bluuebunny/crossref_metadata_2025 huggingface dataset:
Spinal cord regeneration: where fish, frogs and salamanders lead the way, can we follow?
Authors: Diaz Quiroz Juan Felipe , Echeverri Karen
Published: April 2013

Major trauma to the mammalian spinal cord often results in irreversible loss of function, i.e. paralysis, and current therapies ranging from drugs, implantations of stem cells and/or biomaterials, and electrically stimulated nerve regrowth, have so far offered very limited success in improving quality-of-life. However, in marked contrast with this basic shortcoming of ours, certain vertebrate species, including fish and salamanders, display the amazing ability to faithfully regenerate various complex body structures after injury or ablation, restoring full functionality, even in the case of the spinal cord. Despite the inherently strong and obvious translational potential for improving treatment strategies for human patients, our in-depth molecular-level understanding of these decidedly more advanced repair systems remains in its infancy. In the present review, we will discuss the current state of this field, focusing on recent progress in such molecular analyses using various regenerative species, and how these so far relate to the mammalian situation.
Peroxisome membrane proteins: multiple trafficking routes and multiple functions?
Authors: Theodoulou Frederica L. , Bernhardt Kristin , Linka Nicole , Baker Alison
Published: April 2013

PMPs (peroxisome membrane proteins) play essential roles in organelle biogenesis and in co-ordinating peroxisomal metabolism with pathways in other subcellular compartments through transport of metabolites and the operation of redox shuttles. Although the import of soluble proteins into the peroxisome matrix has been well studied, much less is known about the trafficking of PMPs. Pex3 and Pex19 (and Pex16 in mammals) were identified over a decade ago as critical components of PMP import; however, it has proved surprisingly difficult to produce a unified model for their function in PMP import and peroxisome biogenesis. It has become apparent that each of these peroxins has multiple functions and in the present review we focus on both the classical and the more recently identified roles of Pex19 and Pex3 as informed by structural, biochemical and live cell imaging studies. We consider the different models proposed for peroxisome biogenesis and the role of PMP import within them, and propose that the differences may be more perceived than real and may reflect the highly dynamic nature of peroxisomes.
Massive Dirac equation in asymmetric Hulthén potential
Authors: Candemir N. , Bayrak O.
Published: April 2013

One-dimensional effective mass Dirac equation is solved in asymmetric Hulthén potential. Scattering and bound state solutions are obtained in terms of hypergeometric functions. Transmission and reflection coefficients are calculated by matching conditions on the wave function. The necessary conditions for the existence of transmission resonances and supercriticality are derived.
The effect of carrier gas flow rate and source cell temperature on low pressure organic vapor phase deposition simulation by direct simulation Monte Carlo method
Authors: Wada Takao , Ueda Noriaki
Published: April 2013

The process of low pressure organic vapor phase deposition (LP-OVPD) controls the growth of amorphous organic thin films, where the source gases (Alq3 molecule, etc.) are introduced into a hot wall reactor via an injection barrel using an inert carrier gas (N2 molecule). It is possible to control well the following substrate properties such as dopant concentration, deposition rate, and thickness uniformity of the thin film. In this paper, we present LP-OVPD simulation results using direct simulation Monte Carlo-Neutrals (Particle-PLUS neutral module) which is commercial software adopting direct simulation Monte Carlo method. By estimating properly the evaporation rate with experimental vaporization enthalpies, the calculated deposition rates on the substrate agree well with the experimental results that depend on carrier gas flow rate and source cell temperature.
Magnetism dependent phonon anomaly in LaFeAsO observed via inelastic x-ray scattering
Authors: Hahn S. E. , Tucker G. S. , Yan J.-Q. , Said A. H. , Leu B. M. , McCallum R. W. , Alp E. E. , Lograsso T. A. , McQueeney R. J. , Harmon B. N.
Published: April 2013

The phonon dispersion was measured at room temperature (above the Néel temperature TN) along (0,0,L) in the tetragonal phase of LaFeAsO using inelastic x-ray scattering. Magnetostructural effects are well documented in the AFe2As2-based (A = Ca, Sr, Ba, Eu) systems. Only recently have single crystals of LaFeAsO become available. The experimentally observed splitting between two A1g phonon modes at 22 and 26 meV is only reproduced in spin-polarized calculations. Magnetostructural effects similar to those observed in the AFe2As2 materials are confirmed to be present in LaFeAsO. This is discussed in terms of the strong antiferromagnetic correlations that are known to persist above TN and into the tetragonal phase.
A variational characterization and geometric integration for Bertrand curves
Authors: Lucas Pascual , Ortega-Yagües José Antonio
Published: April 2013

In this paper, we introduce a class of functionals, in the three-dimensional semi-Euclidean space \documentclass[12pt]{minimal}\begin{document}$\mathbb {R}^3_q$\end{document}Rq3, having an energy density that depends only on curvature and whose moduli space of trajectories consists of LW-curves, i.e., curves with curvature κ and torsion τ for which there are three real constants λ, μ, ρ such that λκ + μτ = ρ, with λ2 + μ2 > 0. This family of curves includes plane curves, helices, curves of constant curvature, curves of constant torsion, Lancret curves (also called generalized helices), and Bertrand curves. We present an algorithm to construct Bertrand curves in \documentclass[12pt]{minimal}\begin{document}$\mathbb {R}^3_q$\end{document}Rq3 by using an arclength parametrized curve in a totally umbilical surface \documentclass[12pt]{minimal}\begin{document}$\mathbb {S}^2$\end{document}S2, \documentclass[12pt]{minimal}\begin{document}$\mathbb {S}^2_1$\end{document}S12, or \documentclass[12pt]{minimal}\begin{document}$\mathbb {H}^2$\end{document}H2 and prove that every Bertrand curve in \documentclass[12pt]{minimal}\begin{document}$\mathbb {R}^3_q$\end{document}Rq3 can be obtained in this way. A second algorithm is presented for the construction of LW-curves by using a curve of constant slope in the ruled surface Sα whose directrix is a certain curve α with non-zero curvature and whose rulings are generated by its modified Darboux vector field.
Solution of fractional kinetic equation by a class of integral transform of pathway type
Authors: Kumar Dilip
Published: April 2013

Solutions of fractional kinetic equations are obtained through an integral transform named Pα-transform introduced in this paper. The Pα-transform is a binomial type transform containing many class of transforms including the well known Laplace transform. The paper is motivated by the idea of pathway model introduced by Mathai [Linear Algebra Appl. 396, 317–328 (2005)10.1016/j.laa.2004.09.022]. The composition of the transform with differential and integral operators are proved along with convolution theorem. As an illustration of applications to the general theory of differential equations, a simple differential equation is solved by the new transform. Being a new transform, the Pα-transform of some elementary functions as well as some generalized special functions such as H-function, G-function, Wright generalized hypergeometric function, generalized hypergeometric function, and Mittag-Leffler function are also obtained. The results for the classical Laplace transform is retrieved by letting α → 1.
Power spectral distributions of pseudo-turbulent bubbly flows
Authors: Mendez-Diaz S. , Serrano-García J. C. , Zenit R. , Hernández-Cordero J. A.
Published: April 2013

An experimental study was carried out to determinate the power spectral density (PSD) of mono-dispersed bubbly flows in a vertical channel using flying hot-film anemometry. To improve bubble detection, optical fibers were installed in close proximity to the anemometer sensing element; in this way, the collisions of bubbles with the probe can be detected and removed from the signal. Measurements were performed with gas fractions up to 6%. The PSD distributions were found to decay with a power of −3, in agreement with previous studies, but for a much wider range of Reynolds and Weber numbers. Our measurements indicate that the power decay does not depend strongly on the nature of hydrodynamic interactions among bubbles.
Measurement of the elastic modulus of spider mite silk fibers using atomic force microscopy
Authors: Hudson Stephen D. , Zhurov Vladimir , Grbić Vojislava , Grbić Miodrag , Hutter Jeffrey L.
Published: April 2013

Bio-nanomaterials are one of the fastest developing sectors of industry and technology. Spider silk, a highly attractive light-weight biomaterial, has high tensile strength and elasticity and is compatible with human tissues, allowing for many areas of application. In comparison to spider silk fibers with diameters of several micrometers, spider mite silk fibers have much smaller diameters of tens of nanometers, making conventional tensile testing methods impractical. To determine the mechanical properties of adult and larval Tetranychus urticae silk fibers, we have performed three-point bending tests with an atomic force microscope. We found that because of the small diameters of these fibers, axial tension—due to both the applied force and a pre-existing strain—has a significant effect on the fiber response, even in the small-deformation limit. As a result, the typical Euler-Bernoulli-Timoshenko theory cannot be applied. We therefore follow the approach of Heidelberg et al. to develop a mechanical model of the fiber response that accounts for bending, an initial tension in the fibers, and a tension due to elongation during testing. This model provides self-consistent results, allowing us to determine that adult and larval fibers have Young's moduli of 24±3 GPa and 15±3 GPa, respectively. Both adult and larval fibers have an estimated ultimate strength of 200–300 MPa and a toughness of order 9 MJ/m3. We note that with increasing interest in the mechanical properties of very high aspect ratio nanomaterials, the influence of pre-existing tension must be considered in any measurements involving a bending test.
Basis set converged weak interaction energies from conventional and explicitly correlated coupled-cluster approach
Authors: Patkowski Konrad
Published: April 2013

Interaction energies for seven weakly bound dimers involving helium, argon, water, and methane are computed using large correlation-consistent basis sets augmented with bond functions. The estimates of the coupled-cluster singles, doubles, and noniterative triples [CCSD(T)] complete basis set limit are obtained using both the conventional approach and several variants of the explicitly correlated CCSD(T)-F12 method. It is shown that both bond functions and the F12 approach significantly speed up the convergence of the CCSD(T)/aug-cc-pVXZ interaction energies with the basis set cardinal number X. However, the extent of improvement provided by each technique varies with the character of the interactions—the F12 method works best for polar, electrostatics-bound dimers, while for dispersion-dominated complexes the addition of bond functions is more efficient. The convergence rate afforded by different coupled-cluster variants is fairly consistent across the entire attractive region of the potential curve, while the improvement provided by the F12 correction increases along the repulsive wall. The use of large basis sets and the agreement between conventional and explicitly correlated approaches allow us to assess the importance of different residual approximations present in the popular CCSD(T)-F12 implementations.
Tunable resonant properties of perpendicular anisotropy [Co/Pd]/Fe/[Co/Pd] multilayers
Authors: Dou Jian , Pechan Michael J. , Shipton E. , Eibagi N. , Fullerton E. E.
Published: April 2013

We describe the static and dynamic magnetic behaviors of Fe films (thicknesses 2, 4, and 6 nm) sandwiched between Co/Pd multilayers with strong perpendicular magnetic anisotropy. Out-of-plane measurements of both magnetization and ferromagnetic resonance confirm well-defined Fe layer response modified by large perpendicular exchange field arising from the coupling with the Co/Pd. The field/frequency dispersion is linear for all samples with field intercepts increasing with Fe layer thickness. Analysis in terms of shape anisotropy and interfacial exchange model yields a large out-of-plane interfacial coupling of ∼3.0–3.7 erg/cm2 that is mediated by the coupling across thin Pd layers. The value of this interface exchange is also shown to be tunable with interfacial Pd thickness.
Modal and transient dynamics of jet flows
Authors: Garnaud X. , Lesshafft L. , Schmid P. J. , Huerre P.
Published: April 2013

The linear stability dynamics of incompressible and compressible isothermal jets are investigated by means of their optimal initial perturbations and of their temporal eigenmodes. The transient growth analysis of optimal perturbations is robust and allows physical interpretation of the salient instability mechanisms. In contrast, the modal representation appears to be inadequate, as neither the computed eigenvalue spectrum nor the eigenmode shapes allow a characterization of the flow dynamics in these settings. More surprisingly, numerical issues also prevent the reconstruction of the dynamics from a basis of computed eigenmodes. An investigation of simple model problems reveals inherent problems of this modal approach in the context of a stable convection-dominated configuration. In particular, eigenmodes may exhibit an exponential growth in the streamwise direction even in regions where the flow is locally stable.
Photoassisted electron emission from metal-oxide-semiconductor cathodes based on nanocrystalline silicon
Authors: Shimawaki H. , Neo Y. , Mimura H. , Wakaya F. , Takai M.
Published: April 2013

This paper investigates the effect of optical pulses on the electron emission properties of metal-oxide-semiconductor (MOS) cathodes based on nanocrystalline silicon (nc-Si). The emission current is enhanced by about two orders of magnitude by the irradiation of 405 nm laser light. The increase of the emission current under irradiation was proportional to incident laser power. The differential quantum efficiency of the nc-Si based MOS diode itself was estimated to be 3 × 10−2. However, the value of the photoemission current was only 3 × 10−7 due to the short mean free path of hot electron for Pt used as the gate electrode. We obtained a pulsed electron beam from the cathode device by a pulsed laser. The result shows that MOS type cathodes have a suitable structure for optically generating a train of short electron bunches.
Polarity-indicative two-dimensional periodic relief gratings of tethered poly(methyl methacrylate) on silicon surfaces for visualization in volatile organic compound sensing
Authors: Chen Jem-Kun , Wang Jing-Hong , Cheng Chih-Chia , Chang Jia-Yaw , Chang Feng-Chih
Published: April 2013

We grafted poly(methyl methacrylate) (PMMA) from a 200 nm-resolution hole array of photoresist on a silicon substrate as a pillar array of two-dimensional periodic relief grating (2DPRG). The resulting 2DPRGs have been used as detectors of organic solvents in surrounding media, based upon structure change of the 2DPRG as a consequence of the solvent induced reversible swelling-deswelling of PMMA chains, through effective refractive index. Dramatic colors change, purple, green, yellow, and red, was observed by naked eyes along an incident angle of 60°–70° as the surrounding media of PMMA-modified 2DPRG was acetone, tetrahydrofuran, dioxane, and chloroform, respectively.
An atomistic investigation of the impact of in-plane uniaxial stress during solid phase epitaxial regrowth
Authors: Sklenard Benoit , Barbe Jean-Charles , Batude Perrine , Rivallin Pierrette , Tavernier Clement , Cristoloveanu Sorin , Martin-Bragado Ignacio
Published: April 2013

We propose an atomistic comprehensive model based on a lattice kinetic Monte Carlo approach to analyse the impact of in-plane uniaxial stress during solid phase epitaxial regrowth. We observed no influence of tensile stress on the regrowth kinetics. In contrast, compressive stress leads to (i) a reduction of the macroscopic regrowth velocity, (ii) an enhancement of the amorphous/crystalline interface roughness, and (iii) defective Si formation. Our observations are in good agreement with experimental data from the literature. Our atomistic approach also clarifies the interpretation of the interface morphological instability based on the kinetics of microscopic events.
A compact modeling of TiO2-TiO2–x memristor
Authors: Zhang Lu , Chen Zhijie , Joshua Yang J. , Wysocki Bryant , McDonald Nathan , Chen Yiran
Published: April 2013

We developed a spice-compatible compact model of TiO2-TiO2–x memristors based on classic ion transportation theory. Our model is shown to simulate important dynamic memristive properties like real-time memristance switching, which are critical in memristor-based analog circuit designs. The model, as well as its analytical approximation, is validated with the experimentally obtained data from real devices. Minor deviations of our model from the measured data are also analyzed and discussed.
Resolving the EH6/7 level in 4H-SiC by Laplace-transform deep level transient spectroscopy
Authors: Alfieri G. , Kimoto T.
Published: April 2013

We show that Laplace transform deep level transient spectroscopy (LDLTS) is an effective technique for the separation of the overlapping emission rates of the EH6 and EH7 levels, which are known to constitute EH6/7, a mid-gap level in n-type 4H-SiC. The analysis of the electron irradiation dose, electric field dependence, and the effects of carbon interstitials injection on the emission rates of EH6 and EH7 shows that EH7 is dominant over EH6 and confirms that their nature is related to a carbon vacancy.
Identification and mapping of a stripe rust resistance gene in spring wheat germplasm HRMSN-81 from CIMMYT
Authors: Chen Shi-Sheng , Chen Guo-Yue , Yang Cheng , Wei Yu-Ming , Wu Wen-Xiong , He Yuan-Jiang , Liu Ya-Xi , Li Wei , Pu Zhi-En , Lan Xiu-Jin , Zheng You-Liang
Published: April 2013

Pathogens are a reason for low yield in common wheat (Triticum aestivum L.). Stripe rust (or yellow rust), caused by the fungus Puccinia striiformis f. sp. tritici (Pst), is one of the most important foliar diseases of wheat. One of the most cost-effective and environmentally sound ways to control stripe rust is to use plant varieties that are resistant to this pathogen. It is an important task for wheat breeders and pathologists to identify new genes and pyramid them in order to achieve high-level, durable resistance to stripe rust. One spring wheat germplasm, HRMSN-81, with resistance to the most dominant races in China, is identified from the CIMMYT breeding lines. To elucidate the genetic basis of its resistance, HRMSN-81 was crossed with susceptible wheat genotype Taichung 29. Seedlings of the parents were tested with Chinese Pst isolates CYR31, CYR32, and CYR33 under controlled greenhouse conditions, and adult plants of the parents and F1, F2, and F2:3 progeny were inoculated with the epidemic stripe rust mixed races, including CYR31, CYR32, and CYR33, in fields under natural infection.
Genetic analysis showed that HRMSN-81 has a single dominant gene conferring all-stage resistance, temporarily designated as YrHRMSN-81. Resistance gene analogue polymorphism (RGAP), simple sequence repeat (SSR), target region amplified polymorphism (TRAP), and sequence-related amplified polymorphism (SRAP) techniques in combination with bulked segregant analysis (BSA) were used to identify molecular markers linked to the resistance gene. A linkage map consisting of six RGAP, two SSR, one TRAP, and two SRAP markers was constructed for YrHRMSN-81 using 148 F2 plants. The gene was mapped to chromosome arm 2DS by testing the complete set of nulli-tetrasomic lines and selected ditelosomic lines with two RGAP markers and was further confirmed by two chromosome-specific SSR markers. The results of gene characteristics and chromosome locations indicated that YrHRMSN-81 was probably a new stripe rust resistance gene. The two flanking markers Xwgp-180bp (93% polymorphism rate) and Xwmc453 (91% polymorphism rate) detected 100% polymorphism of the 56 tested wheat genotypes when they were used in combination. The identification of the gene YrHRMSN-81 and the determination of the flanking markers should be useful for rapidly transferring it in wheat breeding programs.
LDL receptor and its family members serve as the cellular receptors for vesicular stomatitis virus
Authors: Finkelshtein Danit , Werman Ariel , Novick Daniela , Barak Sara , Rubinstein Menachem
Published: April 2013

Vesicular stomatitis virus (VSV) exhibits a remarkably robust and pantropic infectivity, mediated by its coat protein, VSV-G. Using this property, recombinant forms of VSV and VSV-G-pseudotyped viral vectors are being developed for gene therapy, vaccination, and viral oncolysis and are extensively used for gene transduction in vivo and in vitro. The broad tropism of VSV suggests that it enters cells through a highly ubiquitous receptor, whose identity has so far remained elusive. Here we show that the LDL receptor (LDLR) serves as the major entry port of VSV and of VSV-G-pseudotyped lentiviral vectors in human and mouse cells, whereas other LDLR family members serve as alternative receptors. The widespread expression of LDLR family members accounts for the pantropism of VSV and for the broad applicability of VSV-G-pseudotyped viral vectors for gene transduction.
Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries
Authors: Yi Li , Gebhard Mark C. , Li Qing , Taft Joseph M. , Georgiou George , Iverson Brent L.
Published: April 2013

Myriad new applications of proteases would be enabled by an ability to fine-tune substrate specificity and activity. Herein we present a general strategy for engineering protease selectivity and activity by capitalizing on sequestration of the protease to be engineered within the yeast endoplasmic reticulum (ER). A substrate fusion protein composed of yeast adhesion receptor subunit Aga2, selection and counterselection substrate sequences, multiple intervening epitope tag sequences, and a C-terminal ER retention sequence is coexpressed with a protease library. Cleavage of the substrate fusion protein by the protease eliminates the ER retention sequence, facilitating transport to the yeast surface. Yeast cells that display Aga2 fusions in which only the selection substrate is cleaved are isolated by multicolor FACS with fluorescently labeled antiepitope tag antibodies. Using this system, the Tobacco Etch Virus protease (TEV-P), which strongly prefers Gln at P1 of its canonical ENLYFQ↓S substrate, was engineered to recognize selectively Glu or His at P1. Kinetic analysis indicated an overall 5,000-fold and 1,100-fold change in selectivity, respectively, for the Glu- and His-specific TEV variants, both of which retained high catalytic turnover. Human granzyme K and the hepatitis C virus protease were also shown to be amenable to this unique approach. Further, by adjusting the signaling strategy to identify phosphorylated as opposed to cleaved sequences, this unique system was shown to be compatible with the human Abelson tyrosine kinase.
Murine natural killer cell licensing and regulation by T regulatory cells in viral responses
Authors: Sungur Can M. , Tang-Feldman Yajarayma J. , Ames Erik , Alvarez Maite , Chen Mingyi , Longo Dan L. , Pomeroy Claire , Murphy William J.
Published: April 2013

Natural killer (NK) cells show differential functionality based on their capability of binding to self-MHC consistent with licensing. Here we show in vivo confirmation of the physiologic effects of licensing with differential effects of NK subsets on anti-murine cytomegalovirus (anti-MCMV) responses after syngeneic hematopoietic stem cell transplantation (HSCT) or regulatory T-cell (Treg) depletion. After HSCT, depletion of licensed NK cells led to far greater viral loads in target organs early after infection compared with nondepleted and unlicensed depleted mice. There was a preferential expansion of licensed, C-type lectin-like activating receptor Ly49H+ NK cells with increased IFNγ production after infection in nondepleted mice post-HSCT and after Treg depletion. Adoptive transfer of licensed NK subsets into immunodeficient hosts provided significantly greater MCMV resistance compared with transfer of total NK populations or unlicensed subsets. In non-HSCT mice, only concurrent depletion of Tregs or TGF-β neutralization resulted in detection of NK licensing effects. This suggests that licensed NK cells are the initial and rapidly responding population of NK cells to MCMV infection, but are highly regulated by Tregs and TGF-β.
Increased photosystem II stability promotes H2production in sulfur-deprivedChlamydomonas reinhardtii
Authors: Volgusheva Alena , Styring Stenbjörn , Mamedov Fikret
Published: April 2013

Photobiological H2production is an attractive option for renewable solar fuels. Sulfur-deprived cells ofChlamydomonas reinhardtiihave been shown to produce hydrogen with the highest efficiency among photobiological systems. We have investigated the photosynthetic reactions during sulfur deprivation and H2production in the wild-type and state transition mutant 6 (Stm6) mutant ofChlamydomonas reinhardtii. The incubation period (130 h) was dissected into different phases, and changes in the amount and functional status of photosystem II (PSII) were investigated in vivo by electron paramagnetic resonance spectroscopy and variable fluorescence measurements. In the wild type it was found that the amount of PSII is decreased to 25% of the original level; the electron transport from PSII was completely blocked during the anaerobic phase preceding H2formation. This block was released during the H2production phase, indicating that the hydrogenase withdraws electrons from the plastoquinone pool. This partly removes the block in PSII electron transport, thereby permitting electron flow from water oxidation to hydrogenase. In the Stm6 mutant, which has higher respiration and H2evolution than the wild type, PSII was analogously but much less affected. The addition of the PSII inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea revealed that ∼80% of the H2production was inhibited in both strains. We conclude that (i) at least in the earlier stages, most of the electrons delivered to the hydrogenase originate from water oxidation by PSII, (ii) a faster onset of anaerobiosis preserves PSII from irreversible photoinhibition, and (iii) mutants with enhanced respiratory activity should be considered for better photobiological H2production.
Exosomes reflect the hypoxic status of glioma cells and mediate hypoxia-dependent activation of vascular cells during tumor development
Authors: Kucharzewska Paulina , Christianson Helena C. , Welch Johanna E. , Svensson Katrin J. , Fredlund Erik , Ringnér Markus , Mörgelin Matthias , Bourseau-Guilmain Erika , Bengzon Johan , Belting Mattias
Published: April 2013

Hypoxia, or low oxygen tension, is a major regulator of tumor development and aggressiveness. However, how cancer cells adapt to hypoxia and communicate with their surrounding microenvironment during tumor development remain important questions. Here, we show that secreted vesicles with exosome characteristics mediate hypoxia-dependent intercellular signaling of the highly malignant brain tumor glioblastoma multiforme (GBM). In vitro hypoxia experiments with glioma cells and studies with patient materials reveal the enrichment in exosomes of hypoxia-regulated mRNAs and proteins (e.g., matrix metalloproteinases, IL-8, PDGFs, caveolin 1, and lysyl oxidase), several of which were associated with poor glioma patient prognosis. We show that exosomes derived from GBM cells grown at hypoxic compared with normoxic conditions are potent inducers of angiogenesis ex vivo and in vitro through phenotypic modulation of endothelial cells. Interestingly, endothelial cells were programmed by GBM cell-derived hypoxic exosomes to secrete several potent growth factors and cytokines and to stimulate pericyte PI3K/AKT signaling activation and migration. Moreover, exosomes derived from hypoxic compared with normoxic conditions showed increased autocrine, promigratory activation of GBM cells. These findings were correlated with significantly enhanced induction by hypoxic compared with normoxic exosomes of tumor vascularization, pericyte vessel coverage, GBM cell proliferation, as well as decreased tumor hypoxia in a mouse xenograft model. We conclude that the proteome and mRNA profiles of exosome vesicles closely reflect the oxygenation status of donor glioma cells and patient tumors, and that the exosomal pathway constitutes a potentially targetable driver of hypoxia-dependent intercellular signaling during tumor development.
Deficiency of β-arrestin1 ameliorates collagen-induced arthritis with impaired TH17 cell differentiation
Authors: Li Juan , Wei Bin , Guo Ao , Liu Chang , Huang Shichao , Du Fang , Fan Wei , Bao Chunde , Pei Gang
Published: April 2013

Rheumatoid arthritis (RA) is an inflammatory disease in which interleukin 17 (IL-17)-producing T helper 17 (TH17) cells have been critically involved. We show that in patients with RA, the expression of a multifunctional regulator β-arrestin1 was significantly up-regulated in peripheral and synovial CD4+T cells, which correlated well with active phases of RA. In collagen-induced arthritis, deficiency of β-arrestin1 ameliorated disease with decreased TH17 cell differentiation, proinflammatory cytokine production, synovitis, and cartilage and bone destruction. Further mechanistic study reveals that β-arrestin1 promoted signal transducer and activator of transcription 3 (STAT3) activation required for TH17 cell differentiation through scaffolding the interaction of Janus kinase 1 and STAT3. These findings indicate a critical role for β-arrestin1 in the pathogenesis of collagen-induced arthritis and TH17 cell differentiation and suggest β-arrestin1 as a potential diagnostic biomarker and therapeutic target for RA.
Interference with ERK
Thr188
phosphorylation impairs pathological but not physiological cardiac hypertrophy
Authors: Ruppert Catharina , Deiss Katharina , Herrmann Sebastian , Vidal Marie , Oezkur Mehmet , Gorski Armin , Weidemann Frank , Lohse Martin J. , Lorenz Kristina
Published: April 2013

Extracellular signal-regulated kinases 1 and 2 (ERK1/2) are central mediators of cardiac hypertrophy and are discussed as potential therapeutic targets. However, direct inhibition of ERK1/2 leads to exacerbated cardiomyocyte death and impaired heart function. We have previously identified ERK
Thr188
autophosphorylation as a regulatory phosphorylation of ERK1/2 that is a key factor in cardiac hypertrophy. Here, we investigated whether interference with ERK
Thr188
phosphorylation permits the impairment of ERK1/2-mediated cardiac hypertrophy without increasing cardiomyocyte death. The impact of ERK
Thr188
phosphorylation on cardiomyocyte hypertrophy and cell survival was analyzed in isolated cells and in mice using the mutant ERK2
T188A
, which is dominant-negative for ERK
Thr188
signaling. ERK2
T188A
efficiently attenuated cardiomyocyte hypertrophic responses to phenylephrine and to chronic pressure overload, but it affected neither antiapoptotic ERK1/2 signaling nor overall physiological cardiac function. In contrast to its inhibition of pathological hypertrophy, ERK2
T188A
did not interfere with physiological cardiac growth occurring with age or upon voluntary exercise. A preferential role of ERK
Thr188
phosphorylation in pathological types of hypertrophy was also seen in patients with aortic valve stenosis: ERK
Thr188
phosphorylation was increased 8.5 ± 1.3-fold in high-gradient, rapidly progressing cases (≥40 mmHg gradient), whereas in low-gradient, slowly progressing cases, the increase was not significant. Because interference with ERK
Thr188
phosphorylation (
i
) inhibits pathological hypertrophy and (
ii
) does not impair antiapoptotic ERK1/2 signaling and because ERK
Thr188
phosphorylation shows strong prevalence for aortic stenosis patients with rapidly progressing course, we conclude that interference with ERK
Thr188
phosphorylation offers the possibility to selectively address pathological types of cardiac hypertrophy.
Detergent-mediated incorporation of transmembrane proteins in giant unilamellar vesicles with controlled physiological contents
Authors: Dezi Manuela , Di Cicco Aurelie , Bassereau Patricia , Lévy Daniel
Published: April 2013

Giant unilamellar vesicles (GUVs) are convenient biomimetic systems of the same size as cells that are increasingly used to quantitatively address biophysical and biochemical processes related to cell functions. However, current approaches to incorporate transmembrane proteins in the membrane of GUVs are limited by the amphiphilic nature or proteins. Here, we report a method to incorporate transmembrane proteins in GUVs, based on concepts developed for detergent-mediated reconstitution in large unilamellar vesicles. Reconstitution is performed either by direct incorporation from proteins purified in detergent micelles or by fusion of purified native vesicles or proteoliposomes in preformed GUVs. Lipid compositions of the membrane and the ionic, protein, or DNA compositions in the internal and external volumes of GUVs can be controlled. Using confocal microscopy and functional assays, we show that proteins are unidirectionally incorporated in the GUVs and keep their functionality. We have successfully tested our method with three types of transmembrane proteins. GUVs containing bacteriorhodopsin, a photoactivable proton pump, can generate large transmembrane pH and potential gradients that are light-switchable and stable for hours. GUVs with FhuA, a bacterial porin, were used to follow the DNA injection by T5 phage upon binding to its transmembrane receptor. GUVs incorporating BmrC/BmrD, a bacterial heterodimeric ATP-binding cassette efflux transporter, were used to demonstrate the protein-dependent translocation of drugs and their interactions with encapsulated DNA. Our method should thus apply to a wide variety of membrane or peripheral proteins for producing more complex biomimetic GUVs.
Protein–DNA complexes are the primary sources of replication fork pausing in
Escherichia coli
Authors: Gupta Milind K. , Guy Colin P. , Yeeles Joseph T. P. , Atkinson John , Bell Hazel , Lloyd Robert G. , Marians Kenneth J. , McGlynn Peter
Published: April 2013

Replication fork pausing drives genome instability, because any loss of paused replisome activity creates a requirement for reloading of the replication machinery, a potentially mutagenic process. Despite this importance, the relative contributions to fork pausing of different replicative barriers remain unknown. We show here that
Deinococcus radiodurans
RecD2 helicase inactivates
Escherichia coli
replisomes that are paused but still functional in vitro, preventing continued fork movement upon barrier removal or bypass, but does not inactivate elongating forks. Using RecD2 to probe replisome pausing in vivo, we demonstrate that most pausing events do not lead to replisome inactivation, that transcription complexes are the primary sources of this pausing, and that an accessory replicative helicase is critical for minimizing the frequency and/or duration of replisome pauses. These findings reveal the hidden potential for replisome inactivation, and hence genome instability, inside cells. They also demonstrate that efficient chromosome duplication requires mechanisms that aid resumption of replication by paused replisomes, especially those halted by protein–DNA barriers such as transcription complexes.
A strategy to capture and characterize the synaptic transcriptome
Authors: Puthanveettil Sathyanarayanan V. , Antonov Igor , Kalachikov Sergey , Rajasethupathy Priyamvada , Choi Yun-Beom , Kohn Andrea B. , Citarella Mathew , Yu Fahong , Karl Kevin A. , Kinet Maxime , Morozova Irina , Russo James J. , Ju Jingyue , Moroz Leonid L. , Kandel Eric R.
Published: April 2013

Here we describe a strategy designed to identify RNAs that are actively transported to synapses during learning. Our approach is based on the characterization of RNA transport complexes carried by molecular motor kinesin. Using this strategy in
Aplysia
, we have identified 5,657 unique sequences consisting of both coding and noncoding RNAs from the CNS. Several of these RNAs have key roles in the maintenance of synaptic function and growth. One of these RNAs, myosin heavy chain, is critical in presynaptic sensory neurons for the establishment of long-term facilitation, but not for its persistence.
Quantum critical point and spin fluctuations in lower-mantle ferropericlase
Authors: Lyubutin Igor S. , Struzhkin Viktor V. , Mironovich A. A. , Gavriliuk Alexander G. , Naumov Pavel G. , Lin Jung-Fu , Ovchinnikov Sergey G. , Sinogeikin Stanislav , Chow Paul , Xiao Yuming , Hemley Russell J.
Published: April 2013

Ferropericlase [(Mg,Fe)O] is one of the most abundant minerals of the earth’s lower mantle. The high-spin (HS) to low-spin (LS) transition in the Fe
2+
ions may dramatically alter the physical and chemical properties of (Mg,Fe)O in the deep mantle. To understand the effects of compression on the ground electronic state of iron, electronic and magnetic states of Fe
2+
in (Mg
0.75
Fe
0.25
)O have been investigated using transmission and synchrotron Mössbauer spectroscopy at high pressures and low temperatures (down to 5 K). Our results show that the ground electronic state of Fe
2+
at the critical pressure
P
c
of the spin transition close to
T
= 0 is governed by a quantum critical point (
T
= 0,
P
=
P
c
) at which the energy required for the fluctuation between HS and LS states is zero. Analysis of the data gives
P
c
= 55 GPa. Thermal excitation within the HS or LS states (
T
> 0 K) is expected to strongly influence the magnetic as well as physical properties of ferropericlase. Multielectron theoretical calculations show that the existence of the quantum critical point at temperatures approaching zero affects not only physical properties of ferropericlase at low temperatures but also its properties at
P-T
of the earth’s lower mantle.
Lineage tracing with Axin2 reveals distinct developmental and adult populations of Wnt/β-catenin–responsive neural stem cells
Authors: Bowman Angela N. , van Amerongen Renée , Palmer Theo D. , Nusse Roeland
Published: April 2013

Since the discovery of neural stem cells in the mammalian brain, there has been significant interest in understanding their contribution to tissue homeostasis at both the cellular and molecular level. Wnt/β-catenin signaling is crucial for development of the central nervous system and has been implicated in stem cell maintenance in multiple tissues. Based on this, we hypothesized that the Wnt pathway likely controls neural stem cell maintenance and differentiation along the entire developmental continuum. To test this, we performed lineage tracing experiments using the recently developed tamoxifen-inducible Cre at Axin2 mouse strain to follow the developmental fate of Wnt/β-catenin–responsive cells in both the embryonic and postnatal mouse brain. From as early as embryonic day 8.5 onwards,
Axin2

+

cells can give rise to spatially and functionally restricted populations of adult neural stem cells in the subventricular zone. Similarly, progeny from

Axin2
+

cells labeled from E12.5 contribute to both the subventricular zone and the dentate gyrus of the hippocampus. Labeling in the postnatal brain, in turn, demonstrates the persistence of long-lived, Wnt/β-catenin–responsive stem cells in both of these sites. These results demonstrate the continued importance of Wnt/β-catenin signaling for neural stem and progenitor cell formation and function throughout developmental time.
MPN patients harbor recurrent truncating mutations in transcription factor NF-E2
Authors: Jutzi Jonas S. , Bogeska Ruzhica , Nikoloski Gorica , Schmid Corina A. , Seeger Thalia S. , Stegelmann Frank , Schwemmers Sven , Gründer Albert , Peeken Jan C. , Gothwal Monika , Wehrle Julius , Aumann Konrad , Hamdi Kamar , Dierks Christine , Wang Wei , Döhner Konstanze , Jansen Joop H. , Pahl Heike L.
Published: April 2013

The molecular etiology of myeloproliferative neoplasms (MPNs) remains incompletely understood, despite recent advances incurred through the discovery of several different mutations in MPN patients. We have recently described overexpression of the transcription factor NF-E2 in MPN patients and shown that elevated NF-E2 levels in vivo cause an MPN phenotype and predispose to leukemic transformation in transgenic mice. We report the presence of acquired insertion and deletion mutations in the NF-E2 gene in MPN patients. These result in truncated NF-E2 proteins that enhance wild-type (WT) NF-E2 function and cause erythrocytosis and thrombocytosis in a murine model. NF-E2 mutant cells acquire a proliferative advantage, witnessed by clonal dominance over WT NF-E2 cells in MPN patients. Our data underscore the role of increased NF-E2 activity in the pathophysiology of MPNs.
S1–S3 counter charges in the voltage sensor module of a mammalian sodium channel regulate fast inactivation
Authors: Groome James R. , Winston Vern
Published: April 2013

The movement of positively charged S4 segments through the electric field drives the voltage-dependent gating of ion channels. Studies of prokaryotic sodium channels provide a mechanistic view of activation facilitated by electrostatic interactions of negatively charged residues in S1 and S2 segments, with positive counterparts in the S4 segment. In mammalian sodium channels, S4 segments promote domain-specific functions that include activation and several forms of inactivation. We tested the idea that S1–S3 countercharges regulate eukaryotic sodium channel functions, including fast inactivation. Using structural data provided by bacterial channels, we constructed homology models of the S1–S4 voltage sensor module (VSM) for each domain of the mammalian skeletal muscle sodium channel hNaV1.4. These show that side chains of putative countercharges in hNaV1.4 are oriented toward the positive charge complement of S4. We used mutagenesis to define the roles of conserved residues in the extracellular negative charge cluster (ENC), hydrophobic charge region (HCR), and intracellular negative charge cluster (INC). Activation was inhibited with charge-reversing VSM mutations in domains I–III. Charge reversal of ENC residues in domains III (E1051R, D1069K) and IV (E1373K, N1389K) destabilized fast inactivation by decreasing its probability, slowing entry, and accelerating recovery. Several INC mutations increased inactivation from closed states and slowed recovery. Our results extend the functional characterization of VSM countercharges to fast inactivation, and support the premise that these residues play a critical role in domain-specific gating transitions for a mammalian sodium channel.
Imaging calcium microdomains within entire astrocyte territories and endfeet with GCaMPs expressed using adeno-associated viruses
Authors: Shigetomi Eiji , Bushong Eric A. , Haustein Martin D. , Tong Xiaoping , Jackson-Weaver Olan , Kracun Sebastian , Xu Ji , Sofroniew Michael V. , Ellisman Mark H. , Khakh Baljit S.
Published: April 2013

Intracellular Ca2+ transients are considered a primary signal by which astrocytes interact with neurons and blood vessels. With existing commonly used methods, Ca2+ has been studied only within astrocyte somata and thick branches, leaving the distal fine branchlets and endfeet that are most proximate to neuronal synapses and blood vessels largely unexplored. Here, using cytosolic and membrane-tethered forms of genetically encoded Ca2+ indicators (GECIs; cyto-GCaMP3 and Lck-GCaMP3), we report well-characterized approaches that overcome these limitations. We used in vivo microinjections of adeno-associated viruses to express GECIs in astrocytes and studied Ca2+ signals in acute hippocampal slices in vitro from adult mice (aged ∼P80) two weeks after infection. Our data reveal a sparkling panorama of unexpectedly numerous, frequent, equivalently scaled, and highly localized Ca2+ microdomains within entire astrocyte territories in situ within acute hippocampal slices, consistent with the distribution of perisynaptic branchlets described using electron microscopy. Signals from endfeet were revealed with particular clarity. The tools and experimental approaches we describe in detail allow for the systematic study of Ca2+ signals within entire astrocytes, including within fine perisynaptic branchlets and vessel-associated endfeet, permitting rigorous evaluation of how astrocytes contribute to brain function.
Antimicrobial Stewardship Programs in Florida's Acute Care Facilities
Authors: Abbo Lilian , Lo Kaming , Sinkowitz-Cochran Ronda , Burke Anne Carol , Hopkins Richard S. , Srinivasan Arjun , Hooton Thomas M.
Published: April 2013

We surveyed acute care facilities in Florida to assess components of and barriers to sustained antimicrobial stewardship programs (ASPs). Most respondents with and without ASPs are doing some stewardship-related activities to improve antimicrobial use. Collaborative efforts between facilities and health departments are important to providing better resources for ASPs.
Immigrant Workers and Farm Performance: Evidence from Matched Employer‐Employee Data
Authors: Malchow-Møller Nikolaj , Munch Jakob Roland , Seidelin Claus Aastrup , Skaksen Jan Rose
Published: April 2013

In many developed countries, the agricultural sector has experienced a significant inflow of immigrants. At the same time, agriculture is still in a process of structural transformation, resulting in fewer but larger and presumably more efficient farms. We exploit matched employer‐employee data for Danish farms in 1980–2008 to analyze the micro‐level relationship between these two developments. Farms employing immigrants tend to be both larger than and no less productive than other farms. Furthermore, an increased use of immigrants is associated with an improvement in job creation and revenue, which at least partially seems to reflect a causal effect of immigrants.
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Authors: Yu Danni , Huber Wolfgang , Vitek Olga
Published: April 2013

Motivation: RNA-seq experiments produce digital counts of reads that are affected by both biological and technical variation. To distinguish the systematic changes in expression between conditions from noise, the counts are frequently modeled by the Negative Binomial distribution. However, in experiments with small sample size, the per-gene estimates of the dispersion parameter are unreliable.

Method: We propose a simple and effective approach for estimating the dispersions. First, we obtain the initial estimates for each gene using the method of moments. Second, the estimates are regularized, i.e. shrunk towards a common value that minimizes the average squared difference between the initial estimates and the shrinkage estimates. The approach does not require extra modeling assumptions, is easy to compute and is compatible with the exact test of differential expression.

Results: We evaluated the proposed approach using 10 simulated and experimental datasets and compared its performance with that of currently popular packages edgeR, DESeq, baySeq, BBSeq and SAMseq. For these datasets, sSeq performed favorably for experiments with small sample size in sensitivity, specificity and computational time.

Availability:  http://www.stat.purdue.edu/∼ovitek/Software.html and Bioconductor.

Contact:  ovitek@purdue.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.