bluuebunny/crossref_metadata_2025 huggingface dataset:
Multipurpose EPR loop-gap resonator and cylindrical TE011 cavity for aqueous samples at 94GHz
Authors: Sidabras Jason W. , Mett Richard R. , Froncisz Wojciech , Camenisch Theodore G. , Anderson James R. , Hyde James S.
Published: March 2007

A loop-gap resonator (LGR) and a cylindrical TE011 cavity resonator for use at W band, 94GHz, have been designed and characterized using the Ansoft (Pittsburgh, PA) high frequency structure simulator (HFSS; Version 10.0). Field modulation penetration was analyzed using Ansoft MAXWELL 3D (Version 11.0). Optimizing both resonators to the same sample sizes shows that EPR signal intensities of the LGR and TE011 are similar. The 3dB bandwidth of the LGR, on the order of 1GHz, is a new advantage for high frequency experiments. Ultraprecision electric discharge machining (EDM) was used to fabricate the resonators from silver. The TE011 cavity has slots that are cut into the body to allow penetration of 100kHz field modulation. The resonator body is embedded in graphite, also cut by EDM techniques, for a combination of reasons that include (i) reduced microwave leakage and improved TE011 mode purity, (ii) field modulation penetration, (iii) structural support for the cavity body, and (iv) machinability by EDM. Both resonators use a slotted iris. Variable coupling is provided by a three-stub tuning element. A collet system designed to hold sample tubes has been implemented, increasing repeatability of sample placement and reducing sample vibration noise. Initial results include multiquantum experiments up to 9Q using the LGR to examine 1mM 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) in aqueous solution at room temperature and field modulation experiments using the TE011 cavity to obtain an EPR spectrum of 1μM TEMPO.
Sampling small-scale and large-scale conformational changes in proteins and molecular complexes
Authors: Yun Mi-Ran , Mousseau N. , Derreumaux P.
Published: March 2007

Sampling of small-scale and large-scale motions is important in various computational tasks, such as protein-protein docking and ligand binding. Here, we report further development and applications of the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method generates conformational moves of any complexity and size by identifying and crossing well-defined saddle points connecting energy minima. Simulations on two all-atom proteins and three protein complexes containing between 70 and 300 amino acids indicate that ARTIST opens the door to the full treatment of all degrees of freedom in dense systems such as protein-protein complexes.
Formation of ordered microphase-separated pattern during spin coating of ABC triblock copolymer
Authors: Huang Weihuan , Luo Chunxia , Zhang Jilin , Han Yanchun
Published: March 2007

In this paper, the authors have systematically studied the microphase separation and crystallization during spin coating of an ABC triblock copolymer, polystyrene-b-poly(2-vinylpyridine)-b-poly(ethylene oxide) (PS-b-P2VP-b-PEO). The microphase separation of PS-b-P2VP-b-PEO and the crystallization of PEO blocks can be modulated by the types of the solvent and the substrate, the spinning speed, and the copolymer concentration. Ordered microphase-separated pattern, where PEO and P2VP blocks adsorbed to the substrate and PS blocks protrusions formed hexagonal dots above the P2VP domains, can only be obtained when PS-b-P2VP-b-PEO is dissolved in N,N-dimethylformamide and the films are spin coated onto the polar substrate, silicon wafers or mica. The mechanism of the formation of regular pattern by microphase separation is found to be mainly related to the inducement of the substrate (middle block P2VP wetting the polar substrate), the quick vanishment of the solvent during the early stage of the spin coating, and the slow evaporation of the remaining solvent during the subsequent stage. On the other hand, the probability of the crystallization of PEO blocks during spin coating decreases with the reduced film thickness. When the film thickness reaches a certain value (3.0nm), the extensive crystallization of PEO is effectively prohibited and ordered microphase-separated pattern over large areas can be routinely prepared. When the film thickness exceeds another definite value (12.0nm), the crystallization of PEO dominates the surface morphology. For films with thickness between these two values, microphase separation and crystallization can simultaneously occur.
Structures and magnetic properties of wurtzite Zn1−xCoxO dilute magnetic semiconductor nanocomposites
Authors: Shi Tongfei , Zhu Sanyuan , Sun Zhihu , Wei Shiqiang , Liu Wenhan
Published: March 2007

Cobalt-doped ZnO dilute magnetic semiconductor nanocomposites Zn1−xCoxO with Co concentrations from 0.02 to 0.25 were prepared by the sol-gel method. The magnetic measurement shows paramagnetic behavior for all the samples. The structures of these composites were investigated by x-ray diffraction and fluorescence x-ray absorption fine structure spectroscopy. It is indicated that at low Co concentration (x⩽0.05), the Co atoms are incorporated into the ZnO lattice and located at the substitutional sites of the Zn atoms. At higher Co doping concentration (x⩾0.10), the secondary phase Co3O4 is precipitated. Correlating the magnetic behavior with the structural properties of the Zn1−xCoxO nanocomposites, the authors interpret the paramagnetism to be intrinsic in nature as a result of the low effective doping of Co in ZnO and the lack of oxygen vacancies.
Stabilization of electron emission from nanoneedles with two dimensional graphene sheet structure in a high residual pressure region
Authors: Matsumoto Takahiro , Neo Yoichiro , Mimura Hidenori , Tomita Makoto , Minami Nariyuki
Published: March 2007

A stable field emission (FE) under a high residual pressure (10−5Torr) was obtained by the thermal field operation of a nanoneedle cathode with a two dimensional graphene sheet structure. A high brightness electron emission of the order of 1012Asr−1m−2, as well as stable emission, was achieved. The performance of the stabilized cathode was demonstrated by the construction of a compact FE scanning electron microscope (SEM) system, and clear FE-SEM images were obtained at a residual pressure above 10−5Torr. The emission current fluctuation as a function of cathode temperature was discussed based on the Poisson distribution.
Identification of Mn site in Pb(Zr,Ti)O3 by synchrotron x-ray absorption near-edge structure: Theory and experiment
Authors: Limpijumnong Sukit , Rujirawat Saroj , Boonchun Adisak , Smith M. F. , Cherdhirunkorn B.
Published: March 2007

Synchrotron x-ray absorption near-edge structure (XANES) experiments are performed on Mn-doped PbZr1−xTixO3 samples (PZT) and compared with first-principles XANES simulations. The features of the measured Mn K-edge XANES are consistent with the first-principles XANES of Mn on the Ti∕Zr site and inconsistent with Mn on other sites. The clear agreement between measured and first-principles theoretical XANES spectra reported here is by far the strongest evidence of Mn substituting for Ti∕Zr in PZT. This work illustrates that a first-principles supercell framework, which is popularly used to study impurities in crystals, can be used in conjunction with XANES measurement in order to identify an impurity structure with a high degree of confidence. This approach may thus be broadly applicable to study impurities in other crystals.
Superhard nanocomposite of dense polymorphs of boron nitride: Noncarbon material has reached diamond hardness
Authors: Dubrovinskaia Natalia , Solozhenko Vladimir L. , Miyajima Nobuyoshi , Dmitriev Vladimir , Kurakevych Oleksandr O. , Dubrovinsky Leonid
Published: March 2007

The authors report a synthesis of unique superhard aggregated boron nitride nanocomposites (ABNNCs) showing the enhancement of hardness up to 100% in comparison with single crystal c-BN. Such a great hardness increase is due to the combination of the Hall-Petch and the quantum confinement effects. The decrease of the grain size down to 14nm and the simultaneous formation of the two dense BN phases with hexagonal and cubic structures within the grains at nano- and subnanolevel result in enormous mechanical property enhancement with maximum hardness of 85(5)GPa. Thus, ABNNC is the first non-carbon-based bulk material with the value of hard-ness approaching that of single crystal and polycrystalline diamond and aggregated diamond nanorods. ABNNC also has an unusually high fracture toughness for superhard materials (K1C=15MPam0.5) and wear resistance (WH=11; compare, for industrial polycrystalline diamond, WH=3–4), in combination with high thermal stability (above 1600K in air), making it an exceptional superabrasive.
Velocity controlled anodization nanolithography with an atomic force microscope using Faradaic current feedback
Authors: Johannes Matthew S. , Cole Daniel G. , Clark Robert L.
Published: March 2007

A technique, called velocity controlled anodization nanolithography, is presented that ensures line continuity during atomic force microscope based local anodic oxidation on silicon. Spontaneous current spikes disrupt the generation of uniform silicon oxide patterns during lithography at low humidity. Varying the translational speed during lithography in response to the current fluctuations enables the formation of a more complete and continuous oxide layer. The velocity corrections as a result of control are able to maintain constant current flow through the tip-sample interface. The authors demonstrate that this method is effective for in situ quality control.
Transport limitations and Schottky barrier height in titanium silicide nanowires grown on the Si(111) surface
Authors: Soubiron T. , Stiufiuc R. , Patout L. , Deresmes D. , Grandidier B. , Stiévenard D. , Köble J. , Maier M.
Published: March 2007

The authors have performed electrical measurements at variable temperatures on self-assembled titanium silicide nanowires (NWs) grown on a Si(111) surface. The authors find a metallic I(V) characteristic for the NWs at a temperature of 77K, whereas scanning tunneling spectroscopic measurements obtained at temperatures below 25K yield a rectifying behavior. This behavior indicates that the NWs are electronically decoupled from the Si surface on a voltage range of several hundreds of meV at low temperatures. From these measurements, the authors precisely determine the Schottky barrier height between the NWs and the Si surface.
Ultralow work function of scandium metal gate with tantalum nitride interface layer for n-channel metal oxide semiconductor application
Authors: Hasan Musarrat , Park Hokyung , Yang Hyundoek , Hwang Hyunsang , Jung Hyung-Suk , Lee Jong-Ho
Published: March 2007

The authors have investigated n-channel metal oxide semiconductor compatible metal gate with ultralow work function using tantalum nitride (TaNx)/scandium(Sc) stack layer. By adjusting the deposition condition, the effective work function as low as 4.0eV with improved thermal stability can be obtained. Without TaNx layer, work function of pure Sc gate on HfO2 was about 4.2eV and show thermal instability at high temperature which can be explained by reaction between Sc and HfO2. The authors found that control of TaNx layer is the critical process to maintain thermal stability and work function. The TaNx∕Sc stack process shows promise for future high-k metal gate applications.
Metallic oxide p-I-n junctions with ferroelectric as the barrier
Authors: Yuan J. , Wu H. , Cao L. X. , Zhao L. , Jin K. , Zhu B. Y. , Zhu S. J. , Zhong J. P. , Miao J. , Xu B. , Qi X. Y. , Qiu X. G. , Duan X. F. , Zhao B. R.
Published: March 2007

The authors report the formation of the metallic oxide p-I-n junctions with the ferroelectric (Ba,Sr)TiO3 (BST) as the barrier. The junctions with different thicknesses of BST are investigated. With appropriate thickness, the junctions possess definite parameters, such as the negligible reversed current density (⩽10−7A∕cm2), large breakdown voltage (>7V), and ultrahigh rectification (>2×104) in the bias voltage ⩽2.0V and temperature range from 5to300K. It is under consideration that the built-in field V0, the ferroelectric reversed polarized field Vrp, and the resistivity of the BST layer together decide the transport properties of the junctions.
Tuning optical band gap of vertically aligned ZnO nanowire arrays grown by homoepitaxial electrodeposition
Authors: Anthony Savarimuthu Philip , Lee Jeong In , Kim Jin Kon
Published: March 2007

Vertically aligned ZnO nanowire arrays are grown homoepitaxially on the ZnO seeded indium tin oxide substrate by electrochemical deposition from aqueous solution at low temperature (70°C) without using any template. ZnO nanowires exhibit single crystalline, wurtzite crystal structure determined by transmission electron microscopy and powder x-ray diffraction. The ZnO nanowire arrays show high transmittance in the visible wavelengths. Interestingly, the optical band gap of the ZnO nanowire arrays has been tuned by simply changing zinc salts in the electrodeposition from aqueous solution.
Nuclear spin population and its control toward initialization using an all-electrical submicron scale nuclear magnetic resonance device
Authors: Ota T. , Yusa G. , Kumada N. , Miyashita S. , Hirayama Y.
Published: March 2007

The authors study the nuclear spin population in a GaAs quantum well structure and demonstrate its initialization using an all-electrical nuclear magnetic resonance (NMR) device. In their device, nuclear spins are dynamically polarized in a submicron scale region defined by split gates. The relative population of each nuclear spin state is estimated from resistively detected NMR spectra combined with numerical analysis. They find that nuclear spin populations are determined by electron spin configurations. By applying radio frequency pulses to the strongly polarized nuclear spins, they demonstrate the creation of two-qubit effective pure states, which is a crucial step toward NMR quantum computation.
Tuning electrical properties of conjugated polymer nanowires with the diameter
Authors: Duvail Jean Luc , Long Yunze , Cuenot Stéphane , Chen Zhaojia , Gu Changzhi
Published: March 2007

The role of the nanowire diameter on the electrical properties of isolated poly(3,4-ethylenedioxythiophene) nanowires has been studied systematically by a four-terminal technique. A transition from an insulating to a metallic regime is observed when the diameter decreases from 190to35nm and a transition from a metallic to an insulating regime takes place for the smaller diameters. These results are of importance for the different potential applications based on polymer nanowires or nanotubes.
Vertical flash memory with protein-mediated assembly of nanocrystal floating gate
Authors: Sarkar Joy , Tang Shan , Shahrjerdi Davood , Banerjee Sanjay K.
Published: March 2007

The authors propose and demonstrate a vertical flash memory device incorporating protein-mediated ordering of nanocrystal floating gate to help circumvent density scaling and/or performance limitations of planar flash memory with continuous floating gate. The scalability of the vertical architecture can allow the theoretical maximum array density of 1∕4F2 (F: minimum lithographic pitch), thus circumventing the integration density limitations of planar flash transistor arrays. The nanocrystal floating gate renders reasonable retention, while the protein-mediated ordering of nanocrystals allows scalability and manufacturability. With tunneling program/erase, a memory window of 0.5V, endurance >105cycles, and retention beyond 105s is reported.
Two-dimensional mapping of triaxial strain fields in a multiferroic BiFeO3 thin film using scanning x-ray microdiffraction
Authors: Bark Chung W. , Cho Kyung C. , Koo Yang M. , Tamura Nobumichi , Ryu Sangwoo , Jang Hyun M.
Published: March 2007

The dramatically enhanced polarizations and saturation magnetizations observed in the epitaxially constrained BiFeO3 (BFO) thin films with their pronounced grain-orientation dependence have attracted much attention and are attributed largely to the constrained in-plane strain. Thus, it is highly desirable to directly obtain information on the two-dimensional (2D) distribution of the in-plane strain and its correlation with the grain orientation of each corresponding microregion. Here the authors report a 2D quantitative mapping of the grain orientation and the local triaxial strain field in a 250nm thick multiferroic BFO film using a synchrotron x-ray microdiffraction technique. This direct scanning measurement demonstrates that the deviatoric component of the in-plane strain tensor is between 5×10−3 and 6×10−3 and that the local triaxial strain is fairly well correlated with the grain orientation in that particular region.
Electrochemical route to the synthesis of ultrathin ZnO nanorod/nanobelt arrays on zinc substrate
Authors: Yang Jinhu , Liu Guangming , Lu Jun , Qiu Yongfu , Yang Shihe
Published: March 2007

An electrochemical route has been developed for the synthesis of highly ordered ZnO ultrathin nanorod and hierarchical nanobelt arrays on zinc substrate. A H2 gas sensor based on the ZnO nanobelt array exhibits excellent sensitivity, rapid response, and good reproducibility even at room temperature.
Effect of dislocations on charge carrier mobility–lifetime product in synthetic single crystal diamond
Authors: Lohstroh A. , Sellin P. J. , Wang S. G. , Davies A. W. , Parkin J. , Martin R. W. , Edwards P. R.
Published: March 2007

The authors report correlations between variations in charge transport of electrons and holes in synthetic single crystal diamond and the presence of nitrogen impurities and dislocations. The spatial distribution of these defects was imaged using their characteristic luminescence emission and compared with maps of carrier drift length measured by ion beam induced charge imaging. The images indicate a reduction of electron and hole mobility–lifetime product due to nitrogen impurities and dislocations. Very good charge transport is achieved in selected regions where the dislocation density is minimal.
Controlled assembly of zinc oxide nanowires using dielectrophoresis
Authors: Wang Dingqu , Zhu Rong , Zhou Zhaoying , Ye Xiongying
Published: March 2007

A structure similar to a field effect transistor with two isolated top electrodes comprising the source and drain and a lower substrate electrode as the gate was used for the dielectrophoresis-based assembly of zinc oxide nanowires. The results reveal that the assembly of nanowires is significantly affected by the gap distance between the two top electrodes as well as the magnitude and frequency of the applied electric field. Gate assisted assemblies using direct current and alternating current dielectrophoresis were also investigated and determined to improve the assembly effect of nanowires.
First-principles elastic constants of α- and θ-Al2O3
Authors: Shang Shunli , Wang Yi , Liu Zi-Kui
Published: March 2007

Using an efficient strain-stress method, the first-principles elastic constants cij’s of α-Al2O3 and θ-Al2O3 have been predicted within the local density approximation and the generalized gradient approximation. It is indicated that more accurate calculations of cij’s can be accomplished by the local density approximation. The predicted cij’s of θ-Al2O3 provide helpful guidance for future measurements, especially the predicted negative c15. The present results make the stress estimation in thermally grown oxides containing of α- and θ-Al2O3 possible, which in turn provide helpful insights for preventing the failure of thermal barrier coatings on components in gas-turbine engines.
Role of grain boundary and grain defects on ferromagnetism in Co:ZnO films
Authors: Hsu H. S. , Huang J. C. A. , Chen S. F. , Liu C. P.
Published: March 2007

The annealing effects on magnetism, structure, and ac transport for Co:ZnO films have been systematically investigated. The room temperature saturation magnetization (Ms) varies drastically with Ar or Ar∕H2 annealing processes. By using the impedance spectra, the change in grain boundary and grain defects of these films can be analyzed. The results demonstrate that Ar annealing produces mainly the grain boundary defects which cause the enhancement of Ms. Ar∕H2-annealing creates not only grain boundary defects but also the grain defects, resulting in the stronger enhancement of Ms. Ferromagnetism for Co:ZnO films is influenced by both grain boundaries and grain defects.
Flexible field emitter made of carbon nanotubes microwave welded onto polymer substrates
Authors: Wang C. Y. , Chen T. H. , Chang S. C. , Chin T. S. , Cheng S. Y.
Published: March 2007

The drastic temperature rise of multiwall carbon nanotubes (MWCNTs) in response to microwave irradiation was applied to weld a MWCNT paste on a polymer substrate within a few seconds. It provides a strong bonding between the MWCNT and polymer without thermal damage to the substrate. A flexible field emitter was made from MWCNT microwave welded on polycarbonate, showing excellent electrical conduction and field-emission properties even under bending. The field emitter works with a turn-on voltage of 0.8V∕μm due to the direct electron transfer. By this method, printed circuits and field-emission devices can be processed simultaneously within seconds leading to important applications in flexible electronic devices.
Orientation control of pentacene molecules and transport anisotropy of the thin film transistors by photoaligned polyimide film
Authors: Guo Dong , Sakamoto Kenji , Miki Kazushi , Ikeda Susumu , Saiki Koichiro
Published: March 2007

The authors report preferential in-plane molecular orientation and charge transport anisotropy in pentacene thin film transistors achieved by using a photoaligned polyimide film with large in-plane anisotropy. Polarized infrared absorption spectra indicated that the molecular plane normal of the pentacene preferentially aligned along the average orientation direction of the underlying polyimide backbone structure. Atomic force microscope images showed that the alignment of the polyimide backbone structure significantly modified the pentacene growth process and remarkably increased the grain size. The charge carrier mobility along the polyimide alignment direction was about twice of that perpendicular to it.
Within-plant signaling by volatiles leads to induction and priming of an indirect plant defense in nature
Authors: Heil Martin , Silva Bueno Juan Carlos
Published: March 2007

Plants respond to herbivore attack with the release of volatile organic compounds (VOCs), which can attract predatory arthropods and/or repel herbivores and thus serve as a means of defense against herbivores. Such VOCs might also be perceived by neighboring plants to adjust their defensive phenotype according to the present risk of attack. We exposed lima bean plants at their natural growing site to volatiles of beetle-damaged conspecific shoots. This reduced herbivore damage and increased the growth rate of the exposed plants. To investigate whether VOCs also can serve in signaling processes within the same individual plant we focused on undamaged “receiver” leaves that were either exposed or not exposed to VOCs released by induced “emitter” leaves. Extrafloral nectar secretion by receiver leaves increased when they were exposed to VOCs of induced emitters of neighboring plants or of the same shoot, yet not when VOCs were removed from the system. Extrafloral nectar attracts predatory arthropods and represents an induced defense mechanism. The volatiles also primed extrafloral nectar secretion to show an augmented response to subsequent damage. Herbivore-induced VOCs elicit a defensive response in undamaged plants (or parts of plants) under natural conditions, and they function as external signal for within-plant communication, thus serving also a physiological role in the systemic response of a plant to local damage.
Global extent of horizontal gene transfer
Authors: Choi In-Geol , Kim Sung-Hou
Published: March 2007

Horizontal gene transfer (HGT) is thought to play an important role in the evolution of species and innovation of genomes. There have been many convincing evidences for HGT for specific genes or gene families, but there has been no estimate of the global extent of HGT. Here, we present a method of identifying HGT events within a given protein family and estimate the global extent of HGT in all curated protein domain families (≈8,000) listed in the Pfam database. The results suggest four conclusions: (
i
) for all protein domain families in Pfam, the fixation of genes horizontally transferred is not a rampant phenomenon between organisms with substantial phylogenetic separations (1.1–9.7% of Pfam families surveyed at three taxonomic ranges studied show indication of HGT); (
ii
) however, at the level of domains, >50% of Archaea have one or more protein domains acquired by HGT, and nearly 30–50% of Bacteria did the same when examined at three taxonomic ranges. But, the equivalent value for Eukarya is <10%; (
iii
) HGT will have very little impact in the construction of organism phylogeny, when the construction methods use whole genomes, large numbers of common genes, or SSU rRNAs; and (
iv
) there appears to be no strong preference of HGT for protein families of particular cellular or molecular functions.
Division and differentiation of natural antibody-producing cells in mouse spleen
Authors: Yang Yang , Tung James W. , Ghosn Eliver E. B. , Herzenberg Leonard A. , Herzenberg Leonore A.
Published: March 2007

B-1a cells reside in both the peritoneal cavity and the spleen. LPS stimulates splenic B-1a to differentiate to plasma cells producing natural IgM specific for microbial and self antigens. However, there are conflicting views as to whether the B-1a cells divide before this differentiation occurs, and hence how the resident B-1a population is maintained in the spleen. Studies here resolve this dispute in favor of both sides: we show that (some or all) B-1a cells resident in the spleen respond to LPS by differentiating to plasma cells immediately, without dividing; however, we also show that additional B-1a cells immigrate into the spleen after LPS stimulation and divide at least once before differentiating. Importantly, the studies we presently describe reveal the complex cell migration and differentiation events that collectively underlie the rapid production of natural antibodies in response to
in vivo
LPS stimulation. Thus, the studies present a different view of the roles that B-1a cells play in the early phases of the innate immune response.
Histone hyperacetylation induces demethylation of reelin and 67-kDa glutamic acid decarboxylase promoters
Authors: Dong E. , Guidotti A. , Grayson D. R. , Costa E.
Published: March 2007

Reelin and glutamic acid decarboxylase 67 (GAD
67
) expression down-regulation in GABAergic interneurons of mice exposed to protracted treatment with
l
-methionine (MET) is attributed to
RELN
and
GAD
67
promoter cytosine-5-hypermethylation. This process recruits various transcription repressor proteins [methyl-CpG binding protein (MeCP2) and histone deacetylases (HDACs)] leading to formation of transcriptionally inactive chromatin. Here, we tested the hypothesis that
RELN
and
GAD
67
promoter cytosine-5-hypermethylation induced by a protracted MET treatment is reversible and that repeated administration of HDAC inhibitors influences this process by an activation of DNA-cytosine-5-demethylation. In the frontal cortices of mice receiving MET (5.2 mmol/kg twice a day for 7 days) and killed at 1, 2, 3, 6, and 9 days during MET washout, we measured
RELN
(base pairs −414 to −242) and
GAD
67
(base pairs −1133 to −942) promoter methylation and MeCP2 bound to methylated cytosines of
RELN
(base pairs −520 to −198) and
GAD
67
(base pairs −446 to −760) promoters. Levels of
RELN
and
GAD
67
promoter hypermethylation induced by 7 days of MET treatment declines by ≈50% after 6 days of MET withdrawal. When valproate (VPA) (2 mmol/kg) or MS-275 (0.015–0.12 mmol/kg), two structurally unrelated HDAC inhibitors, was given after MET treatment termination, VPA and MS-275 dramatically accelerated
RELN
and
GAD
67
promoter demethylation in 48–72 h. At these doses, VPA and MS-275 effectively increased the binding of acetylhistone-3 to
RELN
and
GAD
67
promoters, suggesting that histone-3 covalent modifications modulate DNA demethylation in terminally differentiated neurons, supporting the view that, directly or indirectly, HDAC inhibitors may facilitate DNA demethylation.
GGA2- and Ubiquitin-dependent Trafficking of Arn1, the Ferrichrome Transporter ofSaccharomyces cerevisiae
Authors: Kim Youngwoo , Deng Yi , Philpott Caroline C.
Published: March 2007

The intracellular trafficking of Arn1, a ferrichrome transporter in Saccharomyces cerevisiae, is controlled in part by the binding of ferrichrome to the transporter. In the absence of ferrichrome, Arn1 is sorted directly from the Golgi to endosomes. Ferrichrome binding triggers the redistribution of Arn1 to the plasma membrane, whereas ferrichrome transport is associated with the cycling of Arn1 between the plasma membrane and endosomes. Here, we report that the clathrin adaptor Gga2 and ubiquitination by the Rsp5 ubiquitin ligase are required for trafficking of Arn1. Gga2 was required for Golgi-to-endosomal trafficking of Arn1, which was sorted from endosomes to the vacuole for degradation. Trafficking into the vacuolar lumen was dependent on ubiquitination by Rsp5, but ubiquitination was not required for plasma membrane accumulation of Arn1 in the presence of ferrichrome. Retrograde trafficking via the retromer complex or Snx4 was also not required for plasma membrane accumulation. High concentrations of ferrichrome led to higher levels of ubiquitination of Arn1, but they did not induce degradation. Without this ubiquitination, Arn1 remained on the plasma membrane, where it was active for transport. Arn1 was preferentially modified with polyubiquitin chains on a cluster of lysine residues at the amino terminus of the transporter.
Oxa1 Directly Interacts with Atp9 and Mediates Its Assembly into the Mitochondrial F1Fo-ATP Synthase Complex
Authors: Jia Lixia , Dienhart Mary K. , Stuart Rosemary A.
Published: March 2007

The yeast Oxa1 protein is involved in the biogenesis of the mitochondrial oxidative phosphorylation (OXPHOS) machinery. The involvement of Oxa1 in the assembly of the cytochrome oxidase (COX) complex, where it facilitates the cotranslational membrane insertion of mitochondrially encoded COX subunits, is well documented. In this study we have addressed the role of Oxa1, and its sequence-related protein Cox18/Oxa2, in the biogenesis of the F1Fo-ATP synthase complex. We demonstrate that Oxa1, but not Cox18/Oxa2, directly supports the assembly of the membrane embedded Fo-sector of the ATP synthase. Oxa1 was found to physically interact with newly synthesized mitochondrially encoded Atp9 protein in a posttranslational manner and in a manner that is not dependent on the C-terminal, matrix-localized region of Oxa1. The stable manner of the Atp9-Oxa1 interaction is in contrast to the cotranslational and transient interaction previously observed for the mitochondrially encoded COX subunits with Oxa1. In the absence of Oxa1, Atp9 was observed to assemble into an oligomeric complex containing F1-subunits, but its further assembly with subunit 6 (Atp6) of the Fo-sector was perturbed. We propose that by directly interacting with newly synthesized Atp9 in a posttranslational manner, Oxa1 is required to maintain the assembly competence of the Atp9-F1-subcomplex for its association with Atp6.
Ent3p and Ent5p Exhibit Cargo-specific Functions in Trafficking Proteins between theTrans-Golgi Network and the Endosomes in Yeast
Authors: Čopič Alenka , Starr Trevor L. , Schekman Randy
Published: March 2007

The phosphoinositide-binding proteins Ent3p and Ent5p are required for protein transport from the trans-Golgi network (TGN) to the vacuole in Saccharomyces cerevisiae. Both proteins interact with the monomeric clathrin adaptor Gga2p, but Ent5p also interacts with the clathrin adaptor protein 1 (AP-1) complex, which facilitates retention of proteins such as Chs3p at the TGN. When both ENT3 and ENT5 are mutated, Chs3p is diverted from an intracellular reservoir to the cell surface. However, Ent3p and Ent5p are not required for the function of AP-1, but rather they seem to act in parallel with AP-1 to retain proteins such as Chs3p at the TGN. They have all the properties of clathrin adaptors, because they can both bind to clathrin and to cargo proteins. Like AP-1, Ent5p binds to Chs3p, whereas Ent3p facilitates the interaction between Gga2p and the endosomal syntaxin Pep12p. Thus, Ent3p has an additional function in Gga-dependent transport to the late endosome. Ent3p also facilitates the association between Gga2p and clathrin; however, Ent5p can partially substitute for this function. We conclude that the clathrin adaptors AP-1, Ent3p, Ent5p, and the Ggas cooperate in different ways to sort proteins between the TGN and the endosomes.
Conformational Dynamics of the Major Yeast Phosphatidylinositol Transfer Protein Sec14p: Insight into the Mechanisms of Phospholipid Exchange and Diseases of Sec14p-Like Protein Deficiencies
Authors: Ryan Margaret M. , Temple Brenda R.S. , Phillips Scott E. , Bankaitis Vytas A.
Published: March 2007

Molecular dynamics simulations coupled with functional analyses of the major yeast phosphatidylinositol/phosphatidylcholine transfer protein Sec14p identify structural elements involved in regulating the ability of Sec14p to execute phospholipid exchange. The molecular dynamics simulations suggest large rigid body motions within the Sec14p molecule accompany closing and opening of an A10/T4/A11helical gate, and that “state-of-closure” of this helical gate determines access to the Sec14p phospholipid binding cavity. The data also project that conformational dynamics of the helical gate are controlled by a hinge unit (residues F212, Y213, K239, I240, and I242) that links to the N- and C-terminal ends of the helical gate, and by a novel gating module (composed of the B1LB2and A12LT5substructures) through which conformational information is transduced to the hinge. The114TDKDGR119motif of B1LB2plays an important role in that transduction process. These simulations offer new mechanistic possibilities for an important half-reaction of the Sec14p phospholipid exchange cycle that occurs on membrane surfaces after Sec14p has ejected bound ligand, and is reloading with another phospholipid molecule. These conformational transitions further suggest structural rationales for known disease missense mutations that functionally compromise mammalian members of the Sec14-protein superfamily.
MedicCyc: a biochemical pathway database forMedicago truncatula
Authors: Urbanczyk-Wochniak Ewa , Sumner Lloyd W.
Published: March 2007

Motivation: There is an imperative need to integrate functional genomics data to obtain a more comprehensive systems-biology view of the results. We believe that this is best achieved through the visualization of data within the biological context of metabolic pathways. Accordingly, metabolic pathway reconstruction was used to predict the metabolic composition for Medicago truncatula and these pathways were engineered to enable the correlated visualization of integrated functional genomics data.

Results: Metabolic pathway reconstruction was used to generate a pathway database for M. truncatula (MedicCyc), which currently features more than 250 pathways with related genes, enzymes and metabolites. MedicCyc was assembled from more than 225 000 M. truncatula ESTs (MtGI Release 8.0) and available genomic sequences using the Pathway Tools software and the MetaCyc database. The predicted pathways in MedicCyc were verified through comparison with other plant databases such as AraCyc and RiceCyc. The comparison with other plant databases provided crucial information concerning enzymes still missing from the ongoing, but currently incomplete M. truncatula genome sequencing project. MedicCyc was further manually curated to remove non-plant pathways, and Medicago-specific pathways including isoflavonoid, lignin and triterpene saponin biosynthesis were modified or added based upon available literature and in-house expertise. Additional metabolites identified in metabolic profiling experiments were also used for pathway predictions. Once the metabolic reconstruction was completed, MedicCyc was engineered to visualize M. truncatula functional genomics datasets within the biological context of metabolic pathways.

Availability: freely accessible at http://www.noble.org/MedicCyc/

Contact: lwsumner@noble.org
From structure to dynamics of metabolic pathways: application to the plant mitochondrial TCA cycle
Authors: Steuer Ralf , Nesi Adriano Nunes , Fernie Alisdair R. , Gross Thilo , Blasius Bernd , Selbig Joachim
Published: March 2007

Motivation: Mitochondrial metabolism, dominated by the reactions of the tricarboxylic acid (TCA) cycle, is of vital importance for a wide range of metabolic processes. In particular for autotrophic tissue, such as plant leaves, the TCA cycle marks the point of divergence of anabolic pathways and plays an essential role in biosynthesis. However, despite extensive knowledge about its stoichiometric properties, the function and the dynamical capabilities of the TCA cycle remain largely unknown.

Methods and Results: Based on a recently proposed formalism, we investigate the dynamic and functional properties of the mitochondrial TCA cycle of plants. Starting with the structural properties, as described by the elementary flux modes of the system, we aim for the transition from structure to the dynamics of the TCA cycle. Using a parametric description of the system, encompassing all possible differential equations and parameter values, we detect and quantify regimes of different dynamic behavior. Optimizing the system with respect to dynamic stability, we demonstrate that maximal stability is associated with specific (relative) metabolite concentrations and flux values that are subsequently compared to the experimental literature. Our analysis also serves as a general example how to elucidate the transition from the structure to the dynamics of metabolic pathways.

Contact: steuer@agnld.uni-potsdam.de

Supplementary information: Supplementary data are available at Bioinformatics online.
Codelink: an R package for analysis of GE healthcare gene expression bioarrays
Authors: Diez Diego , Alvarez Rebeca , Dopazo Ana
Published: March 2007

Motivation: Microarray-based expression profiles have become a standard methodology in any high-throughput analysis. Several commercial platforms are available, each with its strengths and weaknesses. The R platform for statistical analysis and graphics is a powerful environment for the analysis of microarray data, because it has many integrated statistical methods available as well as the specialized microarray analysis project Bioconductor. Many packages have been added in the last few years increasing the range of possible analysis. Here, we report the availability of a package for reading and analyzing data from GE Healthcare Gene Expression Bioarrays within the R environment.

Availability: The software is implemented in the R language, is open source and available for download free of charge through the Bioconductor (http://www.bioconductor.org) project.

Contact:  diez@kuicr.kyoto-u.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.
Analyzing microarray data using CLANS
Authors: Frickey Tancred , Weiller Georg
Published: March 2007

Summary: Analysis of microarray experiments is complicated by the huge amount of data involved. Searching for groups of co-expressed genes is akin to searching for protein families in a database as, in both cases, small subsets of genes with similar features are to be found within vast quantities of data. CLANS was originally developed to find protein families in large sets of amino acid sequences where the amount of data involved made phylogenetic approaches overly cumbersome. We present a number of improvements that greatly extend the previous version of CLANS and show its application to microarray data as well as its ability of incorporating additional information to facilitate interactive analysis.

Availability: The program is available for download from: http://bioinfoserver.rsbs.anu.edu.au/downloads/clans/

Contact:  Georg.Weiller@anu.edu.au

Supplementary information:  http://bioinfoserver.rsbs.anu.edu.au/programs/clans
ABCGrid: Application for Bioinformatics Computing Grid
Authors: Sun Ying , Zhao Shuqi , Yu Huashan , Gao Ge , Luo Jingchu
Published: March 2007

Summary: We have developed a package named Application for Bioinformatics Computing Grid (ABCGrid). ABCGrid was designed for biology laboratories to use heterogeneous computing resources and access bioinformatics applications from one master node. ABCGrid is very easy to install and maintain at the premise of robustness and high performance. We implement a mechanism to install and update all applications and databases in worker nodes automatically to reduce the workload of manual maintenance. We use a backup task method and self-adaptive job dispatch approach to improve performance. Currently, ABCGrid integrates NCBI_BLAST, Hmmpfam and CE, running on a number of computing platforms including UNIX/Linux, Windows and Mac OS X.

Availability: The source code, executables and documents can be downloaded from http://abcgrid.cbi.pku.edu.cn

Contact:  abcgrid@mail.cbi.pku.edu.cn
Glycan classification with tree kernels
Authors: Yamanishi Yoshihiro , Bach Francis , Vert Jean-Philippe
Published: March 2007

Motivation: Glycans are covalent assemblies of sugar that play crucial roles in many cellular processes. Recently, comprehensive data about the structure and function of glycans have been accumulated, therefore the need for methods and algorithms to analyze these data is growing fast.

Results: This article presents novel methods for classifying glycans and detecting discriminative glycan motifs with support vector machines (SVM). We propose a new class of tree kernels to measure the similarity between glycans. These kernels are based on the comparison of tree substructures, and take into account several glycan features such as the sugar type, the sugar bound type or layer depth. The proposed methods are tested on their ability to classify human glycans into four blood components: leukemia cells, erythrocytes, plasma and serum. They are shown to outperform a previously published method. We also applied a feature selection approach to extract glycan motifs which are characteristic of each blood component. We confirmed that some leukemia-specific glycan motifs detected by our method corresponded to several results in the literature.

Availability: Softwares are available upon request.

Contact:  yoshi@kuicr.kyoto-u.ac.jp

Supplementary information: Datasets are available at the following website: http://web.kuicr.kyoto-u.ac.jp/supp/yoshi/glycankernel/
On detection of multi-band chaotic attractors
Authors: Avrutin Viktor , Eckstein Bernd , Schanz Michael
Published: March 2007

In this work, we present two numerical methods for the detection of the number of bands of a multi-band chaotic attractor. The first method is more efficient but can be applied only for dynamical systems with a continuous system function, whereas the second one is applicable for dynamical systems with a discontinuous system function as well. Using the developed methods, we investigate a one-dimensional piecewise-linear map and report for both cases of a continuous and a discontinuous system functions some new bifurcation scenarios involving multi-band chaotic attractors.
Configurational balance laws for incompatibility in stress space
Authors: Markenscoff Xanthippi , Gupta Anurag
Published: March 2007

Conservation laws have been recently obtained by requiring that a positive definite functional of the stress gradient (the Euler–Lagrange equations of which are the Beltrami–Michell compatibility conditions) be invariant under certain transformations. Here these laws are extended to include body forces, thermal stresses and Kröner's incompatibility tensor as source terms in the configurational balance laws, which allows for the incompatibility in the volume to be measured from surface data. An example is presented.
Experimental evolution of parasite life-history traits inStrongyloides ratti(Nematoda)
Authors: Paterson Steve , Barber Rebecca
Published: March 2007

Evolutionary ecology predicts that parasite life-history traits, including a parasite's survivorship and fecundity within a host, will evolve in response to selection and that their evolution will be constrained by trade-offs between traits. Here, we test these predictions using a nematode parasite of rats,Strongyloides ratti, as a model. We performed a selection experiment by passage of parasite progeny from either early in an infection (‘fast’ lines) or late in an infection (‘slow’ lines). We found that parasite fecundity responded to selection but that parasite survivorship did not. We found a trade-off mediated via conspecific density-dependent constraints; namely, that fast lines exhibit higher density-independent fecundity than slow lines, but fast lines suffered greater reduction in fecundity in the presence of density-dependent constraints than slow lines. We also found that slow lines both stimulate a higher level of IgG1, which is a marker for a Th2-type immune response, and show less of a reduction in fecundity in response to IgG1 levels than for fast lines. Our results confirm the general prediction that parasite life-history traits can evolve in response to selection and indicate that such evolutionary responses may have significant implications for the epidemiology of infectious disease.
A gharial from the Oligocene of Puerto Rico: transoceanic dispersal in the history of a non-marine reptile
Authors: Vélez-Juarbe Jorge , Brochu Christopher A , Santos Hernán
Published: March 2007

The Indian gharial (
Gavialis gangeticus
) is not found in saltwater, but the geographical distribution of fossil relatives suggests a derivation from ancestors that lived in, or were at least able to withstand, saline conditions. Here, we describe a new Oligocene gharial,
Aktiogavialis puertoricensis
, from deltaic–coastal deposits of northern Puerto Rico. It is related to a clade of Neogene gharials otherwise restricted to South America. Its geological and geographical settings, along with its phylogenetic relationships, are consistent with two scenarios: (i) that a single trans-Atlantic dispersal event during the Tertiary explains the South American Neogene gharial assemblage and (ii) that stem gharials were coastal animals and their current restriction to freshwater settings is a comparatively recent environmental shift for the group. This discovery highlights the importance of including fossil information in a phylogenetic context when assessing the ecological history of modern organisms.