bluuebunny/crossref_metadata_2025 huggingface dataset:
Hopping times of two hard disks diffusing in a channel
Authors: Mon K. K. , Percus J. K.
Published: December 2006

A finite difference method was used to solve numerically the multidimensional diffusion equation describing the time evolution of two hard disks diffusing in a narrow hard channel. The authors extract an estimate for the average time τhop needed for the disks to hop pass each other. For narrow channels near the hopping threshold, τhop diverges and is consistent with the scaling prediction of the transition state theory. This provides a much-needed rigorous benchmark to test an approximate solution to the diffusion problem.
Pulse generation and compression via ground and excited states from a grating coupled passively mode-locked quantum dot two-section diode laser
Authors: Kim Jimyung , Choi Myoung-Taek , Delfyett Peter J.
Published: December 2006

The authors generate and compress short pulses via the ground and excited state transitions from a passively mode-locked grating coupled quantum dot two-section diode laser at a repetition rate of 2.7GHz. The selection and isolation of either the ground state or excited state transition were performed by an angle tuning of the grating. The externally compressed pulse widths are 970fs from the ground state and 1.2ps from the excited state transition. The sign of the chirp is up chirped for both state transitions.
Efficient correlation-corrected vibrational self-consistent field computation of OH-stretch frequencies using a low-scaling algorithm
Authors: Benoit David M.
Published: December 2006

The authors present a new computational scheme to perform accurate and fast direct correlation-corrected vibrational self-consistent field (CC-VSCF) computations for a selected number of vibrational modes, which is aimed at predicting a few vibrations in large molecular systems. The method is based on a systematic selection of vibrational mode-mode coupling terms, leading to the direct ab initio construction of a sparse potential energy surface. The computational scaling of the CC-VSCF computation on the generated surface is then further reduced by using a screening procedure for the correlation-correction contributions. The proposed method is applied to the computation of the OH-stretch frequency of five aliphatic alcohols. The authors investigate the influence of different pseudopotential and all-electron basis sets on the quality of the correlated potential energy surfaces computed and on the OH-stretch frequencies calculated for each surface. With the help of these test systems, the authors show that their method offers a computational scaling that is two orders of magnitude lower than a standard CC-VSCF method and that it is of equal accuracy.
Stimulated ion Compton scattering instability of whistlers in plasmas
Authors: Shukla P. K. , Shukla Nitin , Stenflo L.
Published: December 2006

The nonlinear interactions between magnetic field-aligned broadband whistler wave packets (hereafter referred to as whistlerons) and ion quasimodes in magnetized plasmas are considered. By treating the whistlerons as quasiparticles, their nonlinear propagation in a slowly varying medium supported by ion quasimode density perturbations is studied. A nonlinear dispersion relation within the framework of the wave-kinetic (for the whistlerons) and Vlasov (for the ion quasimodes) descriptions is derived. The dispersion relation admits a kinetic modulational instability. The growth rate of the latter is presented. The present result can improve our understanding of the nonlinear propagation of incoherent whistlers, which have been frequently observed in the Earth’s magnetosphere as well as in laboratory plasmas.
Demonstrated fossil-fuel-free energy cycle using magnesium and laser
Authors: Yabe T. , Uchida S. , Ikuta K. , Yoshida K. , Baasandash C. , Mohamed M. S. , Sakurai Y. , Ogata Y. , Tuji M. , Mori Y. , Satoh Y. , Ohkubo T. , Murahara M. , Ikesue A. , Nakatsuka M. , Saiki T. , Motokoshi S. , Yamanaka C.
Published: December 2006

The authors propose an energy cycle based on a renewable fuel. Magnesium is chosen as an energy carrier and is combusted with water to retrieve energy using many power devices. MgO, the combustion residue, is reduced back to Mg by laser radiation generated from solar and other renewable energy sources. They have achieved an energy recovery efficiency of 42.5% for converting MgO to magnesium, using a laser. Combined with a demonstrated 38% efficiency for converting an artificial sunlight source (metal halide lamp) into laser output energy indicates that the proposed energy cycle is already in a feasible range for practical use.
Physical manipulation of biological and chemical syntheses for nanoparticle shape and size control
Authors: Ogale S. B. , Ahmad A. , Pasricha R. , Dhas V. V. , Syed A.
Published: December 2006

A nanosynthesis scheme is demonstrated which renders excellent control of nanoparticle shape, size, and dispersity in a solution based synthesis process. The scheme, termed as percolative microcavity synthesis, involves the use of a granular medium with percolative microcavities which facilitate nearly similar grain size/shape dependent reaction zones limiting intrinsic growth inhomogeneities, enabling particle size/shape control. The viability of the process is demonstrated for the synthesis of gold nanoparticles by a plant extract based biological method as well as a chemical method.
Temperature dependence of serrated flows in compression in a bulk-metallic glass
Authors: Jiang W. H. , Jiang F. , Liu F. X. , Choo H. , Liaw P. K. , Qiu K. Q.
Published: December 2006

The authors investigated the effect of temperature on the plastic-flow and shear-banding behaviors of a Zr-based bulk-metallic glass in compression. The results indicate that at a subambient temperature (194.5K) the plastic deformation of the bulk-metallic glass is still inhomogeneous and is characterized by the serrated flow and shear banding. But, compared to the ambient-temperature results, the subambient temperature moderates serrations in the plastic flow and leads to the formation of fewer shear bands. In view of the spatiotemporality of shear banding, the authors correlate the plastic-flow behaviors to shear-band patterns.
Brownian noise in radiation-pressure-driven micromechanical oscillators
Authors: Rokhsari Hossein , Hossein-Zadeh Mani , Hajimiri Ali , Vahala Kerry
Published: December 2006

The authors demonstrate Brownian-noise-limited operation of an optomechanical oscillator, wherein mechanical oscillations of a silica optical microcavity are sustained by means of radiation pressure. Using phase noise measurement above threshold, it has been shown that the short-term linewidth of mechanical oscillations is fundamentally broadened, limited by thermal equipartition of energy.
Goos-Hänchen shift surface plasmon resonance sensor
Authors: Yin Xiaobo , Hesselink Lambertus
Published: December 2006

A high resolution surface plasmon resonance sensor is proposed and demonstrated by measuring the plasmon resonance enhanced Goos-Hänchen effect at attenuated total internal reflection. The giant Goos-Hänchen shift results from the singular phase retardation at the resonance which leads to the superior sensitivity of the sensor.
Prospects for detection of spin accumulation using submicron planar Andreev array spectroscopy
Authors: Magnus F. , Yates K. A. , Morris B. , Miyoshi Y. , Bugoslavsky Y. , Cohen L. F. , Burnell G. , Blamire M. G. , Josephs-Franks P. W.
Published: December 2006

Andreev spectroscopy can be employed to measure transport spin polarization. Planar Andreev devices have an advantage over point-contact Andreev spectroscopy as they offer greater control over interface quality and the possibility of spatially resolved information about spin polarization using submicron Andreev junction arrays. The authors compare the performance of Pb point contacts onto Cu and Co with that of large area and submicron planar junctions and singularly connected nanoarrays. Planar structures compare favorably to point contacts although the fabrication method influences extracted parameters. The authors find that submicron planar junction reproducibility does not adversely affect the prospects for developing arrays for detection of spin accumulation.
Surface potential shield with aperture structure to improve potential measurement accuracy of scanning Kelvin probe microscopy
Authors: Yang Zhitao , Spencer Michael G.
Published: December 2006

Scanning Kelvin probe microscopy is widely used to measure surface work functions and electrostatic potentials. However, its measurement accuracy suffers from a cantilever effect. The authors introduce a surface potential shield with aperture structure to eliminate cantilever effect. By varying dc biases on the shield, the strength of cantilever effect is deliberately moderated and linear regression can be used to extract the true surface potential. Experimental results show that this approach yields accurate potential measurement, especially when there is only a single potential domain within aperture. A mobile potential shield structure mounted on a micromanipulator can make this approach more versatile.
Strain distribution in epitaxial SrTiO3 thin films
Authors: Zhai Z. Y. , Wu X. S. , Jiang Z. S. , Hao J. H. , Gao J. , Cai Y. F. , Pan Y. G.
Published: December 2006

The lattice strain distributions of epitaxial SrTiO3 films deposited on LaAlO3 were investigated by in situ x-ray diffraction at the temperature range of 25–300K, grazing incident x-ray diffraction, and high resolution x-ray diffraction. The nearly linear temperature dependence of the out-of-plane lattice constant of SrTiO3 was observed in the measured temperature range. The depth distribution of the lattice strain at room temperature for SrTiO3 films includes the surface layer, strained layer, and interface layer.
Retarded oxidation of Si nanowires
Authors: Büttner C. C. , Zacharias M.
Published: December 2006

Retarded thermal oxidation of Si nanowires is investigated. The oxidation behavior strongly depends on the wire curvature. The effect starts to evolve for a curvature larger than 0.05nm, i.e., an original nanowire radius of 35nm. For longer oxidation time and lower oxidation temperature, the effect of retarded oxidation gets stronger. The average values of the oxidation rate for small wires are reduced nearly by a factor of 2 compared to bulk ⟨100⟩ silicon. The authors suggest that the increased stress is responsible for the mechanism of retarded oxidation which cannot be decreased by the viscous flow of the oxide.
Probing adsorption sites on thin oxide films by dynamic force microscopy
Authors: Heyde M. , Simon G. H. , Rust H.-P. , Freund H.-J.
Published: December 2006

Site specific atomically resolved dynamic force spectroscopy measurements were performed on a thin MgO film grown on Ag(001). The microscope is operated in ultrahigh vacuum at low temperature to ensure defined imaging condition, high stability, and drift reduction. Atomically resolved dynamic force microscopy images have been combined with site specific frequency shift versus distance measurements. The frequency shift is measured as a function of z and the lateral displacement. With these measurement characteristics the authors are currently probing inequivalent surface sites on thin MgO films to extract atomic-scale information on surface chemical reactivity and possible adsorption sites for metal atoms and small clusters.
Influence of the substrate orientation on the electronic and optical properties of InAs∕GaAs quantum dots
Authors: Mlinar V. , Peeters F. M.
Published: December 2006

Using three-dimensional k∙p calculation including strain and piezoelectricity the authors predict the variation of electronic and optical properties of InAs∕GaAs quantum dots (QDs) with the substrate orientation. The QD transition energies are obtained for high index substrates, [11k] where k=1,2,3, and are compared with [001]. They find that the QD size in the growth direction determines the degree of influence of the substrate orientation: the flatter the dots, the larger the difference from the reference [001] case.
Structural properties of SrO thin films grown by molecular beam epitaxy on LaAlO3 substrates
Authors: Maksimov O. , Heydemann V. D. , Fisher P. , Skowronski M. , Salvador P. A.
Published: December 2006

SrO films were grown on LaAlO3 substrates by molecular beam epitaxy and characterized using reflection high-energy electron diffraction (RHEED) and x-ray diffraction (XRD). The evolution of the RHEED pattern is discussed as a function of film thickness. 500Å thick SrO films were relaxed and exhibited RHEED patterns indicative of an atomically smooth surface having uniform terrace heights. Films had the epitaxial relationship (001)SrO‖(001)LaAlO3; [010]SrO‖[110]LaAlO3. This 45° in-plane rotation minimizes mismatch and leads to films of high crystalline quality, as verified by Kikuchi lines in the RHEED patterns and narrow rocking curves of the (002) XRD peak.
Oxygen vacancy in monoclinic HfO2: A consistent interpretation of trap assisted conduction, direct electron injection, and optical absorption experiments
Authors: Broqvist Peter , Pasquarello Alfredo
Published: December 2006

The authors calculate energy levels associated with the oxygen vacancy in monoclinic HfO2 using a hybrid density functional which accurately reproduces the experimental band gap. The most stable charge states are obtained for varying Fermi level in the HfO2 band gap. To compare with measured defect levels, they determine total energy differences specific to the considered experiment. Their results show that the oxygen vacancy can consistently account for the defect levels observed in (Poole-Frenkel-type) trap assisted conduction, direct electron injection, and optical absorption experiments.
Strain induced magnetic anisotropy in highly epitaxial CoFe2O4 thin films
Authors: Huang W. , Zhu J. , Zeng H. Z. , Wei X. H. , Zhang Y. , Li Y. R.
Published: December 2006

Cobalt ferrite (CoFe2O4) thin films were epitaxially grown on (001) SrTiO3 and (001) MgO by laser molecular beam epitaxy. Microstructural studies indicate that the CoFe2O4 grown on (001) SrTiO3 with compressive strain are c-oriented island growth mode with rough surface morphology, whereas the films on (001) MgO with tensile strain become c oriented with layer-by-layer mode. Magnetic property studies reveal that the compressive strained CoFe2O4 films on (001) SrTiO3 can significantly enhance out-of-plane magnetization (190emu∕cm3) with a large coercivity (3.8kOe). In contrast, the tensile strained CoFe2O4 films on (001) MgO exhibit weak magnetic anisotropy. These results suggest that strong magnetic anisotropy is highly dependent on the lattice mismatch induced strain.
Control of fine-structure splitting and excitonic binding energies in selected individual InAs∕GaAs quantum dots
Authors: Seguin R. , Schliwa A. , Germann T. D. , Rodt S. , Pötschke K. , Strittmatter A. , Pohl U. W. , Bimberg D. , Winkelnkemper M. , Hammerschmidt T. , Kratzer P.
Published: December 2006

A systematic study of the impact of annealing on the electronic properties of single InAs∕GaAs quantum dots (QDs) is presented. Single QD cathodoluminescence spectra are recorded to trace the evolution of one and the same QD over several steps of annealing. A substantial reduction of the excitonic fine-structure splitting upon annealing is observed. In addition, the binding energies of different excitonic complexes change dramatically. The results are compared to model calculations within 8-band k∙p theory and the configuration interaction method, suggesting a change of electron and hole wave function shape and relative position.
Control of structure, conduction behavior, and band gap of Zn1−xMgxO films by nitrogen partial pressure ratio of sputtering gases
Authors: Cong C. X. , Yao B. , Xing G. Z. , Xie Y. P. , Guan L. X. , Li B. H. , Wang X. H. , Wei Z. P. , Zhang Z. Z. , Lv Y. M. , Shen D. Z. , Fan X. W.
Published: December 2006

Zn 1 − x Mg x O films were grown by radio-frequency reactive magnetron sputtering using mixture of nitrogen and argon as sputtering gases. It was found that Mg concentration, structures, electrical properties, and band gaps of the films can be tuned by changing nitrogen partial pressure ratio of the sputtering gases. The Zn1−xMgxO film consists of wurtzite phase at the ratios from 0% to 50%, mixture of wurtzite and cubic phases at the ratios of 78% to 83%, and cubic phase at 100%. The Mg concentration increased linearly with increasing the ratio. The band gap increases from 3.64eV at x=0.172to4.02eV at x=0.44 for the wurtzite Zn1−xMgxO and reaches 6.30eV for cubic Zn1−xMgxO with x=0.84. All the as-grown Zn1−xMgxO films show high resistivity at room temperature, but transform into p-type conduction after annealing at 600°C for 30min under 10−4Pa, except for the film grown at the ratio of zero.
In
Ga
As
∕
Ga
As
/alkanethiolate radial superlattices
Authors: Deneke Ch. , Zschieschang U. , Klauk H. , Schmidt O. G.
Published: December 2006

A radial InGaAs∕GaAs∕1-hexadecanethiol superlattice is fabricated by the roll-up of a strained InGaAs∕GaAs bilayer passivated with a molecular self-assembled monolayer. The technique allows the formation of multiperiod inorganic/organic hybrid heterostructures. The authors investigate the radial superlattices in a detailed transmission electron microscopy study. The structure consists of 11 tightly bonded semiconductor/organic layers with thicknesses and chemical compositions accurately controlled by epitaxial growth and self-assembly. Their chemical analysis reveals that neither any detectable oxygen contamination nor amorphization is present at the superlattice interfaces.
Experimental study of the subwavelength imaging by a wire medium slab
Authors: Belov Pavel A. , Zhao Yan , Sudhakaran Sunil , Alomainy Akram , Hao Yang
Published: December 2006

An experimental investigation of subwavelength imaging by a wire medium slab is performed. A complex-shaped near field source is used in order to test imaging performance of the device. It is demonstrated that the ultimate bandwidth of operation of the constructed imaging device is 4.5% that coincides with theoretical predictions [P. A. Belov and M. G. Silveirinha, Phys. Rev. E 73, 056607 (2006)]. Within this band the wire medium slab is capable of transmitting images with λ∕15 resolution irrespective of the shape and complexity of the source. Actual bandwidth of operation for particular near-field sources can be larger than the ultimate value, but it strongly depends on the configuration of the source.
Transient thermal properties of high-power diode laser bars
Authors: Ziegler Mathias , Weik Fritz , Tomm Jens W. , Elsaesser Thomas , Nakwaski Włodzimierz , Sarzała Robert P. , Lorenzen Dirk , Meusel Jens , Kozłowska Anna
Published: December 2006

The transient thermal properties of high-power diode laser bars with active and passive cooling are analyzed. Both thermal imaging and the analysis of the thermal wavelength tuning behavior are employed to extract the device temperature as a function of time. A steady-state thermal situation is established with rise times of about 10 and 60ms for active and passive cooling, respectively. The latter number, however, is substantially increased by the particular properties of the external heat sink. Such results are confirmed by model calculations based on the finite element method.
Method to analyze dislocation injection from sharp features in strained silicon structures
Authors: Zhang Zhen , Yoon Juil , Suo Zhigang
Published: December 2006

A microelectronic device usually contains sharp features (e.g., edges and corners) that may intensify stresses, inject dislocations into silicon, and fail the device. The authors describe a method to analyze dislocation injection on the basis of singular stress fields near the sharp features, and apply the method to interpret available experiments of nitride pads on silicon substrates.
Direct writing of silver conductive patterns: Improvement of film morphology and conductance by controlling solvent compositions
Authors: Kim Dongjo , Jeong Sunho , Park Bong Kyun , Moon Jooho
Published: December 2006

The authors have investigated the influence of conductive ink compositions on the quality of ink-jet printed patterns. Controlling the solvent compositions plays an important role of reducing the so-called coffee ring effect. The use of a higher boiling point solvent with lower surface tension such as ethylene glycol enables the formation of a uniform deposit of silver nanoparticles due to surface tension gradient-induced inward Marangoni flow, which can compensate outward convective flow. It is demonstrated that the ink-jet printed film quality is directly related to the resistance difference in the conductive patterns.
D1–D2 dopamine receptor heterooligomers with unique pharmacology are coupled to rapid activation of Gq/11 in the striatum
Authors: Rashid Asim J. , So Christopher H. , Kong Michael M. C. , Furtak Teresa , El-Ghundi Mufida , Cheng Regina , O'Dowd Brian F. , George Susan R.
Published: December 2006

We demonstrate a heteromeric D1–D2 dopamine receptor signaling complex in brain that is coupled to Gq/11 and requires agonist binding to both receptors for G protein activation and intracellular calcium release. The D1 agonist SKF83959 was identified as a specific agonist for the heteromer that activated Gq/11 by functioning as a full agonist for the D1 receptor and a high-affinity partial agonist for a pertussis toxin-resistant D2 receptor within the complex. We provide evidence that the D1–D2 signaling complex can be more readily detected in mice that are 8 months in age compared with animals that are 3 months old, suggesting that calcium signaling through the D1–D2 dopamine receptor complex is relevant for function in the postadolescent brain. Activation of Gq/11 through the heteromer increases levels of calcium/calmodulin-dependent protein kinase IIα in the nucleus accumbens, unlike activation of Gs/olf-coupled D1 receptors, indicating a mechanism by which D1–D2 dopamine receptor complexes may contribute to synaptic plasticity.
Evidence of the existence of the low-density liquid phase in supercooled, confined water
Authors: Mallamace Francesco , Broccio Matteo , Corsaro Carmelo , Faraone Antonio , Majolino Domenico , Venuti Valentina , Liu Li , Mou Chung-Yuan , Chen Sow-Hsin
Published: December 2006

By confining water in a nanoporous structure so narrow that the liquid could not freeze, it is possible to study properties of this previously undescribed system well below its homogeneous nucleation temperature
T

H

= 231 K. Using this trick, we were able to study, by means of a Fourier transform infrared spectroscopy, vibrational spectra (HOH bending and OH-stretching modes) of deeply supercooled water in the temperature range 183 <
T
< 273 K. We observed, upon decreasing temperature, the building up of a new population of hydrogen-bonded oscillators centered around 3,120 cm
−1
, the contribution of which progressively dominates the spectra as one enters into the deeply supercooled regime. We determined that the fractional weight of this spectral component reaches 50% just at the temperature,
T

L

≈ 225 K, where the confined water shows a fragile-to-strong dynamic cross-over phenomenon [Ito, K., Moynihan, C. T., Angell, C. A. (1999)
Nature
398:492–494]. Furthermore, the fact that the corresponding OH stretching spectral peak position of the low-density-amorphous solid water occurs exactly at 3,120 cm
−1
[Sivakumar, T. C., Rice, S. A., Sceats, M. G. (1978)
J. Chem. Phys.
69:3468–3476.] strongly suggests that these oscillators originate from existence of the low-density-liquid phase derived from the occurrence of the first-order liquid–liquid (LL) phase transition and the associated LL critical point in supercooled water proposed earlier by a computer molecular dynamics simulation [Poole, P. H., Sciortino, F., Essmann, U., Stanley, H. E. (1992)
Nature
360:324–328].
Premature myogenic differentiation and depletion of progenitor cells cause severe muscle hypotrophy in
Delta1
mutants
Authors: Schuster-Gossler Karin , Cordes Ralf , Gossler Achim
Published: December 2006

In vertebrates, skeletal myogenesis is initiated by the generation of myoblasts followed by their differentiation to myocytes and the formation of myofibers. The determination of myoblasts and their differentiation are controlled by muscle regulatory factors that are activated at specific stages during myogenesis. During late embryonic and fetal stages a distinct population of resident proliferating progenitor cells is the major source of myogenic cells. How the differentiation of myoblasts and progenitor cells is regulated is not clear. We show that in mouse embryos the Notch ligand Delta1 (
Dll1
) controls both differentiation of early myoblasts and maintenance of myogenic progenitor cells. Early dermomyotome-derived myoblasts are determined normally in
Dll1
mutant embryos, but their differentiation is accelerated, leading to a transient excess of myotomal muscle fibers. Similarly, migratory hypaxial myogenic cells colonize the limb buds and activate muscle regulatory factor expression normally, but muscle differentiation progresses more rapidly. Resident progenitor cells defined by Pax3/Pax7 expression are formed initially, but they are progressively lost and virtually absent at embryonic day 14.5. Muscle growth declines beginning around embryonic day 12, leading to subsequent severe muscle hypotrophy in hypomorphic
Dll1
fetuses. We suggest that premature and excessive differentiation leads to depletion of progenitor cells and cessation of muscle growth, and we conclude that
Dll1
provides essential signals that are required to prevent uncontrolled differentiation early and ensure sustained muscle differentiation during development.
Chemically engineered extracts as an alternative source of bioactive natural product-like compounds
Authors: López Silvia N. , Ramallo I. Ayelen , Sierra Manuel Gonzalez , Zacchino Susana A. , Furlan Ricardo L. E.
Published: December 2006

The access to libraries of molecules with interesting biomolecular properties is a limiting step in the drug discovery process. By virtue of a long molecular evolution process, natural products are recognized as biologically validated starting points in structural space for library development. We introduce here a strategy to generate natural product-like libraries. A semisynthetic mixture of compounds was produced by diversification of a natural product extract through the chemical transformation of common chemical functionalities in natural products into chemical functionalities rarely found in nature. The resulting mixture showed antifungal activity against
Candida albicans
, whereas the starting extract did not show such activity. Bioguided fractionation led to the isolation of a previously undescribed active semisynthetic pyrazole. The result illustrates how biological activity can be generated by designed chemical diversification of a natural product mixture, and represents the proof of principle of an alternative strategy for producing natural product-like libraries from natural products libraries.
Differential fitness costs of reproduction between the sexes
Authors: Penn Dustin J. , Smith Ken R.
Published: December 2006

Natural selection does not necessarily favor maximal reproduction because reproduction imposes fitness costs, reducing parental survival, and offspring quality. Here, we show that parents in a preindustrial population in North America incurred fitness costs from reproduction, and women incurred greater costs than men. We examined the survivorship and reproductive success (Darwinian fitness) of 21,684 couples married between 1860 and 1895 identified in the Utah Population Database. We found that increasing number of offspring (parity) and rates of reproduction were associated with reduced parental survivorship, and significantly more for mothers than fathers. Parental mortality resulted in reduced survival and reproduction of offspring, and the mothers' mortality was more detrimental to offspring than the fathers'. Increasing family size was associated with lower offspring survival, primarily for later-born children, indicating a tradeoff between offspring quantity versus quality. Also, we found that the costs of reproduction increased with age more for women than men. Our findings help to explain some puzzling aspects of human reproductive physiology and behavior, including the evolution of menopause and fertility declines associated with improvements in women's status (demographic transitions).
Functionally important glycosyltransferase gain and loss during catarrhine primate emergence
Authors: Koike Chihiro , Uddin Monica , Wildman Derek E. , Gray Edward A. , Trucco Massimo , Starzl Thomas E. , Goodman Morris
Published: December 2006

A glycosyltransferase, α1,3galactosyltransferase, catalyzes the terminal step in biosynthesis of Galα1,3Galβ1–4GlcNAc-R (αGal), an oligosaccharide cell surface epitope. This epitope or antigenically similar epitopes are widely distributed among the different forms of life. Although abundant in most mammals, αGal is not normally found in catarrhine primates (Old World monkeys and apes, including humans), all of which produce anti-αGal antibodies from infancy onward. Natural selection favoring enhanced resistance to αGal-positive pathogens has been the primary reason offered to account for the loss of αGal in catarrhines. Here, we question the primacy of this immune defense hypothesis with results that elucidate the evolutionary history of
GGTA1
gene and pseudogene loci. One such locus,
GGTA1P
, a processed (intronless) pseudogene (PPG), is present in platyrrhines, i.e., New World monkeys, and catarrhines but not in prosimians. PPG arose in an early ancestor of anthropoids (catarrhines and platyrrhines), and
GGTA1
itself became an unprocessed pseudogene in the late catarrhine stem lineage. Strong purifying selection, denoted by low nonsynonymous substitutions per nonsynonymous site/synonymous substitutions per synonymous site values, preserved
GGTA1
in noncatarrhine mammals, indicating that the functional gene product is subjected to considerable physiological constraint. Thus, we propose that a pattern of alternative and/or more beneficial glycosyltransferase activity had to first evolve in the stem catarrhines before
GGTA1
inactivation could occur. Enhanced defense against αGal-positive pathogens could then have accelerated the replacement of αGal-positive catarrhines by αGal-negative catarrhines. However, we emphasize that positively selected regulatory changes in sugar chain metabolism might well have contributed in a major way to catarrhine origins.
A Large, Uniform Sample of X-Ray-emitting Active Galactic Nuclei from the ROSAT All Sky and Sloan Digital Sky Surveys: The Data Release 5 Sample
Authors: Anderson Scott F. , Margon Bruce , Voges Wolfgang , Plotkin Richard M. , Syphers David , Haggard Daryl , Collinge Matthew J. , Bellovary Jillian , Strauss Michael A. , Agüeros Marcel A. , Hall Patrick B. , Homer L. , Ivezić Željko , Richards Gordon T. , Richmond Michael W. , Schneider Donald P. , Stinson Gregory , Vanden Berk Daniel E. , York Donald G.
Published: December 2006

We describe further results of a program aimed at yielding ∼104 fully characterized optical identifications of ROSAT X-ray sources. Our program employs X-ray data from the ROSAT All Sky Survey (RASS) and both optical imaging and spectroscopic data from the Sloan Digital Sky Survey (SDSS). RASS/SDSS data from 5740 deg2 of sky spectroscopically covered in SDSS Data Release 5 provide an expanded catalog of 7000 confirmed quasars and other active galactic nuclei (AGNs) that are probable RASS identifications. Again, in our expanded catalog the identifications as X-ray sources are statistically secure, with only a few percent of the SDSS AGNs likely to be randomly superposed on unrelated RASS X-ray sources. Most identifications continue to be quasars and Seyfert 1 galaxies with 15 < m < 21 and 0.01 < z < 4, but the total sample size has grown to include very substantial numbers of even quite rare AGNs, e.g., it now includes several hundreds of candidate X-ray-emitting BL Lac objects and narrow-line Seyfert 1 galaxies. In addition to exploring rare subpopulations, such a large total sample may be useful when considering correlations between the X-ray and the optical and may also serve as a resource list from which to select the "best" object (e.g., X-ray-brightest AGN of a certain subclass at a preferred redshift or luminosity) for follow-up X-ray spectral or alternate detailed studies.
Ribosome Biogenesis Is Sensed at the Start Cell Cycle Checkpoint
Authors: Bernstein Kara A. , Bleichert Franziska , Bean James M. , Cross Frederick R. , Baserga Susan J.
Published: December 2006

In the yeast Saccharomyces cerevisiae it has long been thought that cells must reach a critical cell size, called the “setpoint,” in order to allow the Start cell cycle transition. Recent evidence suggests that this setpoint is lowered when ribosome biogenesis is slowed. Here we present evidence that yeast can sense ribosome biogenesis independently of mature ribosome levels and protein synthetic capacity. Our results suggest that ribosome biogenesis directly promotes passage through Start through Whi5, the yeast functional equivalent to the human tumor suppressor Rb. When ribosome biogenesis is inhibited, a Whi5-dependent mechanism inhibits passage through Start before significant decreases in both the number of ribosomes and in overall translation capacity of the cell become evident. This delay at Start in response to decreases in ribosome biogenesis occurs independently of Cln3, the major known Whi5 antagonist. Thus ribosome biogenesis may be sensed at multiple steps in Start regulation. Ribosome biogenesis may thus both delay Start by increasing the cell size setpoint and independently may promote Start by inactivating Whi5.
Two Mammalian Sec16 Homologues Have Nonredundant Functions in Endoplasmic Reticulum (ER) Export and Transitional ER Organization
Authors: Bhattacharyya Dibyendu , Glick Benjamin S.
Published: December 2006

Budding yeast Sec16 is a large peripheral endoplasmic reticulum (ER) membrane protein that functions in generating COPII transport vesicles and in clustering COPII components at transitional ER (tER) sites. Sec16 interacts with multiple COPII components. Although the COPII assembly pathway is evolutionarily conserved, Sec16 homologues have not been described in higher eukaryotes. Here, we show that mammalian cells contain two distinct Sec16 homologues: a large protein that we term Sec16L and a smaller protein that we term Sec16S. These proteins localize to tER sites, and an N-terminal region of each protein is necessary and sufficient for tER localization. The Sec16L and Sec16S genes are both expressed in every tissue examined, and both proteins are required in HeLa cells for ER export and for normal tER organization. Sec16L resembles yeast Sec16 in having a C-terminal conserved domain that interacts with the COPII coat protein Sec23, but Sec16S lacks such a C-terminal conserved domain. Immunoprecipitation data indicate that Sec16L and Sec16S are each present at multiple copies in a heteromeric complex. We infer that mammalian cells have preserved and extended the function of Sec16.
Asymmetric Localization of Calpain 2 during Neutrophil Chemotaxis
Authors: Nuzzi Paul A. , Senetar Melissa A. , Huttenlocher Anna
Published: December 2006

Chemoattractants induce neutrophil polarization through localized polymerization of F-actin at the leading edge. The suppression of rear and lateral protrusions is required for efficient chemotaxis and involves the temporal and spatial segregation of signaling molecules. We have previously shown that the intracellular calcium-dependent protease calpain is required for cell migration and is involved in regulating neutrophil chemotaxis. Here, we show that primary neutrophils and neutrophil-like HL-60 cells express both calpain 1 and calpain 2 and that chemoattractants induce the asymmetric recruitment of calpain 2, but not calpain 1, to the leading edge of polarized neutrophils and differentiated HL-60 cells. Using time-lapse microscopy, we show that enrichment of calpain 2 at the leading edge occurs during early pseudopod formation and that its localization is sensitive to changes in the chemotactic gradient. We demonstrate that calpain 2 is recruited to lipid rafts and that cholesterol depletion perturbs calpain 2 localization, suggesting that its enrichment at the front requires proper membrane organization. Finally, we show that catalytic activity of calpain is required to limit pseudopod formation in the direction of chemoattractant and for efficient chemotaxis. Together, our findings identify calpain 2 as a novel component of the frontness signal that promotes polarization during chemotaxis.
Identification of anN-Acetylglucosamine Transporter That Mediates Hyphal Induction inCandida albicans
Authors: Alvarez Francisco J. , Konopka James B.
Published: December 2006

The sugar N-acetylglucosamine (GlcNAc) plays an important role in nutrient sensing and cellular regulation in a wide range of organisms from bacteria to humans. In the fungal pathogen Candida albicans, GlcNAc induces a morphological transition from budding to hyphal growth. Proteomic comparison of plasma membrane proteins from buds and from hyphae induced by GlcNAc identified a novel hyphal protein (Ngt1) with similarity to the major facilitator superfamily of transporters. An Ngt1-GFP fusion was detected in the plasma membrane after induction with GlcNAc, but not other related sugars. Ngt1-GFP was also induced by macrophage phagocytosis, suggesting a role for the GlcNAc response in signaling entry into phagolysosomes. NGT1 is needed for efficient GlcNAc uptake and for the ability to induce hyphae at low GlcNAc concentrations. High concentrations of GlcNAc could bypass the need for NGT1 to induce hyphae, indicating that elevated intracellular levels of GlcNAc induce hyphal formation. Expression of NGT1 in Saccharomyces cerevisiae promoted GlcNAc uptake, indicating that Ngt1 acts directly as a GlcNAc transporter. Transport mediated by Ngt1 was specific, as other sugars could not compete for the uptake of GlcNAc. Thus, Ngt1 represents the first eukaryotic GlcNAc transporter to be discovered. The presence of NGT1 homologues in the genome sequences of a wide range of eukaryotes from yeast to mammals suggests that they may also function in the cellular processes regulated by GlcNAc, including those that underlie important diseases such as cancer and diabetes.
The Essential Nature of Sphingolipids in Plants as Revealed by the Functional Identification and Characterization of theArabidopsisLCB1 Subunit of Serine Palmitoyltransferase
Authors: Chen Ming , Han Gongshe , Dietrich Charles R. , Dunn Teresa M. , Cahoon Edgar B.
Published: December 2006

Serine palmitoyltransferase (SPT) catalyzes the first step of sphingolipid biosynthesis. In yeast and mammalian cells, SPT is a heterodimer that consists of LCB1 and LCB2 subunits, which together form the active site of this enzyme. We show that the predicted gene for Arabidopsis thaliana LCB1 encodes a genuine subunit of SPT that rescues the sphingolipid long-chain base auxotrophy of Saccharomyces cerevisiae SPT mutants when coexpressed with Arabidopsis LCB2. In addition, homozygous T-DNA insertion mutants for At LCB1 were not recoverable, but viability was restored by complementation with the wild-type At LCB1 gene. Furthermore, partial RNA interference (RNAi) suppression of At LCB1 expression was accompanied by a marked reduction in plant size that resulted primarily from reduced cell expansion. Sphingolipid content on a weight basis was not changed significantly in the RNAi suppression plants, suggesting that plants compensate for the downregulation of sphingolipid synthesis by reduced growth. At LCB1 RNAi suppression plants also displayed altered leaf morphology and increases in relative amounts of saturated sphingolipid long-chain bases. These results demonstrate that plant SPT is a heteromeric enzyme and that sphingolipids are essential components of plant cells and contribute to growth and development.
A phosphate‐binding subsite in bovine pancreatic ribonuclease A can be converted into a very efficient catalytic site
Authors: Moussaoui Mohammed , Cuchillo Claudi M. , Nogués M. Victòria
Published: December 2006

A general acid–base catalytic mechanism is responsible for the cleavage of the phosphodiester bonds of the RNA by ribonuclease A (RNase A). The main active site is formed by the amino acid residues His12, His119, and Lys41, and the process follows an endonucleolytic pattern that depends on the existence of a noncatalytic phosphate‐binding subsite adjacent, on the 3′‐side, to the active site; in this region the phosphate group of the substrate establishes electrostatic interactions through the side chains of Lys7 and Arg10. We have obtained, by means of site‐directed mutagenesis, RNase A variants with His residues both at positions 7 and 10. These mutations have been introduced with the aim of transforming a noncatalytic binding subsite into a putative new catalytic active site. The RNase activity of these variants was determined by the zymogram technique and steady‐state kinetic parameters were obtained by spectrophotometric methods. The variants showed a catalytic efficiency in the same order of magnitude as the wild‐type enzyme. However, we have demonstrated in these variants important effects on the substrate's cleavage pattern. The quadruple mutant K7H/R10H/H12K/H119Q shows a clear increase of the exonucleolytic activity; in this case the original native active site has been suppressed, and, as consequence, its activity can only be associated to the new active site. In addition, the mutant K7H/R10H, with two putative active sites, also shows an increase in the exonucleolytic preference with respect to the wild type, a fact that may be correlated with the contribution of the new active site.
A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo‐oligomers
Authors: Potluri Shobha , Yan Anthony K. , Donald Bruce R. , Bailey‐Kellogg Chris
Published: December 2006

Assignment of nuclear Overhauser effect (NOE) data is a key bottleneck in structure determination by NMR. NOE assignment resolves the ambiguity as to which pair of protons generated the observed NOE peaks, and thus should be restrained in structure determination. In the case of intersubunit NOEs in symmetric homo‐oligomers, the ambiguity includes both the identities of the protons within a subunit, and the identities of the subunits to which they belong. This paper develops an algorithm for simultanous intersubunit NOE assignment and Cn symmetric homo‐oligomeric structure determinations, given the subunit structure. By using a configuration space framework, our algorithm guarantees completeness, in that it identifies structures representing, to within a user‐defined similarity level, every structure consistent with the available data (ambiguous or not). However, while our approach is complete in considering all conformations and assignments, it avoids explicit enumeration of the exponential number of combinations of possible assignments. Our algorithm can draw two types of conclusions not possible under previous methods: (1) that different assignments for an NOE would lead to different structural classes, or (2) that it is not necessary to uniquely assign an NOE, since it would have little impact on structural precision. We demonstrate on two test proteins that our method reduces the average number of possible assignments per NOE by a factor of 2.6 for MinE and 4.2 for CCMP. It results in high structural precision, reducing the average variance in atomic positions by factors of 1.5 and 3.6, respectively.
Contributions of the interdomain loop, amino terminus, and subunit interface to the ligand‐facilitated dimerization of neurophysin: Crystal structures and mutation studies of bovine neurophysin‐I
Authors: Li Xintian , Lee Hunjoong , Wu Jin , Breslow Esther
Published: December 2006

Current evidence indicates that the ligand‐facilitated dimerization of neurophysin is mediated in part by dimerization‐induced changes at the hormone binding site of the unliganded state that increase ligand affinity. To elucidate other contributory factors, we investigated the potential role of neurophysin's short interdomain loop (residues 55–59), particularly the effects of loop residue mutation and of deleting amino‐terminal residues 1–6, which interact with the loop and adjacent residues 53–54. The neurophysin studied was bovine neurophysin‐I, necessitating determination of the crystal structures of des 1–6 bovine neurophysin‐I in unliganded and liganded dimeric states, as well as the structure of its liganded Q58V mutant, in which peptide was bound with unexpectedly increased affinity. Increases in dimerization constant associated with selected loop residue mutations and with deletion of residues 1–6, together with structural data, provided evidence that dimerization of unliganded neurophysin‐I is constrained by hydrogen bonding of the side chains of Gln58, Ser56, and Gln55 and by amino terminus interactions, loss or alteration of these hydrogen bonds, and probable loss of amino terminus interactions, contributing to the increased dimerization of the liganded state. An additional intersubunit hydrogen bond from residue 81, present only in the liganded state, was demonstrated as the largest single effect of ligand binding directly on the subunit interface. Comparison of bovine neurophysins I and II indicates broadly similar mechanisms for both, with the exception in neurophysin II of the absence of Gln55 side chain hydrogen bonds in the unliganded state and a more firmly established loss of amino terminus interactions in the liganded state. Evidence is presented that loop status modulates dimerization via long‐range effects on neurophysin conformation involving neighboring Phe22 as a key intermediary.
Atomic‐resolution crystal structure of thioredoxin from the acidophilic bacterium Acetobacter aceti
Authors: Starks Courtney M. , Francois Julie A. , MacArthur Kelly M. , Heard Brittney Z. , Kappock T. Joseph
Published: December 2006

The crystal structure of thioredoxin (AaTrx) from the acetic acid bacterium Acetobacter aceti was determined at 1 Å resolution. This is currently the highest resolution crystal structure available for any thioredoxin. Thioredoxins facilitate thiol‐disulfide exchange, a process that is expected to be slow at the low pH values encountered in the A. aceti cytoplasm. Despite the apparent need to function at low pH, neither the active site nor the surface charge distribution of AaTrx is notably different from that of Escherichia coli thioredoxin. Apparently the ancestral thioredoxin was sufficiently stable for use in A. aceti or the need to interact with multiple targets constrained the variation of surface residues. The AaTrx structure presented here provides a clear view of all ionizable protein moieties and waters, a first step in understanding how thiol‐disulfide exchange might occur in a low pH cytoplasm, and is a basis for biophysical studies of the mechanism of acid‐mediated unfolding. The high resolution of this structure should be useful for computational studies of thioredoxin function, protein structure and dynamics, and side‐chain ionization.
Human lysosomal DNase IIα contains two requisite PLD‐signature (HxK) motifs: Evidence for a pseudodimeric structure of the active enzyme species
Authors: Schäfer Patrick , Cymerman Iwona A. , Bujnicki Janusz M. , Meiss Gregor
Published: December 2006

Lysosomal DNase IIα is essential for DNA waste removal and auxiliary apoptotic DNA fragmentation in higher eukaryotes. Despite the key role of this enzyme, little is known about its structure–function relationships. Here, mutational and biochemical analyses were used to characterize human DNase IIα variants expressed in mammalian cells. The resulting data strongly support the hypothesis that the enzyme is a monomeric phospholipase D–family member with a pseudodimeric protein fold. According to our results, DNase IIα contains two requisite PLD‐signature motifs (113HTK115 and 295HSK297) in the N‐ and C‐terminal subdomains, respectively, that together form a single active site. Based on these data, we present an experimentally validated structural model of DNase IIα.