bluuebunny/crossref_metadata_2025 huggingface dataset:
Electronic and structural properties of oligophenylene ethynylenes on Au(111) surfaces
Authors: Miao Ling , Seminario Jorge M.
Published: May 2007

The interaction of oligophenylene ethynylene (OPE) on the (111) surface of a gold slab resembling a self-assembled monolayer (SAM) is investigated using ab initio density functional theory calculations. The authors performed a full optimization including all atoms in the OPE and in the slab to better understand OPE adsorption on the surface. It is found that OPE has two energetically favorable adsorption sites on the Au surface with relatively different molecular geometries: the nontop site adsorption greatly modifies the (111) surface structure; however, the extensive electron interactions enable a delocalized electron density distribution, implying an improved conductivity between OPE and Au, and the top site which is 0.9eV higher in energy than the nontop and features weaker Au–S bonds. Interestingly the on top configuration shows a strong spin imbalance along the molecule and the nontop shows a small spin imbalance on the surface. This feature is of strong interest for the development of resonators for the detection of chemical and biological agents. They have also calculated the frequency spectrum of these SAMs, which yield deformations in the gold surface yielding peak frequency shifts specific to each absorption site.
Simulations investigating the effect of a deuterium-tritium-ice coating on the motion of the gold cone surface in a re-entrant cone-guided fast ignition inertial confinement fusion capsule
Authors: Pasley J. , Stephens R.
Published: May 2007

One- and two-dimensional multigroup radiation hydrodynamics simulations have been performed to investigate the motion of the gold plasma generated at the surface of the embedded gold cone in a re-entrant cone-guided inertial confinement fusion capsule. The effect of deuterium-tritium (DT) ice layers, and other possible tampers, of varying thickness, upon the motion of the gold cone plasma has been investigated. The effect of the x-ray drive spectrum incident upon the ice layer is also explored. Ice is shown to tamp the expansion of the gold cone, and whilst denser materials are shown to be more effective in this role, ice does not pollute the ignition region with intermediate-Z ions, which, though preferable to gold contamination, also tend to inhibit the attainment of high fuel-ion temperatures.
Catastrophic onset of fast magnetic reconnection with a guide field
Authors: Cassak P. A. , Drake J. F. , Shay M. A.
Published: May 2007

It was recently shown that the slow (collisional) Sweet-Parker and the fast (collisionless) Hall magnetic reconnection solutions simultaneously exist for a wide range of resistivities; reconnection is bistable [Cassak, Shay, and Drake, Phys. Rev. Lett., 95, 235002 (2005)]. When the thickness of the dissipation region becomes smaller than a critical value, the Sweet-Parker solution disappears and fast reconnection ensues, potentially explaining how large amounts of magnetic free energy can accrue without significant release before the onset of fast reconnection. Two-fluid numerical simulations extending the previous results for anti-parallel reconnection (where the critical thickness is the ion skin depth) to component reconnection with a large guide field (where the critical thickness is the thermal ion Larmor radius) are presented. Applications to laboratory experiments of magnetic reconnection and the sawtooth crash are discussed.
Drag reduction in electro-osmosis of polymer solutions
Authors: Chang Feng-Ming , Tsao Heng-Kwong
Published: May 2007

Electro-osmosis is the preferred transport mechanism in microfluidic systems. Drag reduction in electro-osmosis of polymer solutions is observed due to polymer depletion in the electric double layer (EDL). The well-known Helmholtz-Smoluchowski (HS) equation indicates that the electro-osmosis mobility is inversely proportional to the solution viscosity. For low molecular weight the polymer size (R) is smaller than the EDL thickness (λ) and the HS equation is valid. For high molecular weight (R>λ) the chains in the EDL are partially sheared and the effective viscosity is smaller than the solution viscosity. Salt addition reduces λ and can enhance drag reduction substantially.
Nuclear quadrupole moment of Au197 from high-accuracy atomic calculations
Authors: Yakobi Hana , Eliav Ephraim , Kaldor Uzi
Published: May 2007

The electric field gradient (EFG) at the gold nucleus is calculated using a finite field approach, to make the extraction of the nuclear quadrupole moment Q from experimental nuclear quadrupole coupling constants possible. The four-component Dirac-Coulomb Hamiltonian serves as the framework, 51 of the 79 electrons are correlated by the relativistic Fock-space coupled cluster method with single and double excitations, and the contribution of the Gaunt term, the main part of the Breit interaction, is evaluated. Large basis sets (up to 26s22p18d12f8g5h uncontracted Gaussians) are employed. Energy splittings of the D5∕22 and D3∕22 levels, rather than level shifts, are used to extract the EFG constants, as the former remain linear with Q up to 10−5a.u., whereas the latter display significant nonlinearity even at Q=10−8a.u. Larger Q values lead to larger energy changes and better precision. Excellent agreement (0.1%) is obtained between Q values derived from D5∕22 and D3∕22 data. Systematic errors connected with neglecting triple and higher excitations, truncating the basis and orbital active space, and approximating the Gaunt contribution are evaluated. The final value of Q(Au197) is 521(7)mb. It is lower than the muonic 547(16)mb and agrees within error bounds with the recent value of 510(15)mb obtained from molecular calculations.
Relativistic quaternionic wave equation. II
Authors: Schwartz Charles
Published: May 2007

Further results are reported for the one-component quaternionic wave equation recently introduced. A Lagrangian is found for the momentum-space version of the free equation, and another, nonlocal in time, is found for the complete equation. Further study of multiparticle systems has us looking into the mathematics of tensor products of Hilbert spaces. The principles of linearity and superposition are also clarified to good effect in advancing the quaternionic theory.
Improving the reliability of multiplexed fiber optic low-coherence interferometric sensors by use of novel twin-loop network topologies
Authors: Yang Jun , Yuan Libo , Jin Wei
Published: May 2007

Novel twin-loop network topologies for multiplexing fiber optic low-coherence reflectometric sensors are proposed and theoretically analyzed. The sensing fibers are made by connecting segments of standard single-mode fibers with partial reflections at the fiber joints and are completely passive. Absolute length measurement can be made for each segment of the sensing fiber so that strain or temperature distribution along the entire sensing fiber can be derived. It is expected that novel topologies would help as to improve the reliability of the sensor network by providing multiple accesses to each of the sensing segment so that most of the sensing segments can still be interrogated even when one or more point breakages occur along the transmission fibers. A nine-sensor twin-loop sensing network was constructed and experimentally tested by use of a Michelson low-coherence interferometer, and the results obtained agree with our theoretical prediction. The novel network topologies may be used for large-scale smart structure applications where breakages of transmission fibers may occur during the stages of sensor imbedding, installation, and structure-in-service cycles.
Focal-plane imaging of crossed beams in nonlinear optics experiments
Authors: Bivolaru Daniel , Herring G. C.
Published: May 2007

An application of focal-plane imaging that can be used as a real time diagnostic of beam crossing in various optical techniques is reported. We discuss two specific versions and demonstrate the capability of maximizing system performance with an example in a combined dual-pump coherent anti-Stokes Raman scattering-interferometric Rayleigh scattering experiment (CARS-IRS). We find that this imaging diagnostic significantly reduces beam alignment time and loss of CARS-IRS signals due to inadvertent misalignments.
Remote in vivo imaging of human skin corneocytes by means of an optical fiber bundle
Authors: Dromard Tanguy , Ravaine Valérie , Ravaine Serge , Lévêque Jean-Luc , Sojic Neso
Published: May 2007

Human corneocytes forming the outermost layer of the epidermis (stratum corneum) were imaged in vivo by epifluorescence through a coherent optical fiber bundle. A very simple and rapid method to remotely visualize the cells forming this protective layer of the skin is presented. After the topical application of fluorescein, the distal face of an optical fiber bundle is gently applied perpendicularly onto the labeled skin (contact mode). Remote fluorescence images of the corneocytes are acquired in 50ms through the bundle comprising 30 000 individually cladded 3.5μm diameter optical fibers. The very short focal distance which is an intrinsic characteristic of such bundles, allows visualizing only the most superficial monolayer of cells in contact with the external environment. An image displays about 400–500 cells directly on the human body. The size and the arrangement of the corneocytes can thus be acquired and analyzed in a very simple and easy way. The method is flexible and can be used for any location on the human body. Using a gradient-index lens objective (magnification 2.8×) fused to the distal face of the bundle allows the shape of the corneocytes to be better resolved. In addition, the working distance is 300μm and hence this second approach works in a noncontact imaging mode. Both approaches are complementary and allow providing instantaneously either a global view of the cells with a possible statistical determination of their area or morphological information, which are essential for dermatology and cosmetic sciences. Finally, to improve the quality and the contrast of the recorded images, we tested silica nanoparticles containing fluorescein. In brief, this diagnostic method is nontoxic, painless, easy to use, noninvasive, and nondestructive.
Simultaneous scanning tunneling microscopy and stress measurements to elucidate the origins of surface forces
Authors: Narushima Tetsuya , Kinahan Niall T. , Boland John J.
Published: May 2007

We have developed a new combined measurement system to investigate the underlying origins of forces on solid state surfaces from the viewpoint of atomic surface morphology. This system consists of two main parts: the measurements of force based on displacements and detailed atomic resolution observations of the surface morphology. The former involves a large sample cantilever and a capacitive detection method that provide sufficient resolution to detect changes of a few meV/atom or pN/atom at surfaces. For the latter, a scanning tunneling microscope was incorporated to observe structural changes occurring on the surface of the cantilever sample. Although this combined observation is not trivial, it was accomplished by carefully designing sample dimensions while suppressing the self-oscillation of the cantilever. To demonstrate the performance of this system a preliminary study of the room temperature adsorption of Br2 on the clean Si(111)-7×7 surface is presented.
Droplet evaporation-induced ferritin self-assembled monolayer as a template for nanocrystal flash memory
Authors: Kwon Moonjae , Choi Hyejung , Chang Man , Jo Minseok , Jung Seung-Jae , Hwang Hyunsang
Published: May 2007

A nonvolatile nanocrystal (NC) memory containing a ferritin core was fabricated. A ferritin monolayer was formed through a droplet evaporation technique. High-pressure hydrogen (HP-H2) annealing effectively reduced iron oxide (Fe2O3) to form conductive iron NC. In addition, HP-H2 annealing also improved memory characteristics by passivation of the interface states at Si∕HfO2. The authors observed good memory characteristics, including fast program/erase (P/E) operation, a memory window of 1.75V under ±6V, and a stable memory window up to 104s at 85°C.
CdSe nanowires with controllable growth orientations
Authors: Shan C. X. , Liu Z. , Hark S. K.
Published: May 2007

Epitaxial growths of CdSe nanowires with controllable orientations by metal organic chemical vapor deposition are obtained. Scanning electron microscopy reveals that they preferred to align along different orientations when grown on different GaAs surfaces. The geometrical relationship between their orientations and the substrates can further be changed by changing the growth temperature. They all grow along the ⟨110⟩ direction of the substrates at 480°C, but along the ⟨111⟩ direction at 500°C. X-ray diffraction and transmission electron microscopy confirm that they are single-crystalline wurtzite structured. Photoluminescence measurements on individual CdSe nanowires reveal their good optical properties.
Fast response of InSb Schottky detector
Authors: Kanno Ikuo , Hishiki Shigeomi , Kogetsu Yoshitaka , Nakamura Tatsuya , Katagiri Masaki
Published: May 2007

An InSb Schottky detector, fabricated from an undoped InSb wafer with Hall mobility which is higher than those of previously employed InSb wafers, was used for alpha particle detection. The output pulse of this InSb detector showed a very fast rise time, which was comparable with the output pulses of scintillation detectors.
Electrical study of ferromagnet-oxide-semiconductor diode for a magnetic memory device integrated on silicon
Authors: Kanoun M. , Benabderrahmane R. , Duluard C. , Baraduc C. , Bruyant N. , Bsiesy A. , Achard H.
Published: May 2007

This work focuses on electrical characterization of NiFe∕SiO2∕Si tunnel diodes that can be used for spin injection into silicon in future spintronic devices. Capacitance-voltage characteristics show a large increase of the Si∕SiO2 interfacial state density compared to similar Al∕SiO2∕Si diodes. This result suggests that nickel and/or iron may have diffused across the SiO2 layer. Consistently the current-voltage experimental characteristics have been modeled by using trap assisted electron transport mechanism. These traps may be attributed to ferromagnet atoms in the oxide bulk.
Temperature evolution of the structural properties of monodomain ferroelectric thin film
Authors: Janolin Pierre-Eymeric , Le Marrec Françoise , Chevreul Jacques , Dkhil Brahim
Published: May 2007

The structural evolution of epitaxial monodomain (only 180° domains) ferroelectric PbTiO3 thin film has been investigated, using high-resolution, temperature-dependent, x-ray diffraction. The full set of lattice parameters was obtained from room temperature up to 850K. It allowed the calculation of the different strains stored in the film at room temperature, underlying the difference between the mechanical strain and the misfit strain. The evolution of the misfit strain as a function of temperature was also calculated and was found to be consistent with the theoretical temperature-misfit strain phase diagram. These data strongly suggest that the film remains ferroelectric and tetragonal up to 940K.
Cubic-to-monoclinic phase transition during the epitaxial growth of crystalline Gd2O3 films on Ge(001) substrates
Authors: Molle Alessandro , Wiemer Claudia , Bhuiyan Md. Nurul Kabir , Tallarida Grazia , Fanciulli Marco , Pavia Giuseppe
Published: May 2007

Thin crystalline films of Gd2O3 are grown on an atomically flat Ge(001) surface by molecular beam epitaxy and are characterized in situ by reflection high energy electron diffraction and x-ray photoelectron spectroscopy, and ex situ by x-ray diffraction (XRD), atomic force microscopy (AFM), and transmission electron microscopy. The first stage of the growth corresponds to a cubic (110) structure, with two equiprobable, 90° rotated, in-plane domains. Increasing the thickness of the films, a phase transition from cubic (110) to monoclinic (100) oriented crystallites is observed which keeps the in-plane domain rotation, as evidenced by XRD and AFM.
Photovoltaic probe of cavity polaritons in a quantum cascade structure
Authors: Sapienza Luca , Vasanelli Angela , Ciuti Cristiano , Manquest Christophe , Sirtori Carlo , Colombelli Raffaele , Gennser Ulf
Published: May 2007

The strong coupling between an intersubband excitation in a quantum cascade structure and a photonic mode of a planar microcavity has been detected by angle-resolved photovoltaic measurements. A typical anticrossing behavior, with a vacuum-field Rabi splitting of 16meV at 78K, has been measured, for an intersubband transition at 163meV. These results show that the strong coupling regime between photons and intersubband excitations can be engineered in a quantum cascade optoelectronic device. They also demonstrate the possibility to perform angle-resolved midinfrared photodetection and to develop active devices based on intersubband cavity polaritons.
Control of Fano line shapes by means of photonic crystal structures in a dye-doped polymer
Authors: Harbers Rik , Jochim Selim , Moll Nikolaj , Mahrt Rainer F. , Erni Daniel , Hoffnagle John A. , Hinsberg William D.
Published: May 2007

The emission of a two-dimensional organic photonic crystal structure is investigated. A photon emitted by a molecule in this structure can take two different coupled pathways. It can either be emitted directly into the surroundings or first be transferred to a discrete state of the photonic crystal structure from where it is then emitted. This unique coupling of the pathways results in a particular asymmetric spectral line shape referred to as Fano resonance. By studying the Fano line shape as a function of the quality factor, the authors can gain insights into the coupling between the pathways within the photonic crystal structure.
Morphological change during crystallization of thin amorphous solid water films on Ru(0001)
Authors: Kondo Takahiro , Kato Hiroyuki S. , Bonn Mischa , Kawai Maki
Published: May 2007

The isothermal crystallization process of thin amorphous solid water (ASW) films on Ru(0001) has been investigated in real time by simultaneously employing helium atom scattering, infrared reflection absorption spectroscopy, and isothermal temperature-programmed desorption. The measurements reveal that the crystallization mechanism consists of random nucleation events in the bulk of the ASW films, followed by homogeneous growth. Morphological changes of the solid water film during crystallization expose the water monolayer just above the substrate to the vacuum during the crystallization process.
Fiber optic light collection system for scanning-tunneling-microscope-induced light emission
Authors: Watkins Neil J. , Long James P. , Kafafi Zakya H. , Mäkinen Antti J.
Published: May 2007

We report a compact light collection scheme suitable for retrofitting a scanning tunneling microscope (STM) for STM-induced light emission experiments. The approach uses a pair of optical fibers with large core diameters and high numerical apertures to maximize light collection efficiency and to moderate the mechanical precision required for alignment. Bench tests indicate that efficiency reduction is almost entirely due to reflective losses at the fiber ends, while losses due to fiber misalignment have virtually been eliminated. Photon-map imaging with nanometer features is demonstrated on a stepped Au(111) surface with signal rates exceeding 104counts∕s.
Principal-components analysis of shape fluctuations of single DNA molecules
Authors: Cohen Adam E. , Moerner W. E.
Published: May 2007

Thermal fluctuations agitate molecules in solution over a broad range of times and distances. By passively watching the shape fluctuations of a thermally driven biomolecule, one can infer properties of the underlying interactions that determine the motion. We applied this concept to single molecules of fluorescently labeled λ-DNA, a key model system for polymer physics. In contrast to most other single-molecule DNA experiments, we examined the unstretched, equilibrium state of DNA by using an anti-Brownian electrokinetic trap to confine the center of mass of the DNA without perturbing its internal dynamics. We analyze the long-wavelength conformational normal modes, calculate their spring constants, and measure linear and nonlinear couplings between modes. The modes show strong signs of nonlinear hydrodynamics, a feature of the underlying equations of polymer dynamics that has not previously been reported and is neglected in the widely used Rouse and Zimm approximations.
Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic “fingerprinting”
Authors: Liu Shixin , Bokinsky Gregory , Walter Nils G. , Zhuang Xiaowei
Published: May 2007

Single-molecule FRET is a powerful tool for probing the kinetic mechanism of a complex enzymatic reaction. However, not every reaction intermediate can be identified via a distinct FRET value, making it difficult to fully dissect a multistep reaction pathway. Here, we demonstrate a method using sequential kinetic experiments to differentiate each reaction intermediate by a distinct time sequence of FRET signal (a kinetic “fingerprint”). Our model system, the two-way junction hairpin ribozyme, catalyzes a multistep reversible RNA cleavage reaction, which comprises two structural transition steps (docking/undocking) and one chemical reaction step (cleavage/ligation). Whereas the docked and undocked forms of the enzyme display distinct FRET values, the cleaved and ligated forms do not. To overcome this difficulty, we used Mg
2+
pulse–chase experiments to differentiate each reaction intermediate by a distinct kinetic fingerprint at the single-molecule level. This method allowed us to unambiguously determine the rate constant of each reaction step and fully characterize the reaction pathway by using the chemically competent enzyme–substrate complex. We found that the ligated form of the enzyme highly favors the docked state, whereas undocking becomes accelerated upon cleavage by two orders of magnitude, a result different from that obtained with chemically blocked substrate and product analogs. The overall cleavage reaction is rate-limited by the docking/undocking kinetics and the internal cleavage/ligation equilibrium, contrasting the rate-limiting mechanism of the four-way junction ribozyme. These results underscore the kinetic interdependence of reversible steps on an enzymatic reaction pathway and demonstrate a potentially general route to dissect them.
Restructuring of the dinucleotide-binding fold in an NADP(H) sensor protein
Authors: Zheng Xiaofeng , Dai Xueyu , Zhao Yanmei , Chen Qiang , Lu Fei , Yao Deqiang , Yu Quan , Liu Xinping , Zhang Chuanmao , Gu Xiaocheng , Luo Ming
Published: May 2007

NAD(P) has long been known as an essential energy-carrying molecule in cells. Recent data, however, indicate that NAD(P) also plays critical signaling roles in regulating cellular functions. The crystal structure of a human protein, HSCARG, with functions previously unknown, has been determined to 2.4-Å resolution. The structure reveals that HSCARG can form an asymmetrical dimer with one subunit occupied by one NADP molecule and the other empty. Restructuring of its NAD(P)-binding Rossmann fold upon NADP binding changes an extended loop to an α-helix to restore the integrity of the Rossmann fold. The previously unobserved restructuring suggests that HSCARG may assume a resting state when the level of NADP(H) is normal within the cell. When the NADP(H) level passes a threshold, an extensive restructuring of HSCARG would result in the activation of its regulatory functions. Immunofluorescent imaging shows that HSCARG redistributes from being associated with intermediate filaments in the resting state to being dispersed in the nucleus and the cytoplasm. The structural change of HSCARG upon NADP(H) binding could be a new regulatory mechanism that responds only to a significant change of NADP(H) levels. One of the functions regulated by HSCARG may be argininosuccinate synthetase that is involved in NO synthesis.
Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein
Authors: Stan George , Lorimer George H. , Thirumalai D. , Brooks Bernard R.
Published: May 2007

Escherichia coli
chaperonin, GroEL, helps proteins fold under nonpermissive conditions. During the reaction cycle, GroEL undergoes allosteric transitions in response to binding of a substrate protein (SP), ATP, and the cochaperonin GroES. Using coarse-grained representations of the GroEL and GroES structures, we explore the link between allosteric transitions and the folding of a model SP, a
de novo
-designed four-helix bundle protein, with low spontaneous yield. The ensemble of GroEL-bound SP is less structured than the bulk misfolded structures. Upon binding, which kinetically occurs in two stages, the SP loses not only native tertiary contacts but also experiences a decrease in helical content. During multivalent binding and the subsequent ATP-driven transition of GroEL the SP undergoes force-induced stretching. Upon encapsulation, which occurs upon GroES binding, the SP finds itself in a “hydrophilic” cavity in which it can reach the folded conformation. Surprisingly, we find that the yield of the native state in the expanded GroEL cavity is relatively small even after it remains in it for twice the spontaneous folding time. Thus, in accord with the iterative annealing mechanism, multiple rounds of binding, partial unfolding, and release of the SP are required to enhance the yield of the folded SP.
Deletion of PrBP/δ impedes transport of GRK1 and PDE6 catalytic subunits to photoreceptor outer segments
Authors: Zhang H. , Li S. , Doan T. , Rieke F. , Detwiler P. B. , Frederick J. M. , Baehr W.
Published: May 2007

The mouse
Pde6d
gene encodes a ubiquitous prenyl binding protein, termed PrBP/δ, of largely unknown physiological function. PrBP/δ was originally identified as a putative rod cGMP phosphodiesterase (PDE6) subunit in the retina, where it is relatively abundant. To investigate the consequences of
Pde6d
deletion in retina, we generated a
Pde6d
−/−
mouse by targeted recombination. Although manifesting reduced body weight, the
Pde6d
−/−
mouse was viable and fertile and its retina developed normally. Immunocytochemistry showed that farnesylated rhodopsin kinase (GRK1) and prenylated rod PDE6 catalytic subunits partially mislocalized in
Pde6d
−/−
rods, whereas rhodopsin was unaffected. In
Pde6d
−/−
rod single-cell recordings, sensitivity to single photons was increased and saturating flash responses were prolonged.
Pde6d
−/−
scotopic paired-flash electroretinograms indicated a delay in recovery of the dark state, likely due to reduced levels of GRK1 in rod outer segments. In
Pde6d
−/−
cone outer segments, GRK1 and cone PDE6α′ were present at very low levels and the photopic b-wave amplitudes were reduced by 70%. Thus the absence of PrBP/δ in retina impairs transport of prenylated proteins, particularly GRK1 and cone PDE, to rod and cone outer segments, resulting in altered photoreceptor physiology and a phenotype of a slowly progressing rod/cone dystrophy.
Fetal gene therapy of α-thalassemia in a mouse model
Authors: Han Xiao-Dong , Lin Chin , Chang Judy , Sadelain Michel , Kan Y. W.
Published: May 2007

Fetuses with homozygous α-thalassemia usually die at the third trimester of pregnancy or soon after birth. Hence, the disease could potentially be a target for fetal gene therapy. We have previously established a mouse model of α-thalassemia. These mice mimic the human α-thalassemic conditions and can be used as preclinical models for fetal gene therapy. We tested a lentiviral vector containing the HS 2, 3, and 4 of the β-LCR, a central polypurine tract element, and the β-globin gene promoter directing either the EGFP or the human α-globin gene. We showed that the GFP expression was erythroid-specific and detected in BFU-E colonies and the erythroid progenies of CFU-GEMM. For
in utero
gene delivery, we did yolk sac vessel injection at midgestation of mouse embryos. The recipient mice were analyzed after birth for human α-globin gene expression. In the newborn, human α-globin gene expression was detected in the liver, spleen, and peripheral blood. The human α-globin gene expression was at the peak at 3–4 months, when it reached 20% in some recipients. However, the expression declined at 7 months. Colony-forming assays in these mice showed low abundance of the transduced human α-globin gene in their BFU-E and CFU-GEMM and the lack of its transcript. Thus, lentiviral vectors can be an effective vehicle for delivering the human α-globin gene into erythroid cells
in utero
, but, in the mouse model, delivery at late midgestation could not transduce hematopoietic stem cells adequately to sustain gene expression.
A theory of measuring, electing, and ranking
Authors: Balinski Michel , Laraki Rida
Published: May 2007

The impossibility theorems that abound in the theory of social choice show that there can be no satisfactory method for electing and ranking in the context of the traditional, 700-year-old model. A more realistic model, whose antecedents may be traced to Laplace and Galton, leads to a new theory that avoids all impossibilities with a simple and eminently practical method, “the majority judgement.” It has already been tested.
High relatedness maintains multicellular cooperation in a social amoeba by controlling cheater mutants
Authors: Gilbert Owen M. , Foster Kevin R. , Mehdiabadi Natasha J. , Strassmann Joan E. , Queller David C.
Published: May 2007

The control of cheating is important for understanding major transitions in evolution, from the simplest genes to the most complex societies. Cooperative systems can be ruined if cheaters that lower group productivity are able to spread. Kin-selection theory predicts that high genetic relatedness can limit cheating, because separation of cheaters and cooperators limits opportunities to cheat and promotes selection against low-fitness groups of cheaters. Here, we confirm this prediction for the social amoebaDictyostelium discoideum; relatedness in natural wild groups is so high that socially destructive cheaters should not spread. We illustrate in the laboratory how high relatedness can control a mutant that would destroy cooperation at low relatedness. Finally, we demonstrate that, as predicted, mutant cheaters do not normally harm cooperation in a natural population. Our findings show how altruism is preserved from the disruptive effects of such mutant cheaters and how exceptionally high relatedness among cells is important in promoting the cooperation that underlies multicellular development.
Carotenoid silk coloration is controlled by a carotenoid-binding protein, a product of the
Yellow blood
gene
Authors: Sakudoh Takashi , Sezutsu Hideki , Nakashima Takeharu , Kobayashi Isao , Fujimoto Hirofumi , Uchino Keiro , Banno Yutaka , Iwano Hidetoshi , Maekawa Hideaki , Tamura Toshiki , Kataoka Hiroshi , Tsuchida Kozo
Published: May 2007

Mechanisms for the uptake and transport of carotenoids, essential nutrients for humans, are not well understood in any animal system. The
Y
(
Yellow blood
) gene, a critical cocoon color determinant in the silkworm
Bombyx mori
, controls the uptake of carotenoids into the intestinal mucosa and the silk gland. Here we provide evidence that the
Y
gene corresponds to the intracellular
carotenoid-binding protein
(
CBP
) gene. In the
Y
recessive strain, the absence of an exon, likely due to an incorrect mRNA splicing caused by a transposon-associated genomic deletion, generates a nonfunctional
CBP
mRNA, resulting in colorless hemolymph and white cocoons. Enhancement of carotenoid uptake and coloration of the white cocoon was achieved by germ-line transformation with the
CBP
gene. This study demonstrates the existence of a genetically facilitated intracellular process beyond passive diffusion for carotenoid uptake in the animal phyla, and paves the way for modulating silk color and lipid content through genetic engineering.
Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis
Authors: Hudjashov Georgi , Kivisild Toomas , Underhill Peter A. , Endicott Phillip , Sanchez Juan J. , Lin Alice A. , Shen Peidong , Oefner Peter , Renfrew Colin , Villems Richard , Forster Peter
Published: May 2007

Published and new samples of Aboriginal Australians and Melanesians were analyzed for mtDNA (n= 172) and Y variation (n= 522), and the resulting profiles were compared with the branches known so far within the global mtDNA and the Y chromosome tree. (i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa ≈50–70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlierHomo erectuspopulations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event ≈50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged ≈8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.
Studies on peptide:N-glycanase–p97 interaction suggest that p97 phosphorylation modulates endoplasmic reticulum-associated degradation
Authors: Zhao Gang , Zhou Xiaoke , Wang Liqun , Li Guangtao , Schindelin Hermann , Lennarz William J.
Published: May 2007

During endoplasmic reticulum-associated degradation, the multifunctional AAA ATPase p97 is part of a protein degradation complex. p97 associates via its N-terminal domain with various cofactors to recruit ubiquitinated substrates. It also interacts with alternative substrate-processing cofactors, such as Ufd2, Ufd3, and peptide:N-glycanase (PNGase) in higher eukaryotes. These cofactors determine different fates of the substrates and they all bind outside of the N-terminal domain of p97. Here, we describe a cofactor-binding motif of p97 contained within the last 10 amino acid residues of the C terminus, which is both necessary and sufficient to mediate interactions of p97 with PNGase and Ufd3. The crystal structure of the N-terminal domain of PNGase in complex with this motif provides detailed insight into the interaction between p97 and its substrate-processing cofactors. Phosphorylation of p97's highly conserved penultimate tyrosine residue, which is the main phosphorylation site during T cell receptor stimulation, completely blocks binding of either PNGase or Ufd3 to p97. This observation suggests that phosphorylation of this residue modulates endoplasmic reticulum-associated protein degradation activity by discharging substrate-processing cofactors.
Selective adapter recruitment and differential signaling networks by VEGF vs. shear stress
Authors: Wang Yingxiao , Chang Joann , Chen Kuang-Den , Li Song , Li Julie Yi-Shuan , Wu Chuanyue , Chien Shu
Published: May 2007

Vascular endothelial cells are continuously exposed to mechanical and chemical stimuli, such as shear stress and VEGF, respectively. It is still not clear how cells perceive these stimuli and orchestrate their responses. Studying the molecular mechanism by which shear stress and VEGF regulate the signaling pathways in bovine endothelial aortic cells, we found that VEGF induced a rapid association of VEGF receptor 2 (Flk-1) with Nckβ, but shear stress did not have such an effect. SU1498 (a specific inhibitor of Flk-1) and Nckβ
nm
(a negative mutant of Nckβ) blocked the VEGF-induced ERK and JNK activities. Only SU1498, but not Nckβ
nm
, inhibited the shear-induced ERK activity. Furthermore, neither SU1498 nor Nckβ
nm
had significant effects on the shear-induced JNK activity, which can be blocked by inhibitors of Src family kinase and ROCK kinase. Therefore, mechanical (shear stress) and chemical (VEGF) stimuli diverge at the receptor Flk-1 in terms of the recruitment of the adapter protein Nckβ, and they employ different components of the complex signaling network in regulating downstream molecules, e.g., ERK and JNK.
Crystal structure of RseB and a model of its binding mode to RseA
Authors: Kim Dong Young , Jin Kyeong Sik , Kwon Eunju , Ree Moonhor , Kim Kyeong Kyu
Published: May 2007

The bacterial envelope stress response senses stress signals in the extracytoplasmic compartment, and activates σ
E
-dependent transcription by degrading its antisigma factor RseA. RseB, a binding partner of RseA, plays a pivotal role in regulating this response, but its molecular mechanism is not understood. We therefore determined the crystal structure of
Escherichia coli
RseB at a resolution of 2.4 Å. RseB is composed of two domains linked by a flexible linker and forms a loosely packed dimer with two grooves on each side. This structural feature is confirmed by small-angle scattering in solution. Analysis of the binding of various RseA mutants to RseB allowed us to identify the major RseB-binding motif in RseA. These data, coupled with analysis of small-angle scattering of the RseA/RseB complex in solution, leads us to propose that two RseAs bind to the grooves of the dimeric RseB by conserved residues. The implications for modulating proteolytic cleavage of RseA are discussed.
Data reduction of isotope-resolved LC-MS spectra
Authors: Du Peicheng , Sudha Rajagopalan , Prystowsky Michael B. , Angeletti Ruth Hogue
Published: May 2007

Motivation: Data reduction of liquid chromatography-mass spectrometry (LC-MS) spectra can be a challenge due to the inherent complexity of biological samples, noise and non-flat baseline. We present a new algorithm, LCMS-2D, for reliable data reduction of LC-MS proteomics data.

Results: LCMS-2D can reliably reduce LC-MS spectra with multiple scans to a list of elution peaks, and subsequently to a list of peptide masses. It is capable of noise removal, and deconvoluting peaks that overlap in m/z, in retention time, or both, by using a novel iterative peak-picking step, a ‘rescue’ step, and a modified variable selection method. LCMS-2D performs well with three sets of annotated LC-MS spectra, yielding results that are better than those from PepList, msInspect and the vendor software BioAnalyst.

Availability: The software LCMS-2D is available under the GNU general public license from http://www.bioc.aecom.yu.edu/labs/angellab/as a standalone C program running on LINUX.

Contact: pdu@us.ibm.com
WilcoxCV: an R package for fast variable selection in cross-validation
Authors: Boulesteix Anne-Laure
Published: May 2007

Summary: In the last few years, numerous methods have been proposed for microarray-based class prediction. Although many of them have been designed especially for the case n ≪ p (much more variables than observations), preliminary variable selection is almost always necessary when the number of genes reaches several tens of thousands, as usual in recent data sets. In the two-class setting, the Wilcoxon rank sum test statistic is, with the t-statistic, one of the standard approaches for variable selection. It is well known that the variable selection step must be seen as a part of classifier construction and, as such, be performed based on training data only. When classifier accuracy is evaluated via cross-validation or Monte–Carlo cross-validation, it means that we have to perform p Wilcoxon or t-tests for each iteration, which becomes a daunting task for increasing p. As a consequence, many authors often perform variable selection only once using all the available data, which can induce a dramatic underestimation of error rate and thus lead to misleadingly reporting predictive power. We propose a very fast implementation of variable selection based on the Wilcoxon test for use in cross-validation and Monte Carlo cross-validation (also known as random splitting into learning and test sets). This implementation is based on a simple mathematical formula using only the ranks calculated from the original data set.

Availability: Our method is implemented in the freely available R package WilcoxCV which can be downloaded from the Comprehensive R Archive Network at http://cran.r-project.org/src/contrib/Descriptions/WilcoxCV.html

Contact: boulesteix@slcmsr.org
MutationFinder: a high-performance system for extracting point mutation mentions from text
Authors: Caporaso J. Gregory , Baumgartner William A. , Randolph David A. , Cohen K. Bretonnel , Hunter Lawrence
Published: May 2007

Summary: Discussion of point mutations is ubiquitous in biomedical literature, and manually compiling databases or literature on mutations in specific genes or proteins is tedious. We present an open-source, rule-based system, MutationFinder, for extracting point mutation mentions from text. On blind test data, it achieves nearly perfect precision and a markedly improved recall over a baseline.

Availability: MutationFinder, along with a high-quality gold standard data set, and a scoring script for mutation extraction systems have been made publicly available. Implementations, source code and unit tests are available in Python, Perl and Java. MutationFinder can be used as a stand-alone script, or imported by other applications.

Project URL:  http://bionlp.sourceforge.net

Contact:  gregcaporaso@gmail.com
PLMaddon: a power-law module for the Matlab™ SBToolbox
Authors: Vera Julio , Sun Cheng , Oertel Yvonne , Wolkenhauer Olaf
Published: May 2007

Summary: PLMaddon is a General Public License (GPL) software module designed to expand the current version of the SBToolbox (a Matlab ™ toolbox for systems biology; www.sbtoolbox.org) with a set of functions for the analysis of power-law models, a specific class of kinetic models, set in ordinary differential equations (ODE) and in which the kinetic orders can have positive/negative non-integer values. The module includes functions to generate power-law Taylor expansions of other ODE models (e.g. Michaelis-Menten type models), as well as algorithms to estimate steady-states. The robustness and sensitivity of the models can also be analysed and visualized by computing the power-law's logarithmic gains and sensitivities.

Availability: PLMaddon is an open source module for the analysis of power-law models based on the SBToolbox. The latest version of PLMaddon is freely available from:

www.sbi.uni-rostock.de/plmaddon

The website contains a tutorial with examples, as well as an interactive introductory course on power-law models in systems biology.

Contact: olaf.wolkenhauer@uni-rostock.de
Nucleotide composition string selection in HIV-1 subtyping using whole genomes
Authors: Wu Xiaomeng , Cai Zhipeng , Wan Xiu-Feng , Hoang Tin , Goebel Randy , Lin Guohui
Published: May 2007

Motivation: The availability of the whole genomic sequences of HIV-1 viruses provides an excellent resource for studying the HIV-1 phylogenies using all the genetic materials. However, such huge volumes of data create computational challenges in both memory consumption and CPU usage.

Results: We propose the complete composition vector representation for an HIV-1 strain, and a string scoring method to extract the nucleotide composition strings that contain the richest evolutionary information for phylogenetic analysis. In this way, a large-scale whole genome phylogenetic analysis for thousands of strains can be done both efficiently and effectively. By using 42 carefully curated strains as references, we apply our method to subtype 1156 HIV-1 strains (10.5 million nucleotides in total), which include 825 pure subtype strains and 331 recombinants. Our results show that our nucleotide composition string selection scheme is computationally efficient, and is able to define both pure subtypes and recombinant forms for HIV-1 strains using the 5000 top ranked nucleotide strings.

Availability: The Java executable and the HIV-1 datasets are accessible through ‘http://www.cs.ualberta.ca/~ghlin/src/WebTools/hiv.php

Contact:  ghlin@cs.ualberta.ca

Supplementary information: Supplementary data are available at Bioinformatics online.
Neurogenesis and the spacing effect: Learning over time enhances memory and the survival of new neurons
Authors: Sisti Helene M. , Glass Arnold L. , Shors Tracey J.
Published: May 2007

Information that is spaced over time is better remembered than the same amount of information massed together. This phenomenon, known as the spacing effect, was explored with respect to its effect on learning and neurogenesis in the adult dentate gyrus of the hippocampal formation. Because the cells are generated over time and because learning enhances their survival, we hypothesized that training with spaced trials would rescue more new neurons from death than the same number of massed trials. In the first experiment, animals trained with spaced trials in the Morris water maze outperformed animals trained with massed trials, but there was not a direct effect of trial spacing on cell survival. Rather, animals that learned well retained more cells than animals that did not learn or learned poorly. Moreover, performance during acquisition correlated with the number of cells remaining in the dentate gyrus after training. In the second experiment, the time between blocks of trials was increased. Consequently, animals trained with spaced trials performed as well as those trained with massed, but remembered the location better two weeks later. The strength of that memory correlated with the number of new cells remaining in the hippocampus. Together, these data indicate that learning, and not mere exposure to training, enhances the survival of cells that are generated 1 wk before training. They also indicate that learning over an extended period of time induces a more persistent memory, which then relates to the number of cells that reside in the hippocampus.
Protection from premature habituation requires functional mushroom bodies in Drosophila
Authors: Acevedo Summer F. , Froudarakis Emmanuil I. , Kanellopoulos Alexandros , Skoulakis Efthimios M.C.
Published: May 2007

Diminished responses to stimuli defined as habituation can serve as a gating mechanism for repetitive environmental cues with little predictive value and importance. We demonstrate that wild-type animals diminish their responses to electric shock stimuli with properties characteristic of short- and long-term habituation. We used spatially restricted abrogation of neurotransmission to identify brain areas involved in this behavioral response. We find that the mushroom bodies and, in particular, the α/β lobes appear to guard against habituating prematurely to repetitive electric shock stimuli. In addition to protection from premature habituation, the mushroom bodies are essential for spontaneous recovery and dishabituation. These results reveal a novel modulatory role of the mushroom bodies on responses to repetitive stimuli in agreement with and complementary to their established roles in olfactory learning and memory.