bluuebunny/crossref_metadata_2025 huggingface dataset:
Initial chemical events in shocked octahydro-1,3,5,7-tetranitro-1,3,5,7- tetrazocine: A new initiation decomposition mechanism
Authors: Zhu Weihua , Huang Hui , Huang Hengjian , Xiao Heming
Published: January 2012

We have performed ab initio molecular dynamics simulations in conjunction with the multiscale shock technique to study the initial chemical processes of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under shock wave loading. The results show that the initial decomposition of shocked HMX is triggered by the N–O bond breaking and the ring opening. This will initiate many decomposition reactions and lead to the production of many small radicals at a moment. As the shock compression continues, these small radicals recombine to produce many large radicals and further form ring-shaped radicals. Then, these radicals begin to further decompose. It is also found that the system transiently produces a large number of metallic states under the shock compression. Our simulations thus suggest a new mechanism for the initial chemical processes of shocked HMX and provide fundamental insight into the initial mechanism at the atomistic level, which is of important implication for understanding and development of energetic materials.
Dynamics of solvent-free grafted nanoparticles
Authors: Chremos Alexandros , Panagiotopoulos Athanassios Z. , Koch Donald L.
Published: January 2012

The diffusivity and structural relaxation characteristics of oligomer-grafted nanoparticles have been investigated with simulations of a previously proposed coarse-grained model at atmospheric pressure. Solvent-free, polymer-grafted nanoparticles as well as grafted nanoparticles in a melt were compared to a reference system of bare (ungrafted) particles in a melt. Whereas longer chains lead to a larger hydrodynamic radius and lower relative diffusivity for grafted particles in a melt, bulk solvent-free nanoparticles with longer chains have higher relative diffusivities than their short chain counterparts. Solvent-free nanoparticles with short chains undergo a glass transition as indicated by a vanishing diffusivity, diverging structural relaxation time and the formation of body-centered-cubic-like order. Nanoparticles with longer chains exhibit a more gradual increase in the structural relaxation time with decreasing temperature and concomitantly increasing particle volume fraction. The diffusivity of the long chain nanoparticles exhibits a minimum at an intermediate temperature and volume fraction where the polymer brushes of neighboring particles overlap, but must stretch to fill the interparticle space.
Optimization of power and efficiency of thermoelectric devices with asymmetric thermal contacts
Authors: Yazawa Kazuaki , Shakouri Ali
Published: January 2012

We report the theoretical efficiency of thermoelectric power generation with asymmetric thermal contacts to reservoirs. A key ingredient is the electrical and thermal co-optimization. Generic formula of the maximum power output and the optimum leg length are obtained. The Curzon-Ahlborn limit at maximum power can be rigorously derived when the dimensionless figure-of-merit is very large for any asymmetric thermal contact resistances. The results differ from cyclic thermodynamic engines, and some of the reasons are discussed. We also point out the similarity and differences with single-level quantum dot heat engines, which assume no explicit thermal contact resistance with reservoirs.
Growth sector dependence and mechanism of stress formation in epitaxial diamond growth
Authors: Fischer M. , Gsell S. , Schreck M. , Bergmaier A.
Published: January 2012

Stress generation in epitaxial diamond growth was investigated by μ-Raman spectroscopy and high resolution x-ray diffraction. Intrinsic stress could be varied systematically from compressive to tensile covering a huge range of 5 GPa. The temperature-stress curve for growth on {111}-sectors as compared to {001} shows a shift of −200 °C or +2 GPa. A crucial role of hydrogen in the stress formation process is excluded. Due to the absence of grain boundaries, a model is proposed which is based on the “effective climb” of individual dislocations. The controlled generation of stress profiles offers a powerful concept for strengthening diamond mechanical devices.
Effective energy gap of the double-walled carbon nanotubes with field effect transistors ambipolar characteristics
Authors: Morimoto Takahiro , Kuno Akihiro , Yajima Shota , Ishibashi Koji , Tsuchiya Koji , Yajima Hirofumi
Published: January 2012

We have investigated the transport property of the double-walled carbon nanotubes (DWCNT)-field effect transistor (FET) devices with HfO2 insulating layers at room temperature and 4.2 K. These devices show the ambipolar FET characteristics after deposition of HfO2 insulating layer. The off-regions of ambipolar behavior have clear dependence on their DWCNT diameter. The conversion factor of gate voltages and bias voltages is estimated from low temperature Coulomb Diamond measurement. Using same device structure and dimensions to all devices, these off-regions of threshold voltage are converted to effective energy gap. These energy gaps are in good agreement with theoretical predictions.
Giant electro-mechanical energy conversion in [011] cut ferroelectric single crystals
Authors: Dong Wen D. , Finkel Peter , Amin Ahmed , Lynch Christopher S.
Published: January 2012

Giant electro-mechanical energy conversion is demonstrated under a ferroelectric/ferroelectric phase transformation in [011] cut and poled lead titanate-based relaxor perovskite morphotropic single crystals. It is found that under mechanical pre-stress, a relatively small oscillatory stress drives the material reversibly between rhombohedral and orthorhombic phases with a remarkably high polarization and strain jump induced at zero bias electric field and room temperature. The measured electrical output per cycle is more than an order of magnitude larger than that reported for linear piezoelectric materials. Ideal thermodynamic cycles are presented for this electro-mechanical energy conversion followed by a presentation and discussion of the experimental data.
Plasmon assisted light propagation and Raman scattering hot-spot in end-to-end coupled silver nanowire pairs
Authors: Chikkaraddy Rohit , Singh Danveer , Pavan Kumar G. V.
Published: January 2012

Herein, we report on the experimental observation of light propagation and localization capabilities of end-to-end connected silver nanowire (Ag NW) pairs. By exciting the surface plasmon polaritons at one end of Ag NW pair, we observed relatively intense light emission at the junction and weak light emission at the distal end of the pair. To probe the localization of light at nanowire junction, we captured far-field Raman image of an isolated Ag NW pair adsorbed with rhodamine 6 G and observed enhanced Raman scattering at the nanowire junction. Such nanophotonic modules with light propagation and localization capabilities can be harnessed for multiplexed on-chip plasmonics.
Surface plasmon resonance and surface-enhanced Raman scattering sensing enabled by digital versatile discs
Authors: Dou Xuan , Chung Pei-Yu , Jiang Peng , Dai Jianli
Published: January 2012

We report the simultaneous achievement of sensitive surface plasmon resonance (SPR) and surface-enhanced Raman scattering (SERS) sensing using digital versatile discs (DVDs). The aluminum-covered data tracks of DVDs can efficiently concentrate local electromagnetic field, resulting in an excellent SPR medium (with sensitivity of ∼850 nm per refractive index unit which is higher than that of most available nanofabricated plasmonic substrates) with a small but measurable SERS enhancement. The SPR sensitivity and the optical spectra, as well as the distribution of electric field amplitude, are simulated using a finite-difference time-domain model. The theoretical predictions agree reasonably well with the experimental results.
Enhanced magnetic properties of Dy3+ substituted Ni-Cu-Zn ferrite nanoparticles
Authors: Shirsath Sagar E. , Kadam R. H. , Patange S. M. , Mane M. L. , Ghasemi Ali , Morisako Akimitsu
Published: January 2012

Dy3+ substituted Ni-Cu-Zn (Ni0.4Cu0.4Zn0.2DyxFe2−xO4) ferrite nanoparticles were obtained at 600 °C by synthesizing sol-gel auto-combustion method, and they exhibit a particle size of 12–21 nm. X-ray diffraction patterns confirm the presence of secondary phase of DyFeO3 and Fe2O3 for the Dy3+ substituted samples. Ni-Cu-Zn ferries doped with Dy3+ possess better grain structure and growth than that of pure Ni-Cu-Zn ferrite. The saturation magnetization increases remarkably up to 81 emu/g with increasing the Dy3+ ions. The increased saturation magnetization related to increased exchange interactions between Fe-Fe ions and also with increased particle size. Blocking temperature was found to decrease with increasing Dy3+ substitution. An enhancement in initial permeability and Curie temperature was observed with Dy3+ substitution.
Recoverable electrical transition in a single graphene sheet for application in nonvolatile memories
Authors: Wu Chaoxing , Li Fushan , Zhang Yongai , Guo Tailiang
Published: January 2012

The electrical properties of a resistive-switching memory based on a single graphene sheet suspended on a patterned indium-tin-oxide electrode pair were investigated. Current-voltage measurements on the planar device showed a large ON/OFF ratio (∼106) and excellent retention ability in ambient conditions. Data storage of the device can be realized by applying voltage bias and rewritten after simple heat treatment. Switching mechanisms for the graphene-based memory device were found to be related to the local oxidation of graphene sheet at the graphene/electrode interface.
Communication: Correlation of the instantaneous and the intermediate-time elasticity with the structural relaxation in glassforming systems
Authors: Puosi F. , Leporini D.
Published: January 2012

The elastic models of the glass transition relate the increasing solidity of the glassforming systems with the huge slowing down of the structural relaxation and the viscous flow. The solidity is quantified in terms of the instantaneous shear modulus G∞, i.e., the immediate response to a step change in the strain. By molecular-dynamics simulations of a model polymer system, one shows the virtual absence of correlations between the instantaneous elasticity and the structural relaxation. Instead, a well-defined scaling is evidenced by considering the elastic response observed at intermediate times after the initial fast stress relaxation. The scaling regime ranges from sluggish states with virtually pure elastic response on the picosecond time scale up to high-mobility states where fast restructuring events are more apparent.
Reflection characteristics of a composite planar AMC surface
Authors: Hwang Ruey-Bing , Tsai Yueh-Lin
Published: January 2012

This study investigates the reflection characteristics of a composite Artificial Magnetic Conductor (AMC) surface consisting of multiple orthogonal gradient AMC surfaces arranged in a two-dimensional periodic pattern. The gradient AMC surface in this study consists of square metal patches of variable size printed on a grounded dielectric substrate. Due to the orthogonal placement of the gradient AMC surface, the incident energy of a plane wave normally incident on the composite AMC surface will be reflected into four major lobes away from the impinging direction. To achieve a systematical design, a simple formula based on array antenna theory was developed to determine the reflection pattern of the gradient AMC surface illuminated by a normal incident plane wave. A time-domain full-wave simulation was also carried out to calculate the electromagnetic fields in the structure and the far-field patterns. The scattering patterns of the structure were measured in an electromagnetic anechoic chamber. Results confirm the design principle and procedures in this research. Since such a composite AMC surface can be easily fabricated using the standard printed circuit board technique without via-hole process, it may have potential applications in beam-steering and radar cross section reduction.
Reconsidering the English Question as a Matter of Democratic Politics and Spatial Justice
Authors: Varró Krisztina
Published: January 2012

This paper is concerned with the implications of state territorial decentralization for the management of uneven regional development and spatial justice. It is argued that accounts of post-1997 UK devolution and the treatment of ‘the English question’ with a similar concern have tended to dismiss government policies against the backdrop of an uncritical view of spatial Keynesianism. Furthermore, these accounts have not succeeded in capturing the interconnectedness of the issues of democracy, solidarity, and spatial justice. In order to address these shortcomings I elaborate on a perspective that draws on insights of postfoundational political thought and interprets justice as democratic practice. This perspective reminds us that any notion of solidarity between people sharing a ‘national space’ and, consequently, any understanding of spatial justice is always politically constructed. Accordingly, the main task becomes to ‘unimagine’ the nation as a community of pregiven interests and to examine the obstacles to a meaningful debate on the institutional supports of solidarity.
Devolution, Institutions, and Organisations: Changing Models of Regional Development Agencies
Authors: Danson Mike , Lloyd Greg
Published: January 2012

Prior to devolution, Scotland, Wales, and Northern Ireland each had their own autonomous development organisations to undertake and promote regional economic planning and development within their respective territories. These operated within a national UK regional policy framework. An expectation of devolution was that the development organisations would continue to evolve in different ways according to the prevailing and anticipated economic conditions and differentiated needs and priorities of the regional economies. Indeed, the model was further extended. In England, for example, regional development agencies were established as an integral part of the new intended Regional Assembly infrastructure—providing important economic development delivery functions to the new political bodies. In general terms, a more effective integration of planning, infrastructure provision, business development and investment, and economic development was anticipated at the regional level. This was held as an effective means of contributing to national economic growth and competitiveness objectives: themselves key and pivotal rationales for political devolution. On the basis of benchmarking exercises and academic and policy literature we review and analyse the significant changes that have taken place in the institutions which have been generated across the UK since the late 1990s, presenting and contrasting each nation's and region's experiences with an appreciation of their specific powers and resources.
Quantitative Analysis of Dye Decolourization Reactions in Mixed Micellar Systems of Sodium Dodecyl Sulfate with Tween-20, Tween-80, and Triton X-100
Authors: Lunkim Kimkholhing , Luwang M. Niraj , Srivastava Sri K.
Published: January 2012

The reaction of triphenylmethane dye (ethyl violet) with hydroxyl ion has been investigated in absence and presence of micelles. In micellar solutions, the solubilization of dye carbocation is observed. The reaction rate constant follows pseudo-first order kinetics with respect to the nucleophile. In presence of sodium dodecyl sulfate (SDS) micelles, an inhibitory effect is observed due to repulsion of the nucleophile to the strongly bound dye carbocation in the negatively charged SDS aggregate. The presence of nonionic surfactant reduces the inhibitory effect of the anionic SDS micelles. Quantitative analysis of the micellar data obtained has been done by applying a positive cooperativity model of enzyme catalysis. The value of n (index of cooperativity) has been found to be greater than 1 for all systems under study. The presence of solvents such as ethanol, n-propanol, and n-butanol reduces the inhibitory effect of the micelles.
Phosphorylation-dependent 14-3-3 protein interactions regulate CFTR biogenesis
Authors: Liang Xiubin , Da Paula Ana Carina , Bozóky Zoltán , Zhang Hui , Bertrand Carol A. , Peters Kathryn W. , Forman-Kay Julie D. , Frizzell Raymond A.
Published: January 2012

Cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP/protein kinase A (PKA)–regulated chloride channel whose phosphorylation controls anion secretion across epithelial cell apical membranes. We examined the hypothesis that cAMP/PKA stimulation regulates CFTR biogenesis posttranslationally, based on predicted 14-3-3 binding motifs within CFTR and forskolin-induced CFTR expression. The 14-3-3β, γ, and ε isoforms were expressed in airway cells and interacted with CFTR in coimmunoprecipitation assays. Forskolin stimulation (15 min) increased 14-3-3β and ε binding to immature and mature CFTR (bands B and C), and 14-3-3 overexpression increased CFTR bands B and C and cell surface band C. In pulse-chase experiments, 14-3-3β increased the synthesis of immature CFTR, reduced its degradation rate, and increased conversion of immature to mature CFTR. Conversely, 14-3-3β knockdown decreased CFTR B and C bands (70 and 55%) and elicited parallel reductions in cell surface CFTR and forskolin-stimulated anion efflux. In vitro, 14-3-3β interacted with the CFTR regulatory region, and by nuclear magnetic resonance analysis, this interaction occurred at known PKA phosphorylated sites. In coimmunoprecipitation assays, forskolin stimulated the CFTR/14-3-3β interaction while reducing CFTR's interaction with coat protein complex 1 (COP1). Thus 14-3-3 binding to phosphorylated CFTR augments its biogenesis by reducing retrograde retrieval of CFTR to the endoplasmic reticulum. This mechanism permits cAMP/PKA stimulation to make more CFTR available for anion secretion.
Midbody assembly and its regulation during cytokinesis
Authors: Hu Chi-Kuo , Coughlin Margaret , Mitchison Timothy J.
Published: January 2012

The midbody is a transient structure that connects two daughter cells at the end of cytokinesis, with the principal function being to localize the site of abscission, which physically separates two daughter cells. Despite its importance, understanding of midbody assembly and its regulation is still limited. Here we describe how the structural composition of the midbody changes during progression throughout cytokinesis and explore the functional implications of these changes. Deriving from midzones, midbodies are organized by a set of microtubule interacting proteins that colocalize to a zone of microtubule overlap in the center. We found that these proteins split into three subgroups that relocalize to different parts of the midbody: the bulge, the dark zone, and the flanking zone. We characterized these relocalizations and defined domain requirements for three key proteins: MKLP1, KIF4, and PRC1. Two cortical proteins—anillin and RhoA—localized to presumptive abscission sites in mature midbodies, where they may regulate the endosomal sorting complex required for transport machinery. Finally, we characterized the role of Plk1, a key regulator of cytokinesis, in midbody assembly. Our findings represent the most detailed description of midbody assembly and maturation to date and may help elucidate how abscission sites are positioned and regulated.
Infantile Eczema
Authors: Sandhu Manminder
Published: January 2012

Infantile eczema is an inflammatory itchy skin condition that affects at least 10% of infants at some stage in their lives. It can continue into childhood after the age of 18 months or adolescence where it is referred to as atopic eczema. There are various treatment options for infantile eczema according to its severity. The key role of the GP is to educate parents and carers about the diagnosis and management of eczema and provide support when required.
Delayed Environmental Enrichment Reverses Sevoflurane-induced Memory Impairment in Rats
Authors: Shih Jennifer , May Laura D. V. , Gonzalez Heidi E. , Lee Elaine W. , Alvi Rehan S. , Sall Jeffrey W. , Rau Vinuta , Bickler Philip E. , Lalchandani Gopal R. , Yusupova Marianna , Woodward Elliott , Kang Heejae , Wilk Alan J. , Carlston Colleen M. , Mendoza Mortay V. , Guggenheim Jeremy N. , Schaefer Maximilian , Rowe Allison M. , Stratmann Greg
Published: January 2012

Background

Anesthesia given to immature rodents causes cognitive decline, raising the possibility that the same might be true for millions of children undergoing surgical procedures under general anesthesia each year. We tested the hypothesis that anesthesia-induced cognitive decline in rats is treatable. We also tested if anesthesia-induced cognitive decline is aggravated by tissue injury.

Methods

Seven-day old rats underwent sevoflurane anesthesia (1 minimum alveolar concentration, 4 h) with or without tail clamping. At 4 weeks, rats were randomized to environmental enrichment or normal housing. At 8 weeks rats underwent neurocognitive testing, which consisted of fear conditioning, spatial reference memory, and water maze-based memory consolidation tests, and interrogated working memory, short-term memory, and early long-term memory.

Results

Sevoflurane-treated rats had a greater escape latency when the delay between memory acquisition and memory retrieval was increased from 1 min to 1 h, indicating that short-term memory was impaired. Delayed environmental enrichment reversed the effects of sevoflurane on short-term memory and generally improved many tested aspects of cognitive function, both in sevoflurane-treated and control animals. The performance of tail-clamped rats did not differ from those rats receiving anesthesia alone.

Conclusion

Sevoflurane-induced cognitive decline in rats is treatable. Delayed environmental enrichment rescued the sevoflurane-induced impairment in short-term memory. Tissue injury did not worsen the anesthesia-induced memory impairment. These findings may have relevance to neonatal and pediatric anesthesia.
Transactivation activity of human papillomavirus type 16 E6*I on aldo-keto reductase genes enhances chemoresistance in cervical cancer cells
Authors: Wanichwatanadecha Panata , Sirisrimangkorn Sasinan , Kaewprag Jittranan , Ponglikitmongkol Mathurose
Published: January 2012

The oncogenic E6 proteins produced by high-risk human papillomaviruses (HPVs) are invariably expressed in cervical carcinomas and are multifunctional proteins capable of affecting host-cell proliferation by binding and deregulating key host molecules such as p53. High-risk HPVs, including HPV16, have the unique ability to splice the E6 viral transcript, resulting in the production of a truncated E6 protein known as E6*I whose precise biological function is unclear. This study explored the changes in gene expression of the cervical cancer C33A cell line stably expressing HPV16 E6*I (16E6*I) and observed the upregulation of ten genes. Two of these genes were aldo-keto reductases (AKR1Cs), AKR1C1 and AKR1C3, which have been implicated in drug resistance. The results demonstrated that expression of 16E6*I, but not full-length E6, specifically increased AKR1C1 transcript levels although it did not alter AKR1C2 transcript levels. HPV16 E7 alone also had the ability to cause a moderate increase in AKR1C3 at both mRNA and protein levels. Site-directed mutagenesis of 16E6*I revealed that transactivation activity was abolished in R8A, R10A and T17A 16E6*I mutants without altering their intracellular localization patterns. Loss of transactivation activity of the 16E6*I mutants resulted in a significant loss of AKR1C expression and a decrease in drug resistance. Analysis of the AKR1C1 promoter revealed that, unlike the E6 protein, 16E6*I does not mediate transactivation activity solely through Sp1-binding sites. Taken together, it was concluded that 16E6*I has a novel function in upregulating expression of AKR1C and, in concert with E7, has implications for drug treatment in HPV-mediated cervical cancer.
Lytic Epstein–Barr virus infection in epithelial cells but not in B-lymphocytes is dependent on Blimp1
Authors: Buettner Maike , Lang Anke , Tudor Christiane S. , Meyer Birgit , Cruchley Alan , Barros Mario Henrique M. , Farrell Paul J. , Jäck Hans-Martin , Schuh Wolfgang , Niedobitek Gerald
Published: January 2012

Epstein–Barr virus (EBV) replicates in superficial differentiated cells of oral hairy leukoplakia (OHL). Differentiation of squamous epithelial cells depends on B-lymphocyte-induced maturation protein 1 (Blimp1). Here we show that expression of the EBV immediate-early protein BZLF1 is restricted to Blimp1-positive epithelial cells in OHL. Luciferase assays revealed Blimp1-dependent induction of the BZLF1 promoter Zp in epithelial cell lines. Expression of ZEB1, a negative regulator of Zp, and of Xbp-1, which mediates the Blimp1 effect on Zp in B-cells, was not affected by enforced Blimp1 expression. Moreover, Xbp-1 protein expression was not detected in differentiated epithelial cells of OHL. Thus, Blimp1 induces BZLF1 expression in epithelial cells independently of ZEB1 and Xbp-1. In contrast to epithelial cells of OHL, BZLF1 expression was also observed in Blimp1-negative lymphoid cells in infectious mononucleosis tonsils, suggesting that EBV replication in B-cells may be induced independently of terminal differentiation.
Crystallization and preliminary crystallographic analysis of LipC12, a true lipase isolated through a metagenomics approach
Authors: Martini V. P. , Glogauer A. , Iulek J. , Souza E. M. , Pedrosa F. O. , Krieger N.
Published: January 2012

LipC12, a true lipase from family I.1 of bacterial lipases which was previously isolated through a metagenomics approach, contains 293 amino acids. Among lipases of known three-dimensional structure, it has a sequence identity of 47% to the lipase fromPseudomonas aeruginosaPAO1. Recombinant N-terminally His6-tagged LipC12 protein was expressed inEscherichia coli, purified in a homogenous form and crystallized in several conditions, with the best crystals being obtained using 2.0 Msodium formate and 0.1 Mbis-tris propane pH 7.0. X-ray diffraction data were collected to 2.70 Å resolution. The crystals belonged to the tetragonal space groupP4122, with unit-cell parametersa=b= 58.62,c = 192.60 Å.
Crystallization and preliminary X-ray diffraction analysis of the metalloregulatory protein DtxR fromThermoplasma acidophilum
Authors: Yeo Hyun Ku , Kang Jina , Park Young Woo , Sung Jung-Suk , Lee Jae Young
Published: January 2012

The diphtheria toxin repressor (DtxR) is a metal-ion-dependent transcriptional regulator which regulates genes encoding proteins involved in metal-ion uptake to maintain metal-ion homeostasis. DtxR fromThermoplasma acidophilumwas cloned and overexpressed inEscherichia coli. Crystals of N-terminally His-tagged DtxR were obtained by hanging-drop vapour diffusion and diffracted to 1.8 Å resolution. DtxR was crystallized at 296 K using polyethylene glycol 4000 as a precipitant. The crystals belonged to the orthorhombic space groupP21212, with unit-cell parametersa= 61.14,b= 84.61,c= 46.91 Å, α = β = γ = 90°. The asymmetric unit contained approximately one monomer of DtxR, giving a crystal volume per mass (VM) of 2.22 Å3 Da−1and a solvent content of 44.6%.
Crystallization of oligonucleotides containing A-rich repeats suggests a structural contribution to the autoregulation mechanism of PABP translation
Authors: Kikuchi Keita , Shimizu Satoru , Sato Yoshiteru , Morishita Ella Czarina , Takénaka Akio
Published: January 2012

Eukaryotic poly(A)-binding protein (PABP) commonly binds to the 3′-UTR poly(A) tail of every mRNA, but it also binds to the 5′-UTR of PABP mRNA for autoregulation of its expression. In the sequence of the latter binding site, the contiguous A residues are segmented discretely by the insertion of short pyrimidine oligonucleotides as linkers, so that (A)6–8segments are repeated six times. This differs from the poly(A)-tail sequence, which has a higher binding affinity for PABP. In order to examine whether the A-rich repeats have a functional structure, several RNA/DNA analogues were subjected to crystallization. It was found that some of them could be crystallized. Single crystals thus obtained diffracted to 4.1 Å resolution. The fact that the repeated sequences can be crystallized suggests the possibility that the autoregulatory sequence in PABP mRNA has a specific structure which impedes the binding of PABP. When PABP is excessively produced, it could bind to this sequence by releasing the structure in order to interfere with initiation-complex formation for suppression of PABP translation. Otherwise, PABP at low concentration preferentially binds to the poly(A) tail of PABP mRNA.
Crystallization and preliminary X-ray crystallographic analysis of dioscorin fromDioscorea japonica
Authors: Xue You-Lin , Miyakawa Takuya , Sawano Yoriko , Tanokura Masaru
Published: January 2012

Dioscorin, the major tuber storage protein in yam, has been reported to possess carbonic anhydrase, trypsin inhibitor, angiotensin-converting enzyme (ACE) inhibitor, free-radical scavenger, dehydroascorbate reductase and monodehydroascorbate reductase activities. Recent research has also found that dioscorin can enhance immune modulationviathe toll-like receptor 4 (TLR-4) signal transduction pathway in RAW 264.7 cells, murine bone-marrow cells and human monocytesex vivo. Resolving the structure of dioscorin would help in better understanding its activities and would provide clues to understanding the mechanism of its multiple functions. The full-length protein (residues 1–246) with an additional His6tag at the N-terminus was expressed inEscherichia coliRosetta (DE3) cells. After His-tag cleavage and purification, the protein was crystallized by the sitting-drop vapour-diffusion method at 278 K. An X-ray diffraction data set was collected to a resolution of 2.11 Å using a synchrotron X-ray source. The crystal belonged to space groupC2221, with unit-cell parametersa= 83.5,b= 156.8,c = 83.6 Å, and was estimated to contain two protein molecules per asymmetric unit.
Crystallization and preliminary X-ray analysis ofS-ribosylhomocysteinase fromStreptococcus mutans
Authors: Li Hui , Zhao Hongyan , Zhu Laikuan , Hong Lihua , Zhang Hong , Lin Fanjing , Xu Chunyan , Li Shentao , Zhang Zhimin
Published: January 2012

S-Ribosylhomocysteinase (LuxS) encoded by theluxSgene fromStreptococcus mutansplays a crucial role in the quorum-sensing system. LuxS was solubly expressed inEscherichia coliwith high yield. The purity of the purified target protein, which was identified by SDS–PAGE and MALDI–TOF MS analysis, was >95%. The protein was crystallized using the hanging-drop vapour-diffusion method with PEG 3350 as the primary precipitant. X-ray diffraction data were collected at Beijing Synchrotron Radiation Facility (BSRF). Diffraction by the crystal extended to 2.4 Å resolution and the crystal belonged to space groupC2221, with unit-cell parametersa= 55.3,b= 148.7,c= 82.8 Å.
Crystallization and preliminary X-ray diffraction analysis ofBacillus subtilisYwfE, anL-amino-acid ligase
Authors: Tsuda Takeo , Suzuki Tomomi , Kojima Shuichi
Published: January 2012

Bacillus subtilisYwfE, an L-amino-acid ligase, catalyzes the formation of an α-dipeptide from L-amino acids in an ATP-dependent manner. In order to elucidate the substrate-recognition mode and the reaction mechanism of this ligase, native and selenomethionine-derivatized (SeMet) crystals of YwfE in the presence of ADP, MgCl2and the dipeptide L-Ala-L-Gln were obtained using the hanging-drop vapour-diffusion method. These crystals diffracted to 1.9 and 2.8 Å resolution, respectively. Preliminary SAD phase calculations using the data set from the SeMet crystal suggested that the crystal belonged to the hexagonal space groupP6522, with unit-cell parametersa=b= 90.85,c = 250.31 Å, and contained one molecule in the asymmetric unit with a solvent content of 57.3%.
Expression, purification and preliminary structural analysis of the coiled-coil domain ofDeinococcus radioduransRecN
Authors: Pellegrino Simone , de Sanctis Daniele , McSweeney Sean , Timmins Joanna
Published: January 2012

Deinococcus radioduranshas developed an efficient mechanism which allows the integrity of its entire genome to be fully restored after exposure to very high doses of ionizing radiation. Homologous recombination plays a crucial role in this process. RecN is a protein that belongs to the SMC-like protein family and is suggested to be involved in DNA repair. RecN is composed of a globular domain and an antiparallel coiled-coil region which connects the N- and C-termini. It has been suggested that dimerization of RecN occursviathe coiled-coil domain, but to date there is no structural or biochemical evidence for this. Here, SAXS studies and preliminary X-ray diffraction data of crystals of the purified coiled-coil domain of RecN are presented. The structure was solved by single-wavelength anomalous dispersion using SeMet derivatives, and preliminary electron-density maps support the rod-like model derived from the SAXS data. Model building and refinement are still ongoing.
Crystallization and X-ray diffraction analysis of a novel surface-adhesin protein: protein E fromHaemophilus influenzae
Authors: Singh Birendra , Al Jubair Tamim , Förnvik Karolina , Thunnissen Marjolein M. , Riesbeck Kristian
Published: January 2012

Protein E (PE) is a ubiquitous multifunctional surface protein ofHaemophilusspp. and other bacterial pathogens of thePasteurellaceaefamily.H. influenzaeutilizes PE for attachment to respiratory epithelial cells. In addition, PE interacts directly with plasminogen and the extracellular matrix (ECM) components vitronectin and laminin. Vitronectin is a complement regulator that inhibits the formation of the membrane-attack complex (MAC). PE-mediated vitronectin recruitment at theH. influenzaesurface thus inhibits MAC and protects against serum bactericidal activity. Laminin is an abundant ECM protein and is present in the basement membrane that helps in adherence of H. influenzaeduring colonization. Here, the expression, purification and crystallization of and the collection of high-resolution data for this importantH. influenzaeadhesin are reported. To solve the phase problem for PE, Met residues were introduced and an SeMet variant was expressed and crystallized. Both native and SeMet-containing PE gave plate-like crystals in space groupP21, with unit-cell parametersa= 44,b= 57,c= 61 Å, β = 96°. Diffraction data collected from native and SeMet-derivative crystals extended to resolutions of 1.8 and 2.6 Å, respectively.
Purification, crystallization and preliminary X-ray diffraction analysis of the Hsp40 protein CPIP1 fromNicotiana tabacum
Authors: Griessl Martin H. , Jungkunz Isabel , Sonnewald Uwe , Muller Yves A.
Published: January 2012

Chaperones promote many different molecular processes, including the folding, targeting and degradation of proteins. The best-studied chaperone system consists of the Hsp70s and their co-chaperones the Hsp40s. Chaperone function can be hijacked by viruses in plants.Potato virus Yinteractsviaits coat protein with an Hsp40 fromNicotiana tabacum, referred to as NtCPIP1, in order to regulate replication. To understand the molecular determinants of this mechanism, different variants of NtCPIP1 were expressed, purified and crystallized. While crystals of wild-type NtCPIP1 diffracted to 8.0 Å resolution, the deletion mutant NtCPIP1-Δ(1:127) crystallized in space groupP21212 and diffracted to 2.4 Å resolution.
Refolding, purification and crystallization of the FrpB outer membrane iron transporter fromNeisseria meningitidis
Authors: Saleem Muhammad , Prince Stephen M. , Patel Hema , Chan Hannah , Feavers Ian M. , Derrick Jeremy P.
Published: January 2012

FrpB is an integral outer membrane protein from the human pathogenNeisseria meningitidis. It is a member of the TonB-dependent transporter family and promotes the uptake of iron across the outer membrane. There is also evidence that FrpB is an antigen and hence a potential component of a vaccine against meningococcal meningitis. FrpB incorporating a polyhistidine tag was overexpressed inEscherichia coliinto inclusion bodies. The protein was then solubilized in urea, refolded and purified to homogeneity. Two separate antigenic variants of FrpB were crystallized by sitting-drop vapour diffusion. Crystals of the F5-1 variant diffracted to 2.4 Å resolution and belonged to space groupC2, with unit-cell parametersa= 176.5,b= 79.4,c= 75.9 Å, β = 98.3°. Crystal-packing calculations suggested the presence of a monomer in the asymmetric unit. Crystals of the F3-3 variant also diffracted to 2.4 Å resolution and belonged to space groupP212121, with unit-cell parametersa= 85.3,b = 104.6,c= 269.1 Å. Preliminary analysis suggested the presence of an FrpB trimer in the asymmetric unit.
Crystallization and preliminary X-ray analysis of theClostridium botulinumtype D nontoxic nonhaemagglutinin
Authors: Miyata Keita , Inui Ken , Miyashita Shin-Ichiro , Sagane Yoshimasa , Hasegawa Kimiko , Matsumoto Takashi , Yamano Akihito , Niwa Koichi , Watanabe Toshihiro , Ohyama Tohru
Published: January 2012

Clostridium botulinumproduces botulinum neurotoxin (BoNT) as a large toxin complex assembled with nontoxic nonhaemagglutinin (NTNHA) and/or haemagglutinin components. Complex formation with NTNHA is considered to be critical in eliciting food poisoning because the complex shields the BoNT from the harsh conditions in the digestive tract. In the present study, NTNHA was expressed inEscherichia coliand crystallized. Diffraction data were collected to 3.9 Å resolution. The crystal belonged to the trigonal space groupP321 orP3121/P3221, with unit-cell parametersa=b= 147.85,c= 229.74 Å. The structure of NTNHA will provide insight into the assembly mechanism that produces the unique BoNT–NTNHA complex.
The dynamic cytoskeleton of the developing male germ cell
Authors: Sperry Ann O.
Published: January 2012

Mammalian spermatogenesis is characterised by dramatic cellular change to transform the non‐polar spermatogonium into a highly polarised and functional spermatozoon. The acquisition of cell polarity is a requisite step for formation of viable sperm. The polarity of the spermatozoon is clearly demonstrated by the acrosome at the apical pole of the cell and the flagellum at the opposite end. Spermatogenesis consists of three basic phases: mitosis, meiosis and spermiogenesis. The final phase represents the period of greatest cellular change where cell‐type specific organelles such as the acrosome and the flagellum form, the nucleus migrates to the plasma membrane and elongates, chromatin condenses and residual cytoplasm is removed. An important feature of spermatogenesis is the change in the cytoskeleton that occurs throughout this pathway. In this review, the author will provide an overview of these transformations and provide insight into possible modes of regulation of these rearrangements during spermatogenesis. Although primary focus will be given to the microtubule cytoskeleton, the importance of actin filaments to the cellular transformation of the male germ cell will also be discussed.
Are shoals of minnowPhoxinus phoxinusformed by close kin?
Authors: Bernhardt B. , Lampert K. P. , Leese F. , Mayer C. , Tollrian R.
Published: January 2012

A molecular analysis examining the level of relatedness in shoaling minnowsPhoxinus phoxinuswas conducted. The results revealed that individuals from within the same shoal were not more closely related to each other than to individuals from other shoals. This led to the conclusion that Schreckstoff may be less likely to have evolved in the context of kin selection.
Replication and fine‐mapping of a QTL for recurrent airway obstruction in European Warmblood horses
Authors: Shakhsi‐Niaei M. , Klukowska‐Rötzler J. , Drögemüller C. , Swinburne J. , Ehrmann C. , Saftic D. , Ramseyer A. , Gerber V. , Dolf G. , Leeb T.
Published: January 2012

Recurrent airway obstruction (RAO), or ‘heaves’, is a common performance‐limiting allergic respiratory disease of mature horses. It is related to sensitization and exposure to mouldy hay and has a familial basis with a complex mode of inheritance. In a previous study, we detected a QTL for RAO on ECA 13 in a half‐sib family of European Warmblood horses. In this study, we genotyped additional markers in the family and narrowed the QTL down to about 1.5 Mb (23.7–25.2 Mb). We detected the strongest association with SNP BIEC2‐224511 (24 309 405 bp). We also obtained SNP genotypes in an independent cohort of 646 unrelated Warmblood horses. There was no genome‐wide significant association with RAO in these unrelated horses. However, we performed a genotypic association study of the SNPs on ECA 13 in these unrelated horses, and the SNP BIEC2‐224511 also showed the strongest association with RAO in the unrelated horses (praw = 0.00037). The T allele at this SNP was associated with RAO both in the family and the unrelated horses. Thus, the association study in the unrelated animals provides independent support for the previously detected QTL. The association study allows further narrowing of the QTL interval to about 0.5 Mb (24.0–24.5 Mb). We sequenced the coding regions of the genes in the critical region but did not find any associated coding variants. Therefore, the causative variant underlying this QTL is likely to be a regulatory mutation.
Understanding the evidence for and against the role of breastfeeding in allergy prevention
Authors: Matheson M. C. , Allen K. J. , Tang M. L. K.
Published: January 2012

The relationship between breastfeeding and allergic disease risk has been controversial. This article reviews the current evidence for the role of breastfeeding in the prevention of allergic disease. We found considerable methodological limitations inherent in most studies evaluating the effect of breastfeeding in allergic disease. Nevertheless, since randomized control trials in breast feeding research would be considered unethical, the evidence remains limited to poorer quality observational studies where participation and recall bias can severely affect the objectivity of the data collected. Furthermore, reporting of type of breastfeeding (exclusive, full or partial) may be biased by a participant's inherent belief system of what they think they should be doing. Current evidence is inconclusive regarding the effect of breastfeeding on the development of eczema, with the most recent systemic review reporting no protective effect. There is insufficient data regarding the effects of breastfeeding on objective measures of food allergy at any age. Studies show a paradoxical effect of breastfeeding on the prevention of asthma, with an apparent protective effect against early wheezing illness in the first years of life yet an increased risk of asthma in later life; however, these findings must be interpreted with caution. Existing studies fail to adequately adjust for confounders, including the critical issues of protection against early life respiratory illnesses and reverse causation. Therefore, it is possible that the effect of breastfeeding on early wheezing illness reflects protection against respiratory infection, the predominant trigger of wheezing in early childhood, rather than a true reduction in risk of asthma. In summary, future research that takes into account the potential contribution of confounding factors and effect modifiers is needed to clarify the role of breastfeeding in development of allergic disease and to inform current clinical guidelines on the prevention of allergic disease.
On the use of solute water fronts to measure nitrate adsorption in a Red Ferrosol
Authors: Smiles D. E. , Smith C. J. , Kirkham J.
Published: January 2012

Nitrogen leaching in soils depends on the mobility of nitrate with, and relative to, water. This mobility is affected by anion adsorption at soil surfaces. Our work examines nitrate (NO3−) adsorption during non‐steady, unsaturated absorption of NO3− solution by columns of dry Red Ferrosol (Inceptic Eutrudox), approximating solute transport in unsaturated field soils. The experiments, in which no water flows past the end of the column, show that the application of conventional water and reactive solute flow equations is valid. The profiles of water and NO3−, measured at different horizontal infiltration times, coalesce on to unique curves when plotted as a function of the Boltzmann variable, λ. Anion adsorption delays the NO3− advance relative to that of water. Pragmatically, we use Freundlich and Langmuir equations as convenient mathematical descriptions of how the NO3− is partitioned between the soluble and adsorbed concentrations and conclude that the latter is appropriate for our dataset. We advocate the use of the Langmuir equation (non‐linear form) to obtain the fitting parameters to avoid the need to use ratios of small values, which results in large errors. Absorption of a solution into unsaturated columns of soil provides a powerful method for exploring adsorption: the experiment implicitly tests the water flow equation, the salt flow equation and solute equilibrium between the water‐soluble and adsorbed phases.
Immunohistochemical features of post‐radiation vaginal recurrences of endometrioid carcinomas of the endometrium: role for proteins involved in resistance to apoptosis and hypoxia
Authors: Santacana Maria , Yeramian Andree , Velasco Ana , Bergada Laura , Gatius Sonia , García Virginia , Azueta Ainara , Palacios Jose , Dolcet Xavier , Oliva Esther , Matias‐Guiu Xavier
Published: January 2012

Santacana M, Yeramian A, Velasco A, Bergada L, Gatius S, García V, Azueta A, Palacios J, Dolcet X, Oliva E & Matias‐Guiu X  (2012) Histopathology 60, 460–471  Immunohistochemical features of post‐radiation vaginal recurrences of endometrioid carcinomas of the endometrium: role for proteins involved in resistance to apoptosis and hypoxia

Aims:  Endometrioid carcinoma of the endometrium (EEC) is treated with surgery and radiotherapy. Post‐radiation recurrences are associated with increased risk of metastases. Comparison of the expression of genes important in the development and progression of EEC, and others involved in resistance to apoptosis and hypoxia and adaptation to radiation, was performed between post‐radiation vaginal recurrences (PVRs) and primary EECs. We tried to reproduce the results by exposing an EEC cell line to hypoxia and radiation.

Methods and results:  Immunohistochemistry and tissue microarrays were used to compare 24 PVRs with 82 primary EECs. PVRs exhibited increased expression of p53 (P < 0.0001), cytoplasmic FLICE‐inhibitory protein (FLIP) (P < 0.0001), and Ki67 (P < 0.0001), and nuclear staining for FLIP, nuclear factor kappaB (NF‐κB) family members (p50, P < 0.0001; c‐Rel, P = 0.0077; RelB, P = 0.0157), and β‐catenin (P = 0.0001). Differences regarding p50, hypoxia‐inducible factor 1α (HIF‐1α), and cytoplasmic FLIP were statistically significant when PVRs and primary EECs were matched for histological grade. Exposure of the EEC cell line to hypoxia induced nuclear expression of β‐catenin, FLIP, and HIF‐1α, as well as increased NF‐κB activity. No changes in FLIP, HIF‐1α or NF‐κB were seen when cells were exposed to radiation. Nuclear expression of β‐catenin was seen at 3 Gy, but not at 1 Gy.

Conclusions:  Genes involved in resistance to hypoxia are expressed in PVRs, and may play a role in the development of post‐radiation recurrences.