelps Elizabeth A.
Published: May 2008

Fear responses can be eliminated through extinction, a procedure involving the presentation of fear-eliciting stimuli without aversive outcomes. Extinction is believed to be mediated by new inhibitory learning that acts to suppress fear expression without erasing the original memory trace. This hypothesis is supported mainly by behavioral data demonstrating that fear can recover following extinction. However, a recent report by Myers and coworkers suggests that extinction conducted immediately after fear learning may erase or prevent the consolidation of the fear memory trace. Since extinction is a major component of nearly all behavioral therapies for human fear disorders, this finding supports the notion that therapeutic intervention beginning very soon after a traumatic event will be more efficacious. Given the importance of this issue, and the controversy regarding immediate versus delayed therapeutic interventions, we examined two fear recovery phenomena in both rats and humans: spontaneous recovery (SR) and reinstatement. We found evidence for SR and reinstatement in both rats and humans even when extinction was conducted immediately after fear learning. Thus, our data do not support the hypothesis that immediate extinction erases the original memory trace, nor do they suggest that a close temporal proximity of therapeutic intervention to the traumatic event might be advantageous.
Physiological and Transcriptomic Aspects of Urea Uptake and Assimilation in Arabidopsis Plants
Authors: Mérigout Patricia , Lelandais Maud , Bitton Frédérique , Renou Jean-Pierre , Briand Xavier , Meyer Christian , Daniel-Vedele Françoise
Published: May 2008

Urea is the major nitrogen (N) form supplied as fertilizer in agriculture, but it is also an important N metabolite in plants. Urea transport and assimilation were investigated in Arabidopsis (Arabidopsis thaliana). Uptake studies using 15N-labeled urea demonstrated the capacity of Arabidopsis to absorb urea and that the urea uptake was regulated by the initial N status of the plants. Urea uptake was stimulated by urea but was reduced by the presence of ammonium nitrate in the growth medium. N deficiency in plants did not affect urea uptake. Urea exerted a repressive effect on nitrate influx, whereas urea enhanced ammonium uptake. The use of [15N]urea and [15N]ammonium tracers allowed us to show that urea and ammonium assimilation pathways were similar. Finally, urea uptake was less efficient than nitrate uptake, and urea grown-plants presented signs of N starvation. We also report the first analysis, to our knowledge, of Arabidopsis gene expression profiling in response to urea. Our transcriptomic approach revealed that nitrate and ammonium transporters were transcriptionally regulated by urea as well as key enzymes of the glutamine synthetase-glutamate synthase pathway. AtDUR3, a high-affinity urea transporter in Arabidopsis, was strongly up-regulated by urea. Moreover, our transcriptomic data suggest that other genes are also involved in urea influx.