bluuebunny/crossref_metadata_2025 huggingface dataset:
Photoemission study of oxygen and Au modification of doped copper phthalocyanine
Authors: Ding Huanjun , Gao Yongli
Published: August 2007

The modifications of the electronic structure of heavily Cs-doped copper phthalocyanine (CuPc) by oxygen exposure and by Au deposition have been investigated with ultraviolet and x-ray photoemission spectroscopy. To a certain degree, both oxygen and Au act like p-type dopants and compensate the n-doping effects by Cs in CuPc, including the energy level shift and the gap state. However, the compensation to the electronic structure is incomplete, and it is found that the effect of 1 ML of Au deposition is about equivalent to 300L (1L=10−6torrs) of oxygen exposure. The quenching of the Cs-induced gap state is observed to depend exponentially on the Au deposition. The core level behavior provides additional information on the charge redistribution in the CuPc molecule.
Crystallization, stress, and stress-relieve due to nickel in amorphous silicon thin films
Authors: Zanatta A. R. , Ferri F. A.
Published: August 2007

The structural properties of amorphous silicon (a-Si) films containing 1 and 10 at. % of nickel have been studied by Raman scattering spectroscopy. The films, typically 2 μm thick, were deposited onto crystalline quartz substrates by sputtering a Si+Ni target in an atmosphere of pure argon. For comparison purposes, one Ni-free a-Si film deposited under the same experimental conditions was also investigated. After deposition the films were thermally annealed for cumulative periods of 15 min in the 200–1000 °C temperature range. The present experimental results indicate that: (1) compared to the Ni-free a-Si film, the crystallization of a-SiNi0.01 and a-SiNi0.1 takes place at temperatures ∼200 °C lower; (2) allied to the thermal treatments, the presence of Ni also affects the stress present in the a-Si films; (3) the partial crystallization of the Ni-free Si film increases its original compressive (thermal) stress up to ∼1 GPa; and (4) thermal annealing at temperatures higher than 800 °C induce a stress-relieve in the Ni-containing Si films, which is tentatively attributed to the development of nanostructured features on the surface of the samples.
Exact Heisenberg operator solutions for multiparticle quantum mechanics
Authors: Odake Satoru , Sasaki Ryu
Published: August 2007

Exact Heisenberg operator solutions for independent “sinusoidal coordinates” as many as the degree of freedom are derived for typical exactly solvable multiparticle quantum mechanical systems, the Calogero systems [J. Math. Phys. 12, 419 (1971)] based on any root system. These Heisenberg operator solutions also present the explicit forms of the annihilation-creation operators for various quanta in the interacting multiparticle systems. At the same time they can be interpreted as multivariable generalization of the three term recurrence relations for multivariable orthogonal polynomials constituting the eigenfunctions.
X-ray probe of the polar nanoregions in the relaxor ferroelectric 0.72Pb(Mg1∕3Nb2∕3)O3–0.28PbTiO3
Authors: Guo Zhi , Tai Renzhong , Xu Hongjie , Gao Chen , Pan Guoqiang , Luo Haosu , Namikawa Kazumichi
Published: August 2007

The average, spontaneous (zero field) structure of the polar nanoregions (PNRs) in a single crystal specimen of the relaxor ferroelectric 0.72Pb(Mg1∕3Nb2∕3)O3–0.28PbTiO3 has been characterized above Tm by partially coherent x-ray diffraction. At these temperatures, the PNRs are randomly distributed within the crystal and exhibit dimensions of 17 and 10nm along the [001] and [100] directions, respectively. Based on the results of a previous study [Z. Guo et al., J. Appl. Phys. 101, 053505 (2007)], the long dimension of the PNR is observed to reorient preferentially along the four degenerate diagonal axes [1±1±1], which is believed to contribute to the high electromechanical response in these relaxor materials.
High density single molecule surface patterning with colloidal epitaxy
Authors: Schwartz Jerrod J. , Quake Stephen R.
Published: August 2007

Simple and inexpensive methods for dense surface patterning of single molecules will help realize the massive potential throughput of molecular arrays in biology and nanoscience. To surpass the resolvable density limit imposed by random deposition, the authors have developed a method that uses colloids to pattern single molecules at a fixed length scale. They demonstrate the ability to pattern fluorescently labeled DNA such that ∼38% of the available diffraction-limited regions contain exactly one molecule. This density is slightly less than the theoretical limit suggested by Monte Carlo simulations but surpasses the random deposition limit by more than threefold.
Electrical detection of the ferromagnetic resonance: Spin-rectification versus bolometric effect
Authors: Gui Y. S. , Mecking N. , Wirthmann A. , Bai L. H. , Hu C.-M.
Published: August 2007

The authors have investigated the dc resistance change of a Permalloy microstrip under microwave irradiation. The experimental results demonstrate that both the spin-rectification and the bolometric effects significantly affect the dc resistance change, and the contribution of each can be precisely determined due to their different dependences on the modulation frequency of the microwave. Therefore, both the cone angle of magnetization precession and the thermal relaxation time following microwave heating are obtained.
Domain structure evolution and fatigue cracking of ⟨001⟩-oriented [Pb(Mg1∕3Nb2∕3)O3]0.67(PbTiO3)0.33 ferroelectric single crystals under cyclic electric loading
Authors: Fang F. , Yang W. , Zhang F. C. , Qing H.
Published: August 2007

The authors report on the electrically induced fatigue cracking and phase transition behavior for ⟨001⟩-oriented [Pb(Mg1∕3Nb2∕3)O3]0.67(PbTiO3)0.33 (PMN-PT 67∕33) ferroelectric single crystals under cyclic electric field. For crystals with initial cracks, crack growth and deviation are associated with the transition from the rhombohedral to the tetragonal phase, even though the peak value of the applied cyclic electric field is below the coercive field (Ec). For crystals without initial cracks, numerous microcracks are developed in the crystal as a result of 71° domain switching.
Ultraviolet mechanoluminescence from SrAl2O4:Ce and SrAl2O4:Ce,Ho
Authors: Zhang Hongwu , Yamada Hiroshi , Terasaki Nao , Xu Chao-Nan
Published: August 2007

Phosphors with ultraviolet (UV) mechanoluminescence (ML) SrAl2O4:Ce (SAOCe) and SrAl2O4:Ce,Ho (SAOHoCe) were reported in this letter. The results reveal that the ML emission band is located at 375nm similar to photoluminescent (PL) peak, which indicates that ML is emitted from the same center of Ce3+ ions as PL. Furthermore, the addition of Ho3+ increases the UV ML intensity of SAOHoCe (56nJ∕loadcycle) considerably [approximately two orders of magnitude greater than that of SAOCe (0.21nJ∕loadcycle)]. The formation of many shallow traps (Ho3+−e−) may be responsible for this enhancement.
Dember effect induced photovoltage in perovskite p-n heterojunctions
Authors: Jin Kui-Juan , Zhao Kun , Lu Hui-Bin , Liao Leng , Yang Guo-Zhen
Published: August 2007

An unusual and rather large transient lateral photovoltage (LPV) has been observed in La0.9Sr0.1MnO3∕SrNb0.01Ti0.99O3 and La0.7Sr0.3MnO3∕Si heterojunctions under the nonuniform irradiation of pulsed laser. The irreversible LPVs on both sides of a p-n junction challenge the well established model for LPV in conventional semiconductor p-n junctions, which can be well explained by the Dember effect. Much larger LPV is observed in La0.7Sr0.3MnO3∕Si than that in La0.9Sr0.1MnO3∕SrNb0.01Ti0.99O3. Similar results measured from both substrates of SrNb0.01Ti0.99O3 and Si also support such a Dember effect. Much larger LPVs in heterojunctions than those in simple samples (SrNb0.01Ti0.99O3 or Si) suggest a potential application of Dember effect in heterostructures.
Insulator-to-metal transition in ZnO by electric double layer gating
Authors: Shimotani Hidekazu , Asanuma Haruhiko , Tsukazaki Atsushi , Ohtomo Akira , Kawasaki Masashi , Iwasa Yoshihiro
Published: August 2007

The authors report high-density carrier accumulation and a gate-induced insulator-to-metal transition in ZnO single-crystalline thin-film field effect transistors by adopting electric double layers as gate dielectrics. Hall effect measurements showed that a sheet carrier density of 4.2×1013cm−2 was achieved. The highest sheet conductance at room temperature was ∼1mS, which was sufficient to maintain the metallic state down to 10K. These results strongly suggest the versatility of electric double layer gating for various materials.
Highly optical damage resistant crystal: Zirconium-oxide-doped lithium niobate
Authors: Kong Yongfa , Liu Shiguo , Zhao Yanjun , Liu Hongde , Chen Shaolin , Xu Jingjun
Published: August 2007

Usage of lithium niobate in nonlinear optics is seriously hampered by optical damage, in particular, where high intensity is needed. Doping with magnesium can improve its resistance against optical damage. However, since a rather large dopant concentration is required (more than 4.6mol% MgO) and since the distribution coefficient is unfavorable, it is difficult to grow crystals of high optical quality. The authors show that by doping with zirconium, one can obtain at the same time a higher resistance against optical damage, a lower doping threshold (only 2.0mol% ZrO2), a distribution coefficient near 1.0, and a low coercive field that is only one-third of that of congruent LiNbO3. These properties suggest that zirconium-doped lithium niobate is an excellent choice for nonlinear optical applications.
Surface phonon polariton mode of wurtzite structure AlxGa1−xN (⩽x⩽1) thin films
Authors: Ng S. S. , Hassan Z. , Abu Hassan H.
Published: August 2007

Surface phonon polariton (SPP) mode of wurtzite structure AlxGa1−xN (0⩽x⩽1) thin films is investigated experimentally and theoretically. The influences of the alloy composition x on the position and the line width of SPP mode are reported. The results showed that the SPP absorption peak exhibits one-mode behavior and is subjected to broadening as x is increased. Reasonable agreement between the experimental and the theoretical results is also obtained. Finally, the composition dependence of the SPP mode with bowing parameter of −72.5cm−1 is determined.
Observation of room temperature ferromagnetic behavior in cluster-free, Co doped HfO2 films
Authors: Chang Y. H. , Soo Y. L. , Lee W. C. , Huang M. L. , Lee Y. J. , Weng S. C. , Sun W. H. , Hong M. , Kwo J. , Lee S. F. , Ablett J. M. , Kao C.-C.
Published: August 2007

Extensive structural and magnetic analyses of Hf1−xCoxO2 thin films grown by molecular beam epitaxy are reported. Nearly cobalt cluster-free film with x=0.04–0.1 was obtained via 100°C growth, and Co ions are inferred to be located at interstitial site. Ferromagnetic behavior was observed up to 300K in both magnetization curves and temperature dependence of the moment. Via post-oxygen-annealing studies, a qualitative correlation between saturation magnetization and oxygen vacancy concentration is established, consistent with the impurity-band exchange model, and that the occurrence of ferromagnetic insulator behavior in the Co doped HfO2 is more probable than Co doped ZnO, TiO2, and SnO2 systems for doping concentrations under cation percolation threshold.
High quality SrTiO3 tunnel barrier obtained by pulsed laser deposition
Authors: Fix T. , Da Costa V. , Ulhaq-Bouillet C. , Colis S. , Dinia A. , Bouzehouane K. , Barthélémy A.
Published: August 2007

The quality of a SrTiO3 tunnel barrier deposited by pulsed laser deposition on SrTiO3 (001)‖Sr2FeMoO6 is investigated. Epitaxy and two-dimensional growth are obtained and the root-mean-square roughness is 0.3nm. The distribution of the local current measured by conductive atomic force microscopy indicates that hot spots are almost absent. The standard deviation of the barrier thickness distribution is lower than 0.05nm. Current-voltage characteristics of patterned magnetic tunnel junctions provide evidence of the high quality of the barrier. The electrical properties of the SrTiO3 barrier are at least as good as the ones obtained by sputtering or e-beam evaporation.
Magnetic coupling in Ge nanoparticles
Authors: Liou Y. , Lee M. S. , You K. L.
Published: August 2007

Ferromagnetism in Ge nanoparticles fabricated by inert gas condensation was investigated. The magnetization was influenced by both the size and the density of Ge nanoparticles. The size was determined by the helium pressure and the density was controlled by depositing Ge nanoparticles on Si substrates at different locations. As the density was increased, the interparticle distance was reduced, which enhanced the magnetic coupling among Ge nanoparticles. The magnetism in Ge nanoparticles was attributed to both the quantum size effect and the magnetic coupling among Ge nanoparticles. By capping a layer over the Ge nanoparticles the magnetization was also enhanced.
Ultrafine nanoporous gold by low-temperature dealloying and kinetics of nanopore formation
Authors: Qian L. H. , Chen M. W.
Published: August 2007

A low-temperature dealloying technique was developed to tailor the characteristic length scale of nanoporous gold for advanced functional applications. By systematically investigating the kinetics of nanopore formation during free corrosion, the authors experimentally demonstrated that the dealloying process is controlled by the diffusion of gold atoms at alloy/electrolyte interfaces, which strongly relies on the reaction temperatures. Low dealloying temperatures significantly reduce the interfacial diffusivity of gold atoms and result in an ultrafine nanoporous structure that has been proved to be useful with improved chemical and physical properties.
Optical investigations and exciton localization in high quality Zn1−xMgxO–ZnO single quantum wells
Authors: Al-Suleiman M. , El-Shaer A. , Bakin A. , Wehmann H.-H. , Waag A.
Published: August 2007

This work investigates the photoluminescence properties of Zn1−xMgxO–ZnO single quantum wells, which have been fabricated by molecular-beam epitaxy. With increasing temperature from 13to300K the single quantum well-related emission peaks exhibit an irregular S-shaped (redshift-blueshift-redshift) behavior, which is in contrast with that ascribed to band gap shrinkage (redshift). In order to clarify the origin of this behavior, the temperature dependence of the integral photoluminescence intensity of the quantum well emission was studied and the relevant activation energies were calculated and correlated to its full width at half maximum, band offsets, and monolayer fluctuations.
Genetic inhibition of cardiac ERK1/2 promotes stress-induced apoptosis and heart failure but has no effect on hypertrophy
in vivo
Authors: Purcell Nicole H. , Wilkins Benjamin J. , York Allen , Saba-El-Leil Marc K. , Meloche Sylvain , Robbins Jeffrey , Molkentin Jeffery D.
Published: August 2007

MAPK signaling pathways function as critical regulators of cellular differentiation, proliferation, stress responsiveness, and apoptosis. One branch of the MAPK signaling pathway that culminates in ERK1/2 activation is hypothesized to regulate the growth and adaptation of the heart to both physiologic and pathologic stimuli, given its known activation in response to virtually every stress- and agonist-induced hypertrophic stimulus examined to date. Here we investigated the requirement of ERK1/2 signaling in mediating the cardiac hypertrophic growth response in
Erk1
−/−
and
Erk2
+/−
mice, as well as in transgenic mice with inducible expression of an ERK1/2-inactivating phosphatase in the heart, dual-specificity phosphatase 6. Although inducible expression of dual-specificity phosphatase 6 in the heart eliminated ERK1/2 phosphorylation at baseline and after stimulation without affecting any other MAPK, it did not diminish the hypertrophic response to pressure overload stimulation, neuroendocrine agonist infusion, or exercise. Similarly,
Erk1
−/−
and
Erk2
+/−
mice showed no reduction in pathologic or physiologic stimulus-induced cardiac growth
in vivo
. However, blockade or deletion of cardiac ERK1/2 did predispose the heart to decompensation and failure after long-term pressure overload in conjunction with an increase in myocyte TUNEL. Thus, ERK1/2 signaling is not required for mediating physiologic or pathologic cardiac hypertrophy
in vivo
, although it does play a protective role in response to pathologic stimuli.
How gene order is influenced by the biophysics of transcription regulation
Authors: Kolesov Grigory , Wunderlich Zeba , Laikova Olga N. , Gelfand Mikhail S. , Mirny Leonid A.
Published: August 2007

What are the forces that shape the structure of prokaryotic genomes: the order of genes, their proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are believed to promote the proximity of functionally related genes and the formation of operons. However, forces that influence the structure of the genome beyond the level of a single operon remain unknown. Here, we show that the biophysical mechanism by which regulatory proteins search for their sites on DNA can impose constraints on genome structure. Using simulations, we demonstrate that rapid and reliable gene regulation requires that the transcription factor (TF) gene be close to the site on DNA the TF has to bind, thus promoting the colocalization of TF genes and their targets on the genome. We use parameters that have been measured in recent experiments to estimate the relevant length and times scales of this process and demonstrate that the search for a cognate site may be prohibitively slow if a TF has a low copy number and is not colocalized. We also analyze TFs and their sites in a number of bacterial genomes, confirm that they are colocalized significantly more often than expected, and show that this observation cannot be attributed to the pressure for coregulation or formation of selfish gene clusters, thus supporting the role of the biophysical constraint in shaping the structure of prokaryotic genomes. Our results demonstrate how spatial organization can influence timing and noise in gene expression.
The Atg5–Atg12 conjugate associates with innate antiviral immune responses
Authors: Jounai Nao , Takeshita Fumihiko , Kobiyama Kouji , Sawano Asako , Miyawaki Atsushi , Xin Ke-Qin , Ishii Ken J. , Kawai Taro , Akira Shizuo , Suzuki Koichi , Okuda Kenji
Published: August 2007

Autophagy is an essential process for physiological homeostasis, but its role in viral infection is only beginning to be elucidated. We show here that the Atg5–Atg12 conjugate, a key regulator of the autophagic process, plays an important role in innate antiviral immune responses. Atg5-deficient mouse embryonic fibroblasts (MEFs) were resistant to vesicular stomatitis virus replication, which was largely due to hyperproduction of type I interferons in response to immunostimulatory RNA (isRNA), such as virus-derived, double-stranded, or 5′-phosphorylated RNA. Similar hyperresponse to isRNA was also observed in Atg7-deficient MEFs, in which Atg5–Atg12 conjugation is impaired. Overexpression of Atg5 or Atg12 resulted in Atg5–Atg12 conjugate formation and suppression of isRNA-mediated signaling. Molecular interaction studies indicated that the Atg5–Atg12 conjugate negatively regulates the type I IFN production pathway by direct association with the retinoic acid-inducible gene I (RIG-I) and IFN-β promoter stimulator 1 (IPS-1) through the caspase recruitment domains (CARDs). Thus, in contrast to its role in promoting the bactericidal process, a component of the autophagic machinery appears to block innate antiviral immune responses, thereby contributing to RNA virus replication in host cells.
Norepinephrine enables the induction of associative long-term potentiation at thalamo-amygdala synapses
Authors: Tully Keith , Li Yan , Tsvetkov Evgeny , Bolshakov Vadim Y.
Published: August 2007

Emotional arousal, linked to a surge of norepinephrine (NE) in the amygdala, leads to creation of stronger and longer-lasting memories. However, little is known about the synaptic mechanisms of such modulatory NE influences. Long-term potentiation (LTP) in auditory inputs to the lateral nucleus of the amygdala was recently linked to the acquisition of fear memory. Therefore we explored whether LTP induction at thalamo-amygdala projections, conveying the acoustic conditioned stimulus information to the amygdala during fear conditioning, is under adrenergic control. Using whole-cell recordings from amygdala slices, we show that NE suppresses GABAergic inhibition of projection neurons in the lateral amygdala and enables the induction of LTP at thalamo-amygdala synapses under conditions of intact GABA
A
receptor-mediated inhibition. Our data indicate that the NE effects on the efficacy of inhibition could result from a decrease in excitability of local circuit interneurons, without direct effects of NE on release machinery of the GABA-containing vesicles or the size of single-quanta postsynaptic GABA
A
receptor-mediated responses. Thus, adrenergic modulation of local interneurons may contribute to the formation of fear memory by gating LTP in the conditioned stimulus pathways.
The circadian clock stops ticking during deep hibernation in the European hamster
Authors: Revel Florent G. , Herwig Annika , Garidou Marie-Laure , Dardente Hugues , Menet Jérôme S. , Masson-Pévet Mireille , Simonneaux Valérie , Saboureau Michel , Pévet Paul
Published: August 2007

Hibernation is a fascinating, yet enigmatic, physiological phenomenon during which body temperature and metabolism are reduced to save energy. During the harsh season, this strategy allows substantial energy saving by reducing body temperature and metabolism. Accordingly, biological processes are considerably slowed down and reduced to a minimum. However, the persistence of a temperature-compensated, functional biological clock in hibernating mammals has long been debated. Here, we show that the master circadian clock no longer displays 24-h molecular oscillations in hibernating European hamsters. The clock genes
Per1
,
Per2
, and
Bmal1
and the clock-controlled gene
arginine vasopressin
were constantly expressed in the suprachiasmatic nucleus during deep torpor, as assessed by radioactive
in situ
hybridization. Finally, the melatonin rhythm-generating enzyme, arylalkylamine
N
-acetyltransferase, whose rhythmic expression in the pineal gland is controlled by the master circadian clock, no longer exhibits day/night changes of expression but constantly elevated mRNA levels over 24 h. Overall, these data provide strong evidence that in the European hamster the molecular circadian clock is arrested during hibernation and stops delivering rhythmic output signals.
Mendel's green cotyledon gene encodes a positive regulator of the chlorophyll-degrading pathway
Authors: Sato Yutaka , Morita Ryouhei , Nishimura Minoru , Yamaguchi Hiroyasu , Kusaba Makoto
Published: August 2007

Mutants that retain greenness of leaves during senescence are known as “stay-green” mutants. The most famous stay-green mutant is Mendel's green cotyledon pea, one of the mutants used in determining the law of genetics. Pea plants homozygous for this recessive mutation (known as
i
at present) retain greenness of the cotyledon during seed maturation and of leaves during senescence. We found tight linkage between the
I
locus and stay-green gene originally found in rice,
SGR
. Molecular analysis of three
i
alleles including one with no
SGR
expression confirmed that the
I
gene encodes SGR in pea. Functional analysis of
sgr
mutants in pea and rice further revealed that leaf functionality is lowered despite a high chlorophyll
a
(Chl
a
) and chlorophyll
b
(Chl
b
) content in the late stage of senescence, suggesting that SGR is primarily involved in Chl degradation. Consistent with this observation, a wide range of Chl–protein complexes, but not the ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunit, were shown to be more stable in
sgr
than wild-type plants. The expression of
OsCHL
and
NYC1
, which encode the first enzymes in the degrading pathways of Chl
a
and Chl
b
, respectively, was not affected by
sgr
in rice. The results suggest that SGR might be involved in activation of the Chl-degrading pathway during leaf senescence through translational or posttranslational regulation of Chl-degrading enzymes.
Identification of IRS-1 Ser-1101 as a target of S6K1 in nutrient- and obesity-induced insulin resistance
Authors: Tremblay Frédéric , Brûlé Sophie , Hee Um Sung , Li Yu , Masuda Kohei , Roden Michael , Sun Xiao Jian , Krebs Michael , Polakiewicz Roberto D. , Thomas George , Marette André
Published: August 2007

S6K1 has emerged as a critical signaling component in the development of insulin resistance through phosphorylation and inhibition of IRS-1 function. This effect can be triggered directly by nutrients such as amino acids or by insulin through a homeostatic negative-feedback loop. However, the role of S6K1 in mediating IRS-1 phosphorylation in a physiological setting of nutrient overload is unresolved. Here we show that S6K1 directly phosphorylates IRS-1 Ser-1101
in vitro
in the C-terminal domain of the protein and that mutation of this site largely blocks the ability of amino acids to suppress IRS-1 tyrosine and Akt phosphorylation. Consistent with this finding, phosphorylation of IRS-1 Ser-1101 is increased in the liver of obese
db/db
and wild-type, but not
S6K1
−/−
, mice maintained on a high-fat diet and is blocked by siRNA knockdown of S6K1 protein. Finally, infusion of amino acids in humans leads to the concomitant activation of S6K1, phosphorylation of IRS-1 Ser-1101, a reduction in IRS-1 function, and insulin resistance in skeletal muscle. These findings indicate that nutrient- and hormonal-dependent activation of S6K1 causes insulin resistance in mice and humans, in part, by mediating IRS-1 Ser-1101 phosphorylation.
Increases in nitrogen uptake rather than nitrogen-use efficiency support higher rates of temperate forest productivity under elevated CO
2
Authors: Finzi Adrien C. , Norby Richard J. , Calfapietra Carlo , Gallet-Budynek Anne , Gielen Birgit , Holmes William E. , Hoosbeek Marcel R. , Iversen Colleen M. , Jackson Robert B. , Kubiske Mark E. , Ledford Joanne , Liberloo Marion , Oren Ram , Polle Andrea , Pritchard Seth , Zak Donald R. , Schlesinger William H. , Ceulemans Reinhart
Published: August 2007

Forest ecosystems are important sinks for rising concentrations of atmospheric CO
2
. In previous research, we showed that net primary production (NPP) increased by 23 ± 2% when four experimental forests were grown under atmospheric concentrations of CO
2
predicted for the latter half of this century. Because nitrogen (N) availability commonly limits forest productivity, some combination of increased N uptake from the soil and more efficient use of the N already assimilated by trees is necessary to sustain the high rates of forest NPP under free-air CO
2
enrichment (FACE). In this study, experimental evidence demonstrates that the uptake of N increased under elevated CO
2
at the Rhinelander, Duke, and Oak Ridge National Laboratory FACE sites, yet fertilization studies at the Duke and Oak Ridge National Laboratory FACE sites showed that tree growth and forest NPP were strongly limited by N availability. By contrast, nitrogen-use efficiency increased under elevated CO
2
at the POP-EUROFACE site, where fertilization studies showed that N was not limiting to tree growth. Some combination of increasing fine root production, increased rates of soil organic matter decomposition, and increased allocation of carbon (C) to mycorrhizal fungi is likely to account for greater N uptake under elevated CO
2
. Regardless of the specific mechanism, this analysis shows that the larger quantities of C entering the below-ground system under elevated CO
2
result in greater N uptake, even in N-limited ecosystems. Biogeochemical models must be reformulated to allow C transfers below ground that result in additional N uptake under elevated CO
2
.
DNA transposition target immunity and the determinants of the MuB distribution patterns on DNA
Authors: Tan Xin , Mizuuchi Michiyo , Mizuuchi Kiyoshi
Published: August 2007

MuB, an ATP-dependent DNA-binding protein, is critical for the selection of target sites on the host chromosome during the phage Mu transposition. We developed a multichannel fluidic system to study the MuB–DNA interaction dynamics at the single DNA molecule level by total internal reflection fluorescence microscopy. We analyzed the distribution of MuB along DNA during the assembly and disassembly of MuB polymers on immobilized DNA molecules. The results reveal the absence of a significant correlation of MuB polymer distribution between the assembly and disassembly phases. These observations argue against a model in which MuB polymers on DNA represent a mixture of higher and lower affinity forms, with higher affinity forms being the first to appear and the last to disappear. Instead, assembly and disassembly of MuB polymers involve independent stochastic events. Additionally, we demonstrate that MuB disassembles from the polymer ends at a higher rate than from internal regions of the polymer and MuA stimulates MuB disassembly both at the polymer ends and internally.
Effects of light on development of mammalian zygotes
Authors: Takenaka Manami , Horiuchi Toshitaka , Yanagimachi Ryuzo
Published: August 2007

It is generally assumed that light has no effect on the physiology of oocytes, zygotes, or early embryos. Therefore, little or no attention has been paid to lighting conditions during the handling of these cells
in vitro
. Here we show that cool white fluorescent light, rich in short-wavelength visible light and commonly used in research and clinical laboratories, produces more reactive oxygen species in mouse and hamster zygotes than does warm white fluorescent light. Mouse blastocysts that developed from zygotes shielded from light best developed to term fetuses followed by those exposed to warm white fluorescent light and then by those exposed to cool white fluorescent light. We hypothesized that light is one of the physical factors affecting embryonic environment and that its effects on cultured mammalian zygotes and embryos should not be overlooked.
Human cardiac stem cells
Authors: Bearzi Claudia , Rota Marcello , Hosoda Toru , Tillmanns Jochen , Nascimbene Angelo , De Angelis Antonella , Yasuzawa-Amano Saori , Trofimova Irina , Siggins Robert W. , LeCapitaine Nicole , Cascapera Stefano , Beltrami Antonio P. , D'Alessandro David A. , Zias Elias , Quaini Federico , Urbanek Konrad , Michler Robert E. , Bolli Roberto , Kajstura Jan , Leri Annarosa , Anversa Piero
Published: August 2007

The identification of cardiac progenitor cells in mammals raises the possibility that the human heart contains a population of stem cells capable of generating cardiomyocytes and coronary vessels. The characterization of human cardiac stem cells (hCSCs) would have important clinical implications for the management of the failing heart. We have established the conditions for the isolation and expansion of c-
kit
-positive hCSCs from small samples of myocardium. Additionally, we have tested whether these cells have the ability to form functionally competent human myocardium after infarction in immunocompromised animals. Here, we report the identification
in vitro
of a class of human c-
kit
-positive cardiac cells that possess the fundamental properties of stem cells: they are self-renewing, clonogenic, and multipotent. hCSCs differentiate predominantly into cardiomyocytes and, to a lesser extent, into smooth muscle cells and endothelial cells. When locally injected in the infarcted myocardium of immunodeficient mice and immunosuppressed rats, hCSCs generate a chimeric heart, which contains human myocardium composed of myocytes, coronary resistance arterioles, and capillaries. The human myocardium is structurally and functionally integrated with the rodent myocardium and contributes to the performance of the infarcted heart. Differentiated human cardiac cells possess only one set of human sex chromosomes excluding cell fusion. The lack of cell fusion was confirmed by the Cre-
lox
strategy. Thus, hCSCs can be isolated and expanded
in vitro
for subsequent autologous regeneration of dead myocardium in patients affected by heart failure of ischemic and nonischemic origin.
Two distinct arginine methyltransferases are required for biogenesis of Sm-class ribonucleoproteins
Authors: Gonsalvez Graydon B. , Tian Liping , Ospina Jason K. , Boisvert François-Michel , Lamond Angus I. , Matera A. Gregory
Published: August 2007

Small nuclear ribonucleoproteins (snRNPs) are core components of the spliceosome. The U1, U2, U4, and U5 snRNPs each contain a common set of seven Sm proteins. Three of these Sm proteins are posttranslationally modified to contain symmetric dimethylarginine (sDMA) residues within their C-terminal tails. However, the precise function of this modification in the snRNP biogenesis pathway is unclear. Several lines of evidence suggest that the methyltransferase protein arginine methyltransferase 5 (PRMT5) is responsible for sDMA modification of Sm proteins. We found that in human cells, PRMT5 and a newly discovered type II methyltransferase, PRMT7, are each required for Sm protein sDMA modification. Furthermore, we show that the two enzymes function nonredundantly in Sm protein methylation. Lastly, we provide in vivo evidence demonstrating that Sm protein sDMA modification is required for snRNP biogenesis in human cells.
Maintaining the proper connection between the centrioles and the pericentriolar matrix requires Drosophila Centrosomin
Authors: Lucas Eliana P. , Raff Jordan W.
Published: August 2007

Centrosomes consist of two centrioles surrounded by an amorphous pericentriolar matrix (PCM), but it is unknown how centrioles and PCM are connected. We show that the centrioles in Drosophila embryos that lack the centrosomal protein Centrosomin (Cnn) can recruit PCM components but cannot maintain a proper attachment to the PCM. As a result, the centrioles “rocket” around in the embryo and often lose their connection to the nucleus in interphase and to the spindle poles in mitosis. This leads to severe mitotic defects in embryos and to errors in centriole segregation in somatic cells. The Cnn-related protein CDK5RAP2 is linked to microcephaly in humans, but cnn mutant brains are of normal size, and we observe only subtle defects in the asymmetric divisions of mutant neuroblasts. We conclude that Cnn maintains the proper connection between the centrioles and the PCM; this connection is required for accurate centriole segregation in somatic cells but is not essential for the asymmetric division of neuroblasts.
OPA1 processing controls mitochondrial fusion and is regulated by mRNA splicing, membrane potential, and Yme1L
Authors: Song Zhiyin , Chen Hsiuchen , Fiket Maja , Alexander Christiane , Chan David C.
Published: August 2007

OPA1, a dynamin-related guanosine triphosphatase mutated in dominant optic atrophy, is required for the fusion of mitochondria. Proteolytic cleavage by the mitochondrial processing peptidase generates long isoforms from eight messenger RNA (mRNA) splice forms, whereas further cleavages at protease sites S1 and S2 generate short forms. Using OPA1-null cells, we developed a cellular system to study how individual OPA1 splice forms function in mitochondrial fusion. Only mRNA splice forms that generate a long isoform in addition to one or more short isoforms support substantial mitochondrial fusion activity. On their own, long and short OPA1 isoforms have little activity, but, when coexpressed, they functionally complement each other. Loss of mitochondrial membrane potential destabilizes the long isoforms and enhances the cleavage of OPA1 at S1 but not S2. Cleavage at S2 is regulated by the i-AAA protease Yme1L. Our results suggest that mammalian cells have multiple pathways to control mitochondrial fusion through regulation of the spectrum of OPA1 isoforms.
Cross-competition of CD8+ T cells shapes the immunodominance hierarchy during boost vaccination
Authors: Kastenmuller Wolfgang , Gasteiger Georg , Gronau Julian H. , Baier Robert , Ljapoci Ronny , Busch Dirk H. , Drexler Ingo
Published: August 2007

CD8+ T cell responses directed against multiple pathogen-derived epitopes are characterized by defined immunodominance hierarchy patterns. A possible explanation for this phenomenon is that CD8+ T cells of different specificities compete for access to epitopes on antigen-presenting cells, and that the outcome of this so-called cross-competition reflects the number of induced T cells. In our study using a vaccinia virus infection model, we found that T cell cross-competition is highly relevant during boost vaccination, thereby shaping the immunodominance hierarchy in the recall. We demonstrate that competition was of no importance during priming and was unaffected by the applied route of immunization. It strongly depended on the timing of viral antigen expression in infected APCs, and it was characterized by poor proliferation of T cells recognizing epitopes derived from late viral proteins. To our knowledge, this is the first demonstration of the functional importance of T cell cross-competition during a viral infection. Our findings provide a basis for novel strategies for how boost vaccination to defined antigens can be selectively improved. They give important new insights into the design of more efficient poxviral vectors for immunotherapy.
Natively unstructured regions in proteins identified from contact predictions
Authors: Schlessinger Avner , Punta Marco , Rost Burkhard
Published: August 2007

Motivation: Natively unstructured (also dubbed intrinsically disordered) regions in proteins lack a defined 3D structure under physiological conditions and often adopt regular structures under particular conditions. Proteins with such regions are overly abundant in eukaryotes, they may increase functional complexity of organisms and they usually evade structure determination in the unbound form. Low propensity for the formation of internal residue contacts has been previously used to predict natively unstructured regions.

Results: We combined PROFcon predictions for protein-specific contacts with a generic pairwise potential to predict unstructured regions. This novel method, Ucon, outperformed the best available methods in predicting proteins with long unstructured regions. Furthermore, Ucon correctly identified cases missed by other methods. By computing the difference between predictions based on specific contacts (approach introduced here) and those based on generic potentials (realized in other methods), we might identify unstructured regions that are involved in protein–protein binding. We discussed one example to illustrate this ambitious aim. Overall, Ucon added quality and an orthogonal aspect that may help in the experimental study of unstructured regions in network hubs.

Availability:  http://www.predictprotein.org/submit_ucon.html

Contact:  as2067@columbia.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Con-Struct Map: a comparative contact map analysis tool
Authors: Chung Jo-Lan , Beaver John E. , Scheeff Eric D. , Bourne Philip E.
Published: August 2007

Summary: Con-Struct Map is a graphical tool for the comparative study of protein structures. The tool detects potential conserved residue contacts shared by multiple protein structures by superimposing their contact maps according to a multiple structure alignment. In general, Con-Struct Map allows the study of structural changes resulting from, e.g. sequence substitutions, or alternatively, the study of conserved components of a structure framework across structurally aligned proteins. Specific applications include the study of sequence-structure relationship in distantly related proteins and the comparisons of wild type and mutant proteins.

Availability:  http://pdbrs3.sdsc.edu/ConStructMap/viewer_argument_generator/singleArguments

Contact:  bourne@sdsc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
A Laboratory Information Management System (LIMS) for a high throughput genetic platform aimed at candidate gene mutation screening
Authors: Voegele C. , Tavtigian S.V. , de Silva D. , Cuber S. , Thomas A. , Le Calvez-Kelm F.
Published: August 2007

Summary: High throughput mutation screening in an automated environment generates large data sets that have to be organized and stored reliably. Complex multistep workflows require strict process management and careful data tracking. We have developed a Laboratory Information Management Systems (LIMS) tailored to high throughput candidate gene mutation scanning and resequencing that respects these requirements. Designed with a client/server architecture, our system is platform independent and based on open-source tools from the database to the web application development strategy. Flexible, expandable and secure, the LIMS, by communicating with most of the laboratory instruments and robots, tracks samples and laboratory information, capturing data at every step of our automated mutation screening workflow. An important feature of our LIMS is that it enables tracking of information through a laboratory workflow where the process at one step is contingent on results from a previous step.

Availability: Script for MySQL database table creation and source code of the whole JSP application are freely available on our website: http://www-gcs.iarc.fr/lims/.

Contact:  voegele@iarc.fr

Supplementary information: System server configuration, database structure and additional details on the LIMS and the mutation screening workflow are available on our website: http://www-gcs.iarc.fr/lims/
Is Partial-Dimension Convergence a Problem for Inferences from MCMC Algorithms?
Authors: Gill Jeff
Published: August 2007

Increasingly, political science researchers are turning to Markov chain Monte Carlo methods to solve inferential problems with complex models and problematic data. This is an enormously powerful set of tools based on replacing difficult or impossible analytical work with simulated empirical draws from the distributions of interest. Although practitioners are generally aware of the importance of convergence of the Markov chain, many are not fully aware of the difficulties in fully assessing convergence across multiple dimensions. In most applied circumstances, every parameter dimension must be converged for the others to converge. The usual culprit is slow mixing of the Markov chain and therefore slow convergence towards the target distribution. This work demonstrates the partial convergence problem for the two dominant algorithms and illustrates these issues with empirical examples.
Differential Contribution of Sodium Channel Subtypes to Action Potential Generation in Unmyelinated Human C-type Nerve Fibers
Authors: Lang Philip M. , Hilmer Verena B. , Grafe Peter
Published: August 2007

Background

Multiple voltage-dependent sodium channels (Na(v)) contribute to action potentials and excitability of primary nociceptive neurons. The aim of the current study was to characterize subtypes of Na(v) that contribute to action potential generation in peripheral unmyelinated human C-type nerve fibers.

Methods

Registration of C-fiber compound action potentials and determination of membrane threshold was performed by a computerized threshold tracking program. Nerve fibers were stimulated with a 1-ms current pulse either alone or after a small ramp current lasting 300 ms.

Results

Compound C-fiber action potentials elicited by supramaximal 1-ms current pulses were rather resistant to application of tetrodotoxin (30-90 nM). However, the same concentrations of tetrodotoxin strongly reduced the peak height and elevated membrane threshold of action potentials evoked at the end of a 300-ms current ramp. A similar effect was observed during application of lidocaine and mexiletine (50 microM each).

Conclusions

These data indicate that more than one type of Na(v) contributes to the generation of action potentials in unmyelinated human C-type nerve fibers. The peak height of an action potential produced by a short electrical impulse is dependent on the activation of tetrodotoxin-resistant ion channels. In contrast, membrane threshold and action potential peak height at the end of a slow membrane depolarization are regulated by a subtype of Na(v) with high sensitivity to low concentrations of tetrodotoxin, lidocaine, and mexiletine. The electrophysiologic and pharmacologic characteristics may indicate the functional activity of the Na(v) 1.7 subtype of voltage-dependent sodium channels.
Neonatal Exposure to a Combination of N -Methyl-d-aspartate and γ-Aminobutyric Acid Type A Receptor Anesthetic Agents Potentiates Apoptotic Neurodegeneration and Persistent Behavioral Deficits
Authors: Fredriksson Anders , Pontén Emma , Gordh Torsten , Eriksson Per
Published: August 2007

Background

During the brain growth spurt, the brain develops and modifies rapidly. In rodents this period is neonatal, spanning the first weeks of life, whereas in humans it begins during the third trimester and continues 2 yr. This study examined whether different anesthetic agents, alone and in combination, administered to neonate mice, can trigger apoptosis and whether behavioral deficits occur later in adulthood.

Methods

Ten-day-old mice were injected subcutaneously with ketamine (25 mg/kg), thiopental (5 mg/kg or 25 mg/kg), propofol (10 mg/kg or 60 mg/kg), a combination of ketamine (25 mg/kg) and thiopental (5 mg/kg), a combination of ketamine (25 mg/kg) and propofol (10 mg/kg), or control (saline). Fluoro-Jade staining revealed neurodegeneration 24 h after treatment. The behavioral tests--spontaneous behavior, radial arm maze, and elevated plus maze (before and after anxiolytic)--were conducted on mice aged 55-70 days.

Results

Coadministration of ketamine plus propofol or ketamine plus thiopental or a high dose of propofol alone significantly triggered apoptosis. Mice exposed to a combination of anesthetic agents or ketamine alone displayed disrupted spontaneous activity and learning. The anxiolytic action of diazepam was less effective when given to adult mice that were neonatally exposed to propofol.

Conclusion

This study shows that both a gamma-aminobutyric acid type A agonist (thiopental or propofol) and an N-methyl-D-aspartate antagonist (ketamine) during a critical stage of brain development potentiated neonatal brain cell death and resulted in functional deficits in adulthood. The use of thiopental, propofol, and ketamine individually elicited no or only minor changes.