bluuebunny/crossref_metadata_2025 huggingface dataset:
Cryogenic ion trapping systems with surface-electrode traps
Authors: Antohi P. B. , Schuster D. , Akselrod G. M. , Labaziewicz J. , Ge Y. , Lin Z. , Bakr W. S. , Chuang I. L.
Published: January 2009

We present two simple cryogenic rf ion trap systems in which cryogenic temperatures and ultra high vacuum pressures can be reached in as little as 12 h. The ion traps are operated either in a liquid helium bath cryostat or in a low vibration closed cycle cryostat. The fast turn around time and availability of buffer gas cooling made the systems ideal for testing surface-electrode ion traps. The vibration amplitude of the closed cycled cryostat was found to be below 106 nm. We evaluated the systems by loading surface-electrode ion traps with S88r+ ions using laser ablation, which is compatible with the cryogenic environment. Using Doppler cooling we observed small ion crystals in which optically resolved ions have a trapped lifetime over 2500 min.
Quenching of He-induced intensity enhancement effect in H and D emission produced by Nd-doped yttrium aluminum garnet laser irradiation on solid targets in low pressure helium gas
Authors: Kurniawan Koo Hendrik , Lie Tjung Jie , Suliyanti Maria Margaretha , Pardede Marincan , Abdulmadjid Syahrun Nur , Kagawa Kiichiro , Tjia May On
Published: January 2009

An experimental study was performed on the N2-induced quenching of He-induced intensity enhancement effect in reduced-pressure plasma emission produced by Nd-YAG irradiation on solid zircaloy and porous fossil samples. The spatial distributions and temporal variations in the emission intensities show pronounced intensity quenching effects on the He I 667.9 nm, H I 656.2 nm, and D I 656.1 nm emission lines in both samples when a tiny amount (5% by volume) of nitrogen was added to helium gas, while leaving the spatial and temporal intensity profiles of the heavier Zr and Ca atoms virtually unaffected. In both cases of different ambient gases, the spatial and temporal variations in the He, H, and D emission intensities exhibit distinct features and changes, which are clearly distinguishable from those observed on the Zr and Ca emission lines, which were mainly produced by the shock-wave induced thermal excitation process. The analysis of these data unambiguously revealed the presence of an additional and distinct “He-assisted” excitation mechanism in the He plasma, which was further suggested to be related to the He metastable excited state. The quenching effect was therefore explained as a consequence of energy depletion of the He metastable excited state triggered by the Penning ionization process induced by the presence of nitrogen. This also explains the relatively insensitive response of the Zr and Ca emission intensity profiles to nitrogen addition despite the increased plasma electron density resulting from the ionization process.
Branch-point energies and band discontinuities of III-nitrides and III-/II-oxides from quasiparticle band-structure calculations
Authors: Schleife A. , Fuchs F. , Rödl C. , Furthmüller J. , Bechstedt F.
Published: January 2009

Using quasiparticle band structures based on modern electronic-structure theory, we calculate the branch-point energies for zinc blende (GaN, InN), rocksalt (MgO, CdO), wurtzite (AlN, GaN, InN, ZnO), and rhombohedral crystals (In2O3). For InN, CdO, ZnO, and also In2O3 the branch-point energies are located within the lowest conduction band. These predictions are in agreement with observations of surface electron accumulation (InN, CdO) or conducting behavior of the oxides (ZnO, In2O3). The results are used to predict natural band offsets for the materials investigated.
Modification of graphene properties due to electron-beam irradiation
Authors: Teweldebrhan D. , Balandin A. A.
Published: January 2009

The authors report micro-Raman investigation of changes in the single and bilayer graphene crystal lattice induced by the low and medium energy electron-beam irradiation (5–20 keV). It was found that the radiation exposures result in the appearance of the strong disorder D band around 1345 cm−1, indicating damage to the lattice. The D and G peak evolution with increasing radiation dose follows the amorphization trajectory, which suggests graphene’s transformation to the nanocrystalline and then to amorphous form. The results have important implications for graphene characterization and device fabrication, which rely on the electron microscopy and focused ion beam processing.
Flexible photodetectors on plastic substrates by use of printing transferred single-crystal germanium membranes
Authors: Yuan Hao-Chih , Shin Jonghyun , Qin Guoxuan , Sun Lei , Bhattacharya Pallab , Lagally Max G. , Celler George K. , Ma Zhenqiang
Published: January 2009

This letter presents studies of multiwavelength flexible photodetectors on a plastic substrate by use of printing transferred single-crystal germanium (Ge) membranes. Ge membranes of 250nm thickness with selectively ion-implantation doped regions were released from a germanium-on-insulator substrate and integrated with a 175-μm-thick polyethylene terephthalate substrate via a dry printing technique. Photodiodes configured in lateral p-i-n configuration using the flexible Ge membranes with an intrinsic region width of 10μm exhibit an external quantum efficiency that varies from 5% at 411nm to 42% at 633nm under −1V bias condition. These results demonstrate the potential of utilizing single-crystal Ge-membrane photodiodes for imaging applications and as solar cells on objects with arbitrary curvatures and shapes.
High performance quantum cascade lasers based on three-phonon-resonance design
Authors: Wang Qi Jie , Pflügl Christian , Diehl Laurent , Capasso Federico , Edamura Tadataka , Furuta Shinichi , Yamanishi Masamichi , Kan Hirofumi
Published: January 2009

A quantum cascade laser structure based on three-phonon-resonance design is proposed and demonstrated. Devices, emitting at a wavelength of 9 μm, processed into buried ridge waveguide structures with a 3 mm long, 16 μm wide cavity and a high-reflection (HR) coating have shown peak output powers of 1.2 W, slope efficiencies of 1 W/A, threshold current densities of 1.1 kA/cm2, and high wall-plug efficiency of 6% at 300 K. A 3 mm long, 12 μm wide buried-heterostructure device without a HR coating exhibited continuous wave output power of as high as 65 mW from a single facet at 300 K.
Achieving a noninteracting magnetic nanoparticle system through direct control of interparticle spacing
Authors: Yang H. T. , Hasegawa D. , Takahashi M. , Ogawa T.
Published: January 2009

Monodisperse magnetite (Fe3O4) nanoparticles (NPs) were synthesized and coated using a SiO2 shell with controlled thickness ranging from 3.0 to 20.0 nm. The temperature-dependent zero-field-cooled (ZFC) and field-cooled (FC) magnetizations of the 7.5 nm Fe3O4 NPs with systematically increasing interparticle spacing were studied using the continuous and intermittent cooling protocol. The experimental evidence from dc magnetization and simulated ZFC/FC curves reveal that the increasing interparticle spacing modulated the collective magnetic behavior by effectively lowering the interparticle dipolar coupling, and for 7.5 nm Fe3O4 NPs a noninteracting particle system formed with interparticle spacing above 31.5 nm.
Single-parameter quantized charge pumping in high magnetic fields
Authors: Kaestner B. , Leicht C. , Kashcheyevs V. , Pierz K. , Siegner U. , Schumacher H. W.
Published: January 2009

We study single-parameter quantized charge pumping via a semiconductor quantum dot in high magnetic fields. The quantum dot is defined between two top gates in an AlGaAs/GaAs heterostructure. Application of an oscillating voltage to one of the gates leads to pumped current plateaus in the gate characteristic, corresponding to controlled transfer of integer multiples of electrons per cycle. In a perpendicular-to-plane magnetic field the plateaus become more pronounced indicating an improved current quantization. Current quantization is sustained up to magnetic fields where full spin polarization of the device can be expected.
Observation of excited states in a graphene quantum dot
Authors: Schnez S. , Molitor F. , Stampfer C. , Güttinger J. , Shorubalko I , Ihn T. , Ensslin K.
Published: January 2009

We demonstrate that excited states in single-layer graphene quantum dots can be detected via direct transport experiments. Coulomb diamond measurements show distinct features of sequential tunneling through an excited state. Moreover, the onset of inelastic cotunneling in the diamond region could be detected. For low magnetic fields, the positions of the single-particle energy levels fluctuate on the scale of a flux quantum penetrating the dot area. For higher magnetic fields, the transition to the formation of Landau levels is observed. Estimates based on the linear energy-momentum relation of graphene give carrier numbers of the order of 10 for our device.
Determination of third order elastic constants in a complex solid applying coda wave interferometry
Authors: Payan C. , Garnier V. , Moysan J. , Johnson P. A.
Published: January 2009

In this letter we describe the development of coda wave interferometry to determine acoustoelastically derived third order nonlinear coefficients of a highly complex material, concrete. Concrete, a structurally heterogeneous and volumetrically mechanically damaged material, is an example of a class of materials that exhibit strong multiple scattering as well as significant elastic nonlinear response. We show that intense scattering can be applied to robustly determine velocity changes at progressively increasing applied stress using coda wave interferometry, and thereby extract nonlinear coefficients.
Local strain behavior of bulk metallic glasses under tension studied by in situ x-ray diffraction
Authors: Wang X. D. , Bednarcik J. , Franz H. , Lou H. B. , He Z. H. , Cao Q. P. , Jiang J. Z.
Published: January 2009

The uniaxial tensile behavior of Zr62Al8Ni13Cu17, Cu46Zr46Al8, Zr48Cu43Al7Ag2, and La62Al14(Cu5/6Ag1/6)14Co5Ni5 bulk metallic glasses (BMGs) has been investigated by using in situ synchrotron radiation diffraction technique. It is found that the local strain is basically homogeneously distributed at low stress. However, heterogeneity appears obviously when the stress is close to the fracture strength. The amplitude of fluctuation in local strain for four BMGs could relate to the distribution of excess free volume within the medium range order.
Self-pulsing 104 A cm−2 current density discharges in dielectric barrier Al/Al2O3 microplasma devices
Authors: Yarmolich D. , Krasik Ya. E. , Stambulchik E. , Bernshtam V. , Yoon J. K. , Herrera B. , Park S.-J. , Eden J. G.
Published: January 2009

Excitation of Al/Al2O3 microplasma devices with 50 μs, 800 V pulses produces, in Ar/H2 gas mixtures at 600 Torr, ∼6 A current pulses with a duration of ∼30 ns. Corresponding to peak current and power densities of ∼104 A/cm2 and ∼2.5 GW/cm3, respectively, these pulses are generated in a 10 μs burst in which the voltage self-pulses at a repetition frequency of ∼3 MHz. Analysis of the Hα, Hβ, and Ar II emission line profiles yields a plasma density of ∼1017 cm−3, and the emission of O IV ions suggests the presence of energetic electrons. Images of the microplasma indicate that the plasma is initiated by surface flashover and extends ∼200 μm outside the microcavity.
Complete photonic bandgaps in the visible range from spherical layer structures in dichromate gelatin emulsions
Authors: Hung Jenny , Kok Mang Hin , Tam Wing Yim
Published: January 2009

We have fabricated spherical layer structures that exhibit complete photonic bandgaps in the visible range in dichromate gelatin emulsions by holographic interference. The complete bandgap was not a result of the high dielectric contrast but was due to the fact that the spherical layer structure was isotropic with equal spacing in all accessible directions. Angular dependence spectral measurements of the spherical layer structures were in good agreement with the expected results from an ideal structure of dielectric concentric spherical shells with equal spacing. Our fabrication technique and results could pave the way for new applications using complete bandgap photonic crystals.
Dependence of zeta potential on polyelectrolyte moving through a solid-state nanopore
Authors: Kejian Ding , Weimin Sun , Haiyan Zhang , Xianglei Peng , Honggang Hu
Published: January 2009

This paper presents a method for establishing the relationship between the zeta potential and the movement of polyelectrolyte through a solid-state nanopore by employing electrostatic-hydrodynamic theory. The influence of the salt concentration, the surface charge density, the zeta potential, and the relationship between them are discussed. For a selected polyelectrolyte driven by an electric field, the dependence of the zeta potential on the velocity of polyelectrolyte translocation is shown, which demonstrates that polyelectrolyte movement is mediated by the zeta potential and predicts that surface charge modification can become an effective means for managing and regulating polyelectrolyte translocation.
The use of nanocavities for the fabrication of ultrathin buried oxide layers
Authors: Ou Xin , Kögler Reinhard , Mücklich Arndt , Skorupa Wolfgang , Möller Wolfhard , Wang Xi , Vines Lasse
Published: January 2009

A continuous buried oxide layer with a thickness of only 58 nm is formed in silicon by oxygen implantation at 185 keV with a very low ion fluence of 1×1017 cm−2 and subsequent He implantation. Due to the implanted He efficient oxygen gettering occurs at the implantation induced damage and results in the accumulation of the implanted oxygen as well as of oxygen indiffused from the annealing atmosphere. The morphology and the resistivity of the resulting silicon-on-insulator structure are analyzed by cross section transmission electron microscopy and by cross section scanning spreading resistance microscopy.
Bricks, Butter, and Slices of Cucumber: Investigating Semantic Influences in Amodal Completion
Authors: Vrins Sven , de Wit Tessa C J , van Lier Rob
Published: January 2009

Objects in our world are partly occluded by other objects or sometimes even partly by themselves. Amodal completion is a visual process that enables us to perceive these objects as complete and is influenced by both local object information, present at contour intersections, and overall (global) object shape. In contrast, object semantics have been demonstrated to play no role in amodal completion but do so only by means of subjective methods. In the present study, object semantics were operationalised by material hardness of familiar objects which was varied to test whether it leaves amodal completion unaffected. Specifically, we investigated the perceived form of joined naturalistic objects that differ in perceived material hardness, employing the primed matching paradigm. In experiments 1 and 2, probing three different prime durations, amodal completion of a notched circular object changes systematically with the hardness of the object it was joined to. These results are in line with the view that amodal completion is inseparable from general object interpretation, during which object semantics may dominate.
Nonequilibrium scale selection mechanism for columnar jointing
Authors: Goehring Lucas , Mahadevan L. , Morris Stephen W.
Published: January 2009

Crack patterns in laboratory experiments on thick samples of drying cornstarch are geometrically similar to columnar joints in cooling lava found at geological sites such as the Giant's Causeway. We present measurements of the crack spacing from both laboratory and geological investigations of columnar jointing, and show how these data can be collapsed onto a single master scaling curve. This is due to the underlying mathematical similarity between theories for the cracking of solids induced by differential drying or by cooling. We use this theory to give a simple quantitative explanation of how these geometrically similar crack patterns arise from a single dynamical law rooted in the nonequilibrium nature of the phenomena. We also give scaling relations for the characteristic crack spacing in other limits consistent with our experiments and observations, and discuss the implications of our results for the control of crack patterns in thin and thick solid films.
Wnt/β-catenin signaling is required for CNS, but not non-CNS, angiogenesis
Authors: Daneman Richard , Agalliu Dritan , Zhou Lu , Kuhnert Frank , Kuo Calvin J. , Barres Ben A.
Published: January 2009

Despite the importance of CNS blood vessels, the molecular mechanisms that regulate CNS angiogenesis and blood−brain barrier (BBB) formation are largely unknown. Here we analyze the role of Wnt/β-catenin signaling in regulating the formation of CNS blood vessels. First, through the analysis of TOP-Gal Wnt reporter mice, we identify that canonical Wnt/β-catenin signaling is specifically activated in CNS, but not non-CNS, blood vessels during development. This activation correlates with the expression of different Wnt ligands by neural progenitor cells in distinct locations throughout the CNS, including Wnt7a and Wnt7b in ventral regions and Wnt1, Wnt3, Wnt3a, and Wnt4 in dorsal regions. Blockade of Wnt/β-catenin signaling in vivo specifically disrupts CNS, but not non-CNS, angiogenesis. These defects include reduction in vessel number, loss of capillary beds, and the formation of hemorrhagic vascular malformations that remain adherent to the meninges. Furthermore, we demonstrate that Wnt/β-catenin signaling regulates the expression of the BBB-specific glucose transporter glut-1. Taken together these experiments reveal an essential role for Wnt/β-catenin signaling in driving CNS-specific angiogenesis and provide molecular evidence that angiogenesis and BBB formation are in part linked.
Artificial ligand binding within the HIF2α PAS-B domain of the HIF2 transcription factor
Authors: Scheuermann Thomas H. , Tomchick Diana R. , Machius Mischa , Guo Yan , Bruick Richard K. , Gardner Kevin H.
Published: January 2009

The hypoxia-inducible factor (HIF) basic helix–loop–helix Per-aryl hydrocarbon receptor nuclear translocator (ARNT)-Sim (bHLH-PAS) transcription factors are master regulators of the conserved molecular mechanism by which metazoans sense and respond to reductions in local oxygen concentrations. In humans, HIF is critically important for the sustained growth and metastasis of solid tumors. Here, we describe crystal structures of the heterodimer formed by the C-terminal PAS domains from the HIF2α and ARNT subunits of the HIF2 transcription factor, both in the absence and presence of an artificial ligand. Unexpectedly, the HIF2α PAS-B domain contains a large internal cavity that accommodates ligands identified from a small-molecule screen. Binding one of these ligands to HIF2α PAS-B modulates the affinity of the HIF2α:ARNT PAS-B heterodimer in vitro. Given the essential role of PAS domains in forming active HIF heterodimers, these results suggest a presently uncharacterized ligand-mediated mechanism for regulating HIF2 activity in endogenous and clinical settings.
A G-protein γ subunit mimic is a general antagonist of prion propagation in
Saccharomyces cerevisiae
Authors: Ishiwata Masao , Kurahashi Hiroshi , Nakamura Yoshikazu
Published: January 2009

The Gpg1 protein is a Gγ subunit mimic implicated in the G-protein glucose-signaling pathway in
Saccharomyces cerevisiae
, and its function is largely unknown. Here we report that Gpg1 blocks the maintenance of [
PSI
+
], an aggregated prion form of the translation termination factor Sup35. Although the
GPG1
gene is normally not expressed, over-expression of
GPG1
inhibits propagation of not only [
PSI
+
] but also [
PIN
+
], [
URE3
] prions, and the toxic polyglutamine aggregate in
S. cerevisiae
. Over-expression of Gpg1 does not affect expression and activity of Hsp104, a protein-remodeling factor required for prion propagation, showing that Gpg1 does not target Hsp104 directly. Nevertheless, prion elimination by Gpg1 is weakened by over-expression of Hsp104. Importantly, Gpg1 protein is prone to self-aggregate and transiently colocalized with Sup35NM-prion aggregates when expressed in [
PSI
+
] cells. Genetic selection and characterization of loss-of-activity
gpg1
mutations revealed that multiple mutations on the hydrophobic one-side surface of predicted α-helices of the Gpg1 protein hampered the activity. Prion elimination by Gpg1 is unaffected in the
gpa2
Δ and
gpb1
Δ strains lacking the supposed physiological G-protein partners of Gpg1. These findings suggest a general inhibitory interaction of the Gpg1 protein with other transmissible and nontransmissible amyloids, resulting in prion elimination. Assuming the ability of Gpg1 to form G-protein heterotrimeric complexes, Gpg1 is likely to play a versatile function of reversing the prion state and modulating the G-protein signaling pathway.
Specific transbilayer translocation of dolichol-linked oligosaccharides by an endoplasmic reticulum flippase
Authors: Sanyal Sumana , Menon Anant K.
Published: January 2009

The oligosaccharide donor for protein
N
-glycosylation, Glc
3
Man
9
GlcNAc
2
-PP-dolichol, is synthesized via a multistep pathway that starts on the cytoplasmic face of the endoplasmic reticulum (ER) and ends in the lumen where the glycosylation reaction occurs. This necessitates transbilayer translocation or flipping of the lipid intermediate Man
5
GlcNAc
2
-PP-dolichol (M5-DLO) across the ER membrane. The mechanism by which M5-DLO—or any other lipid—is flipped across the ER is unknown, except that specific transport proteins or flippases are required. We recently demonstrated M5-DLO flipping activity in proteoliposomes reconstituted from detergent-solubilized ER membrane proteins and showed that it was ATP-independent and required a trypsin-sensitive protein that sedimented at approximately 4S. By using an activity-enriched fraction devoid of glycerophospholipid flippase activity, we now report that M5-DLO is rapidly flipped in the reconstituted system with a time constant τ <2 min, whereas its triantennary structural isomer is flipped slowly with τ >200 min. DLOs larger than M5-DLO are also poorly translocated, with τ ranging from approximately 10 min to >200 min. We conclude that (i) the number and arrangement of mannoses in the DLO glycan has a profound effect on the ability of the DLO to be translocated by the flippase, (ii) glycan size
per se
does not dictate whether a DLO will be flipped, and (iii) the flippase is highly specific for M5-DLO. Our results suggest a simple structural model for the interaction between the DLO head group and the flippase.
Spectral methods in machine learning and new strategies for very large datasets
Authors: Belabbas Mohamed-Ali , Wolfe Patrick J.
Published: January 2009

Spectral methods are of fundamental importance in statistics and machine learning, because they underlie algorithms from classical principal components analysis to more recent approaches that exploit manifold structure. In most cases, the core technical problem can be reduced to computing a low-rank approximation to a positive-definite kernel. For the growing number of applications dealing with very large or high-dimensional datasets, however, the optimal approximation afforded by an exact spectral decomposition is too costly, because its complexity scales as the cube of either the number of training examples or their dimensionality. Motivated by such applications, we present here 2 new algorithms for the approximation of positive-semidefinite kernels, together with error bounds that improve on results in the literature. We approach this problem by seeking to determine, in an efficient manner, the most informative subset of our data relative to the kernel approximation task at hand. This leads to two new strategies based on the Nyström method that are directly applicable to massive datasets. The first of these—based on sampling—leads to a randomized algorithm whereupon the kernel induces a probability distribution on its set of partitions, whereas the latter approach—based on sorting—provides for the selection of a partition in a deterministic way. We detail their numerical implementation and provide simulation results for a variety of representative problems in statistical data analysis, each of which demonstrates the improved performance of our approach relative to existing methods.
Photosynthetic metabolism of C
3
plants shows highly cooperative regulation under changing environments: A systems biological analysis
Authors: Luo Ruoyu , Wei Haibin , Ye Lin , Wang Kankan , Chen Fan , Luo Lijun , Liu Lei , Li Yuanyuan , Crabbe M. James C. , Jin Li , Li Yixue , Zhong Yang
Published: January 2009

We studied the robustness of photosynthetic metabolism in the chloroplasts of C
3
plants under drought stress and at high CO
2
concentration conditions by using a method called Minimization of Metabolic Adjustment Dynamic Flux Balance Analysis (M_DFBA). Photosynthetic metabolism in the chloroplasts of C
3
plants applies highly cooperative regulation to minimize the fluctuation of metabolite concentration profiles in the face of transient perturbations. Our work suggests that highly cooperative regulation assures the robustness of the biological system and that there is closer cooperation under perturbation conditions than under normal conditions. This results in minimizing fluctuations in the profiles of metabolite concentrations, which is the key to maintaining a system's function. Our methods help in understanding such phenomena and the mechanisms of robustness for complex metabolic networks in dynamic processes.
Biodegradable dendritic positron-emitting nanoprobes for the noninvasive imaging of angiogenesis
Authors: Almutairi Adah , Rossin Raffaella , Shokeen Monica , Hagooly Aviv , Ananth Ashwin , Capoccia Benjamin , Guillaudeu Steve , Abendschein Dana , Anderson Carolyn J. , Welch Michael J. , Fréchet Jean M. J.
Published: January 2009

A biodegradable positron-emitting dendritic nanoprobe targeted at α
v
β
3
integrin, a biological marker known to modulate angiogenesis, was developed for the noninvasive imaging of angiogenesis. The nanoprobe has a modular multivalent core-shell architecture consisting of a biodegradable heterobifunctional dendritic core chemoselectively functionalized with heterobifunctional polyethylene oxide (PEO) chains that form a protective shell, which imparts biological stealth and dictates the pharmacokinetics. Each of the 8 branches of the dendritic core was functionalized for labeling with radiohalogens. Placement of radioactive moieties at the core was designed to prevent in vivo dehalogenation, a potential problem for radiohalogens in imaging and therapy. Targeting peptides of cyclic arginine–glycine–aspartic acid (RGD) motifs were installed at the terminal ends of the PEO chains to enhance their accessibility to α
v
β
3
integrin receptors. This nanoscale design enabled a 50-fold enhancement of the binding affinity to α
v
β
3
integrin receptors with respect to the monovalent RGD peptide alone, from 10.40 nM to 0.18 nM IC
50
. Cell-based assays of the
125
I-labeled dendritic nanoprobes using α
v
β
3
-positive cells showed a 6-fold increase in α
v
β
3
receptor-mediated endocytosis of the targeted nanoprobe compared with the nontargeted nanoprobe, whereas α
v
β
3
-negative cells showed no enhancement of cell uptake over time. In vivo biodistribution studies of
76
Br-labeled dendritic nanoprobes showed excellent bioavailability for the targeted and nontargeted nanoprobes. In vivo studies in a murine hindlimb ischemia model for angiogenesis revealed high specific accumulation of
76
Br-labeled dendritic nanoprobes targeted at α
v
β
3
integrins in angiogenic muscles, allowing highly selective imaging of this critically important process.
Deadly competition between sibling bacterial colonies
Authors: Be'er Avraham , Zhang H. P. , Florin E.-L. , Payne Shelley M. , Ben-Jacob Eshel , Swinney Harry L.
Published: January 2009

Bacteria can secrete a wide array of antibacterial compounds when competing with other bacteria for the same resources. Some of these compounds, such as bacteriocins, can affect bacteria of similar or closely related strains. In some cases, these secretions have been found to kill sibling cells that belong to the same colony. Here, we present experimental observations of competition between 2 sibling colonies of
Paenibacillus dendritiformis
grown on a low-nutrient agar gel. We find that neighboring colonies (growing from droplet inoculation) mutually inhibit growth through secretions that become lethal if the level exceeds a well-defined threshold. In contrast, within a single colony developing from a droplet inoculation, no growth inhibition is observed. However, growth inhibition and cell death are observed if material extracted from the agar between 2 growing colonies is introduced outside a growing single colony. To interpret the observations, we devised a simple mathematical model for the secretion of an antibacterial compound. Simulations of this model illustrate how secretions from neighboring colonies can be deadly, whereas secretions from a single colony growing from a droplet are not.
Ab initioStudy on Structures and Isomerization of Magnesium Fluorosilylenoid H2SiFMgF
Authors: Zhang Yi-jian , Li Mei-jiang , Lai Guo-qiao , Feng Da-cheng , Feng Sheng-yu
Published: January 2009

The structures and isomerization of magnesium fluorosilylenoid H2SiFMgF were investigated by ab initio molecular orbital theory. Four equilibrium structures and three isomeric transition states were located and fully optimized at the B3LYP/6-31G(d,p) and G3MP2B3 levels, respectively. Based on the B3LYP/6-31G(d,p) optimized geometries, harmonic frequencies of various structures were obtained and 29Si chemical shifts were calculated. The solvent effects were investigated by means of the polarizable continuum model using THF as a solvent at B3LYP/6-31G(d,p) level. Isomerization paths for isomers were confirmed by intrinsic reaction coordinate calculations. The calculated results show that tetrahedral structure has the lowest energy and is the most stable; tetrahedral, three-membered ring, and p-complex structures are suggested to be the experimentally detectable ones; and -complex structure has the highest energy and will not exist.
Theoretical Studies on the Structure and Spectrum of Imidazole-Chloranil Charge Transfer Complex
Authors: Wang Hai-long , Lu Tong-tong , He Tian-jing , Chen Dong-ming
Published: January 2009

UV-Vis absorption spectra of the molecular complex formed by imidazole (Im) and chloranil (CA) were measured in chloroform. The stoichiometry of the imidazole-chloranil (Im-CA) complex was determined as 1:1 by applying BenesiHildebrand's equation and Job's continuous variation method. Density function theory (DFT) and MP2 calculations were performed to study the structures and the binding energies of the Im-CA complex. The calculations located four conformations (denoted as S1S4) for the Im-CA complex, two edge(Im)-to-face(CA) linked and two edge(Im)-to-edge(CA) linked. It was found that the edge-to-face conformers are more stable than the edge-to-edge ones. The bonding characteristics of these conformers were investigated with natural population analysis (NPA), topological analysis of electron density, and natural bond orbital (NBO) analysis. It was revealed that the edge-to-face conformers are charge-transfer (CT) complexes whereas the edge-to-edge conformers are the hydrogen bond complexes. For the most stable conformation of the Im-CA complex (S1), the charge transfer interaction of the imidazole n(N15) lone pair orbital with the chloranil *(C1 = O7) orbital plays a crucial role in the Im-CA binding, and the binding is further strengthened by the O7 H20 hydrogen bond. The electronic excitation energies of the complex (S1) were calculated with time-dependent DFT (TDDFT), and the observed UV-Visible spectrum of the complex was analyzed based on the computed results.
Mesoporous Silica Materials Synthesized via Sol-Gel Methods Modified with Ionic Liquid and Surfactant Molecules
Authors: Xu Cun-ying , Tang Ru-lan , Hua Yi-xin , Zhang Peng-xiang
Published: January 2009

Mesoporous silica materials were synthesized via a sol-gel method employing a room temperature ionic liquid (1-butyl-3-methylimidazolium tetrafluoroborate, [bmim][BF4]) as a new solvent medium and further modified with surfactant (hexadecyl-trimethyl-ammonium bromide, CTAB) as a pore templating material. The synthesized samples were characterized by the transmission electron microscopy, X-ray diffraction, and N2 adsorption-desorption techniques. The results indicated that the mesoporous silica synthesized by using [bmim][BF4] and CTAB as mixed templates showed better mesostructural order and smaller pore size, compared with mesoporous silica materials synthesized by using single [bmim][BF4] as template under the same conditions. This indicates that the presence of surfactant can affect the microstructures of silica prepared by the present synthesis method.
Essential Role of hIST1 in Cytokinesis
Authors: Agromayor Monica , Carlton Jez G. , Phelan John P. , Matthews Daniel R. , Carlin Leo M. , Ameer-Beg Simon , Bowers Katherine , Martin-Serrano Juan
Published: January 2009

The last steps of multivesicular body (MVB) formation, human immunodeficiency virus (HIV)-1 budding and cytokinesis require a functional endosomal sorting complex required for transport (ESCRT) machinery to facilitate topologically equivalent membrane fission events. Increased sodium tolerance (IST) 1, a new positive modulator of the ESCRT pathway, has been described recently, but an essential function of this highly conserved protein has not been identified. Here, we describe the previously uncharacterized KIAA0174 as the human homologue of IST1 (hIST1), and we report its conserved interaction with VPS4, CHMP1A/B, and LIP5. We also identify a microtubule interacting and transport (MIT) domain interacting motif (MIM) in hIST1 that is necessary for its interaction with VPS4, LIP5 and other MIT domain-containing proteins, namely, MITD1, AMSH, UBPY, and Spastin. Importantly, hIST1 is essential for cytokinesis in mammalian cells but not for HIV-1 budding, thus providing a novel mechanism of functional diversification of the ESCRT machinery. Last, we show that the hIST1 MIM activity is essential for cytokinesis, suggesting possible mechanisms to explain the role of hIST1 in the last step of mammalian cell division.
Biochemical Analyses of Human IST1 and Its Function in Cytokinesis
Authors: Bajorek Monika , Morita Eiji , Skalicky Jack J. , Morham Scott G. , Babst Markus , Sundquist Wesley I.
Published: January 2009

The newly described yeast endosomal sorting complexes required for transport (ESCRT) protein increased sodium tolerance-1 (Ist1p) binds the late-acting ESCRT proteins Did2p/charged MVB protein (CHMP) 1 and Vps4p and exhibits synthetic vacuolar protein sorting defects when combined with mutations in the Vta1p/LIP5–Vps60p/CHMP5 complex. Here, we report that human IST1 also functions in the ESCRT pathway and is required for efficient abscission during HeLa cell cytokinesis. IST1 binding interactions with VPS4, CHMP1, LIP5, and ESCRT-I were characterized, and the IST1–VPS4 interaction was investigated in detail. Mutational and NMR spectroscopic studies revealed that the IST1 terminus contains two distinct MIT interacting motifs (MIM1 and MIM2) that wrap around and bind in different groves of the MIT helical bundle. IST1, CHMP1, and VPS4 were recruited to the midbodies of dividing cells, and depleting either IST1 or CHMP1 proteins blocked VPS4 recruitment and abscission. In contrast, IST1 depletion did not inhibit human immunodeficiency virus-1 budding. Thus, IST1 and CHMP1 act together to recruit and modulate specific VPS4 activities required during the final stages of cell division.
A Fluorescently Tagged C-Terminal Fragment of p47phoxDetects NADPH Oxidase Dynamics during Phagocytosis
Authors: Li Xing Jun , Tian Wei , Stull Natalie D. , Grinstein Sergio , Atkinson Simon , Dinauer Mary C.
Published: January 2009

The assembly of cytosolic p47phoxand p67phoxwith flavocytochrome b558at the membrane is crucial for activating the leukocyte NADPH oxidase that generates superoxide for microbial killing. p47phoxand p67phoxare linked via a high-affinity, tail-to-tail interaction involving a proline-rich region (PRR) and a C-terminal SH3 domain (SH3b), respectively, in their C-termini. This interaction mediates p67phoxtranslocation in neutrophils, but is not required for oxidase activity in model systems. Here we examined phagocytosis-induced NADPH oxidase assembly, showing the sequential recruitment of YFP-tagged p67phoxto the phagosomal cup, and, after phagosome internalization, a probe for PI(3)P followed by a YFP-tagged fragment derived from the p47phoxPRR. This fragment was recruited in a flavocytochrome b558-dependent, p67phox-specific, and PI(3)P-independent manner. These findings indicate that p47PRR fragment probes the status of the p67phoxSH3b domain and suggest that the p47phox/p67phoxtail-to-tail interaction is disrupted after oxidase assembly such that the p67phox-SH3b domain becomes accessible. Superoxide generation was sustained within phagosomes, indicating that this change does not correlate with loss of enzyme activity. This study defines a sequence of events during phagocytosis-induced NADPH oxidase assembly and provides experimental evidence that intermolecular interactions within this complex are dynamic and modulated after assembly on phagosomes.
Cu, Zn Superoxide Dismutase and NADP(H) Homeostasis Are Required for Tolerance of Endoplasmic Reticulum Stress inSaccharomyces cerevisiae
Authors: Tan Shi-Xiong , Teo Mariati , Lam Yuen T. , Dawes Ian W. , Perrone Gabriel G.
Published: January 2009

Genome-wide screening for sensitivity to chronic endoplasmic reticulum (ER) stress induced by dithiothreitol and tunicamycin (TM) identified mutants deleted for Cu, Zn superoxide dismutase (SOD) function (SOD1, CCS1) or affected in NADPH generation via the pentose phosphate pathway (TKL1, RPE1). TM-induced ER stress led to an increase in cellular superoxide accumulation and an increase in SOD1 expression and Sod1p activity. Prior adaptation of the hac1 mutant deficient in the unfolded protein response (UPR) to the superoxide-generating agent paraquat reduced cell death under ER stress. Overexpression of the ER oxidoreductase Ero1p known to generate hydrogen peroxide in vitro, did not lead to increased superoxide levels in cells subjected to ER stress. The mutants lacking SOD1, TKL1, or RPE1 exhibited decreased UPR induction under ER stress. Sensitivity of the sod1 mutant to ER stress and decreased UPR induction was partially rescued by overexpression of TKL1 encoding transketolase. These data indicate an important role for SOD and cellular NADP(H) in cell survival during ER stress, and it is proposed that accumulation of superoxide affects NADP(H) homeostasis, leading to reduced UPR induction during ER stress.
Heme Oxygenase-1 Contributes to an Alternative Macrophage Activation Profile Induced by Apoptotic Cell Supernatants
Authors: Weis Nicole , Weigert Andreas , von Knethen Andreas , Brüne Bernhard
Published: January 2009

Apoptotic cells (AC) are rapidly engulfed by professional phagocytes such as macrophages to avoid secondary necrosis and thus inflammation. Recognition of AC polarizes macrophages toward an anti-inflammatory phenotype, which shows homology to an alternatively activated M2 macrophage. However, mechanistic details provoking these phenotype alterations are incompletely understood. Here, we demonstrate a biphasic up-regulation of heme oxygenase-1 (HO-1), a protein that bears an antiapoptotic as well as an anti-inflammatory potential, in primary human macrophages, which were exposed to the supernatant of AC. Although the first phase of HO-1 induction at 6 h was accomplished by AC-derived sphingosine-1-phosphate (S1P) acting via S1P receptor 1, the second wave of HO-1 induction at 24 h was attributed to autocrine signaling of vascular endothelial growth factor A (VEGFA), whose expression and release were facilitated by S1P. Whereas VEGFA release from macrophages was signal transducer and activator of transcription (STAT) 1-dependent, vascular endothelial growth factor itself triggered STAT1/STAT3 heterodimer formation, which bound to and activated the HO-1 promoter. Knockdown of HO-1 proved its relevance in facilitating enhanced expression of the antiapoptotic proteins Bcl-2 and Bcl-XL, as well as the anti-inflammatory adenosine receptor A2A. These findings suggest that HO-1, which is induced by AC-derived S1P, is critically involved in macrophage polarization toward an M2 phenotype.
PanCGH: a genotype-calling algorithm for pangenome CGH data
Authors: Bayjanov Jumamurat R. , Wels Michiel , Starrenburg Marjo , van Hylckama Vlieg Johan E. T. , Siezen Roland J. , Molenaar Douwe
Published: January 2009

Motivation: Pangenome arrays contain DNA oligomers targeting several sequenced reference genomes from the same species. In microbiology, these can be employed to investigate the often high genetic variability within a species by comparative genome hybridization (CGH). The biological interpretation of pangenome CGH data depends on the ability to compare strains at a functional level, particularly by comparing the presence or absence of orthologous genes. Due to the high genetic variability, available genotype-calling algorithms can not be applied to pangenome CGH data.

Results: We have developed the algorithm PanCGH that incorporates orthology information about genes to predict the presence or absence of orthologous genes in a query organism using CGH arrays that target the genomes of sequenced representatives of a group of microorganisms. PanCGH was tested and applied in the analysis of genetic diversity among 39 Lactococcus lactis strains from three different subspecies (lactis.cremoris, hordniae) and isolated from two different niches (dairy and plant). Clustering of these strains using the presence/absence data of gene orthologs revealed a clear separation between different subspecies and reflected the niche of the strains.

Contact:  J.Bayjanov@cmbi.ru.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses
Authors: Barker Michael S. , Dlugosch Katrina M. , Reddy A. Chaitanya C. , Amyotte Sarah N. , Rieseberg Loren H.
Published: January 2009

Summary: Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. The program was created to knit together 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences.

Availability: SCARF is freely available at http://msbarker.com/software.htm, and is released under the open source GPLv3 license (http://www.opensource.org/licenses/gpl-3.0.html.

Contact:  msbarker@indiana.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
DichroCalc—circular and linear dichroism online
Authors: Bulheller Benjamin M. , Hirst Jonathan D.
Published: January 2009

Motivation: Circular dichroism (CD) is widely used in studies of protein folding. The CD spectrum of a protein can be estimated from its structure alone, using the well-established matrix method. In the last decade, a related spectroscopy, linear dichroism (LD), has been increasingly applied to study the orientation of proteins in solution. However, matrix method calculations of LD spectra have not been presented before. DichroCalc makes both CD and LD calculations available in an easy-to-use fashion.

Results: DichroCalc can be used without registration and calculates CD and LD spectra using a variety of matrix method parameters. PDB files can be uploaded as input or retrieved via their PDB code and a Perl-based parser is offered for easy handling of PDB files.

Availability:  http://comp.chem.nottingham.ac.uk/dichrocalc and http://comp.chem.nottingham.ac.uk/parsepdb

Contact:  jonathan.hirst@nottingham.ac.uk
Considering multiple-species attributes to understand better the effects of successive changes in protection status on a coral reef fish assemblage
Authors: Preuss Bastien , Pelletier Dominique , Wantiez Laurent , Letourneur Yves , Sarramégna Sébastien , Kulbicki Michel , Galzin René , Ferraris Jocelyne
Published: January 2009

Preuss, B., Pelletier, D., Wantiez, L., Letourneur, Y., Sarramégna, S., Kulbicki, M., Galzin, R., and Ferraris, J. 2009. Considering multiple-species attributes to understand better the effects of successive changes in protection status on a coral reef fish assemblage. – ICES Journal of Marine Science, 66: 170–179. The response of fish assemblages to changes in protection status is a major issue for both biodiversity conservation and fishery management. In New Caledonia, the Aboré reef marine reserve harbours more than 500 fish species, and has been subjected to changes in protection status since 1988. The present study investigates the impact of these changes on a wide subset of species (213), based on underwater visual counts collected before the opening and after the closure to fishing of this marine protected area (MPA). We analysed the spatial and temporal variability in fish assemblage attributable to protection status, explicitly considering habitat. To understand the successive responses of fish assemblage to fishing and protection, the assessment models included four criteria defining species groups that partition the fish assemblage: trophic regime, adult size, mobility, and interest for fishing. We could therefore identify the negative impact of opening the MPA to fishing on piscivores and highly mobile species. Surprisingly, target species were not affected more than non-target species. Model results were used to identify species groups that respond to fishing and protection. These results utilize fisheries-related criteria to provide new insight into the response of fish assemblages to protection from the perspective of MPA monitoring.
Identifying eastern Baltic cod nursery grounds using hydrodynamic modelling: knowledge for the design of Marine Protected Areas
Authors: Hinrichsen Hans-Harald , Kraus Gerd , Böttcher Uwe , Köster Fritz
Published: January 2009

Hinrichsen, H-H., Kraus, G., Böttcher, U., and Köster, F. 2009. Identifying eastern Baltic cod nursery grounds using hydrodynamic modelling: knowledge for the design of Marine Protected Areas. – ICES Journal of Marine Science, 66: 101–108. Knowledge of the spatial and temporal distribution of juvenile cod is essential to closing the life cycle in population dynamic models, and it is a prerequisite for the design of Marine Protected Areas (MPAs) aiming at the protection of juveniles. In this study, we use a hydrodynamic model to examine the spatial distribution of eastern Baltic cod larvae and early juveniles. The transport patterns of the larvae spawned at the three major spawning grounds in the central Baltic Sea were investigated by drift model simulations for the period 1979–2004. We analysed potential habitats for their suitability for juvenile settlement, i.e. the change from pelagic to demersal life. The results revealed a clear dependence of the probability for successful settling on wind-induced drift of larval cod, which is controlled by the local atmospheric conditions over the Baltic Sea. Furthermore, we found evidence that the final destinations of juvenile cod drift routes are affected by decadal climate variability. Application of the methodology to MPA design is discussed, e.g. identifying the overlap of areas with a high probability of successful juvenile cod settlement and regions of high fishing effort in small-meshed fisheries targeting sprat and herring.