bluuebunny/crossref_metadata_2025 huggingface dataset:
Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates
Authors: Bailly Xavier , Giuntini Elisa , Sexton M Connor , Lower Ryan P J , Harrison Peter W , Kumar Nitin , Young J Peter W
Published: May 2011

We investigated the genomic diversity of a local population of the symbiotic bacterium Sinorhizobium medicae, isolated from the roots of wild Medicago lupulina plants, in order to assess genomic diversity, to identify genomic regions influenced by duplication, deletion or strong selection, and to explore the composition of the pan-genome. Partial genome sequences of 12 isolates were obtained by Roche 454 shotgun sequencing (average 5.3 Mb per isolate) and compared with the published sequence of S. medicae WSM 419. Homologous recombination appears to have less impact on the polymorphism patterns of the chromosome than on the chromid pSMED01 and megaplasmid pSMED02. Moreover, pSMED02 is a hot spot of insertions and deletions. The whole chromosome is characterized by low sequence polymorphism, consistent with the high density of housekeeping genes. Similarly, the level of polymorphism of symbiosis genes (low) and of genes involved in polysaccharide synthesis (high) may reflect different selection. Finally, some isolates carry genes that may confer adaptations that S. medicae WSM 419 lacks, including homologues of genes encoding rhizobitoxine synthesis, iron uptake, response to autoinducer-2, and synthesis of distinct polysaccharides. The presence or absence of these genes was confirmed by PCR in each of these 12 isolates and a further 27 isolates from the same population. All isolates had rhizobitoxine genes, while the other genes were co-distributed, suggesting that they may be on the same mobile element. These results are discussed in relation to the ecology of Medicago symbionts and in the perspective of population genomics studies.
Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation
Authors: Santoro Alyson E , Casciotti Karen L
Published: May 2011

Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98–99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonia (NH3) to nitrite (NO2−). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (15ɛNH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal 15ɛNH3 ranged from 13‰ to 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by 15ɛNH3 is similar.
Validity of Weight Loss to Estimate Improvement in Body Composition in Individuals Attending a Wellness Center
Authors: Cruz Paulina , Johnson Bruce D. , Karpinski Susan C. , Limoges Katherine A. , Warren Beth A. , Olsen Kerry D. , Somers Virend K. , Jensen Michael D. , Clark Matthew M. , Lopez‐Jimenez Francisco
Published: May 2011

The accuracy of weight loss in estimating successful changes in body composition (BC), namely fat mass (FM) loss, is not known and was addressed in our study. To assess the correlation between change in body weight and change in FM, fat% and fat‐free mass (FFM), 465 participants (41% male; 41 ± 13 years), who met the criteria for weight change assessment at a wellness center, underwent air‐displacement plethysmography (ADP). Body weight and BC were measured at the same time. We categorized the change in body weight, FM and FFM as an increase if there was >1 kg gain, a decrease if there was >1 kg loss and no change if the difference was ≤1 kg. We estimated the diagnostic performance of weight change to identify improvement in BC. After a median time of 132 days, there was a mean weight change was 2.4 kg. From the 255 people who lost >1 kg of weight, 216 (84.7%) had lost >1 kg of FM, but 69 (27.1%) had lost >1 kg of FFM. Of the 143 people with no weight change, 42 (29.4%) had actually lost >1 kg of FM. Of the 67 who gained >1 kg of weight at follow‐up, in 23 (34.3%) this was due to an increase in FFM but not in FM. Weight change had a NPV of 73%. Our results indicate that favorable improvements in BC may go undetected in almost one‐third of people whose weight remains the same and in one‐third of people who gain weight after attending a wellness center. These results underscore the potential role of BC measurements in people attempting lifestyle changes.
Validation of Ussing Chamber Technology to Study Satiety Hormone Release From Human Duodenal Specimens
Authors: Geraedts Maartje C.P. , Troost Freddy J. , De Ridder Rogier J. , Bodelier Alexander G.L. , Masclee Ad A.M. , Saris Wim H.M.
Published: May 2011

By developing novel screening technologies to test effects of food ingredients on hormone release, which are comparable to the in vivo situation, fewer tests may have to be performed using volunteers, whereas it still provides information that can be extrapolated to the human situation. In an in vivo intervention study, 10 lean (BMI: 20–25 kg/m2) and 10 obese (BMI >30 kg/m2) were recruited. All subjects randomly received pea protein (PP) solutions or placebo, orally and intraduodenally. Cholecystokinin (CCK) and glucagon like peptide 1 (GLP‐1) release was measured over 2 h. During the oral interventions, gastrointestinal (GI) fluids were retrieved. For the present ex vivo study, duodenal biopsies were taken and placed in Ussing chambers. The luminal side was exposed to PP, placebo, intraduodenal fluid after oral PP‐intake and oral placebo–intake in vivo, and a commercial pea‐hydrolysate for 2 h. CCK and GLP‐1 levels were measured at the serosal side. After intraduodenal PP administration in vivo, the area under the curve (AUC) for both CCK and GLP‐1 was significantly increased in both lean and obese subjects. In the ex vivo study, exposure to PP resulted in significantly elevated levels of CCK and GLP‐1 compared to all other test solutions. These results indicate that the ex vivo Ussing chamber technology is a valid alternative for in vivo studies, and may therefore serve as a suitable screening tool for studying the effects of nutritional compounds on the release of satiety hormones.
Observations of Marketing on Food Packaging Targeted to Youth in Retail Food Stores
Authors: Grigsby‐Toussaint Diana S. , Moise Imelda K. , Geiger Sarah D.
Published: May 2011

There is growing evidence that exposure to food marketing influences dietary preferences among youth. Few studies exploring this association, however, have focused on the retail food store environment where families negotiate the influence of food and beverage marketing on purchasing practices. Consequently, we sought to examine: (i) the extent to which foods marketed on the internet and television to youth are also available and marketed in retail food stores, and (ii) whether differences exist in the marketing practices across store types and by neighborhood racial composition. In 2008, a cross‐sectional survey of 118 food stores was conducted in four Midwestern cities in the United States. Results showed that 82% of stores assessed carried items commonly marketed to youth via television or the internet. The items most likely to have some type of marketing technique were noncarbonated drinks (97.7%), fruit and cereal bars (76.9%), and soda (62.2%). Grocery stores were significantly more likely than convenience stores to have marketing for breads and pastries (34.6% vs. 17.9%), breakfast cereals (52.0% vs. 22.9%), cookies and crackers (54.2% vs. 25.3%), dairy (70.8% vs. 42.7%), and ice cream (23.8% vs. 9.8%). Stores located in black neighborhoods were significantly more likely to have marketing, in comparison to white neighborhoods, for breads and pastries (35.7% vs. 17.1%), breakfast cereals (44.4% vs. 25.0%), and cookies and crackers (48.1% vs. 26.3%). Our results highlight the importance of examining food marketing techniques in the retail food store environment, where visual cues from television and the internet may be reinforced.
Changes in the Obesity Phenotype Within Canadian Children and Adults, 1981 to 2007–2009
Authors: Janssen Ian , Shields Margot , Craig Cora L. , Tremblay Mark S.
Published: May 2011

We investigated whether the relationships between BMI, waist circumference (WC), and sum of 5 skinfolds (S5S) have changed over time in Canadians. Anthropometric data on 7–69 year old from national representative surveys conducted in 1981 (n = 15,688) and 2007–2009 (n = 4,987) were examined. WC and S5S were regressed on BMI while controlling for age in each survey by sex and age group (child, adult). The results indicate that increases in WC and SFS for a one unit increase in BMI were higher in 2007–2009 than in 1981. For example, in 20–69 year old women in 1981 an increase in BMI of 1 kg/m2 was associated with corresponding increases of 1.98 cm in WC and 6.10 mm in SFS; these values increased to 2.22 cm and 7.60 mm, respectively, in 2007–2009. In conclusion, present day Canadians have higher WC and skinfold thickness values for a given BMI than Canadians did 30 years ago.
Nonthermal illumination effects on ultra-shallow junction formation
Authors: Vaidyanathan Ramakrishnan , Felch Susan , Graoui Houda , Foad Majeed A. , Kondratenko Yevgeniy , Seebauer Edmund G.
Published: May 2011

In this letter, we present direct and unambiguous experimental evidence for nonthermal illumination effects in boron or arsenic implanted silicon. Both, dopant diffusion and activation vary significantly with illumination. Depending on annealing temperature, diffusion is either enhanced or inhibited. The results have significant implications for modeling and formation of ultrashallow junctions.
Electron shear-flow-driven instability in magnetized plasmas with magnetic field gradient
Authors: Saleem Hamid , Eliasson Bengt
Published: May 2011

It is found that the zero-order current associated with electron shear flow produces a drift wave in magnetized plasmas, which can become unstable under certain conditions. This wave will be particularly important in low density and low temperature plasmas of heavy ions. As an example, numerical estimates are presented for a barium plasma with parameters compatible with experiments.
Levi-Civita cylinders with fractional angular deficit
Authors: Krisch J. P. , Glass E. N.
Published: May 2011

The angular deficit factor in the Levi-Civita vacuum metric has been parametrized using a Riemann-Liouville fractional integral. This introduces a new parameter into the general relativistic cylinder description, the fractional index α. When the fractional index is continued into the negative α region, new behavior is found in the Gott-Hiscock cylinder and in an Israel shell.
Electric field and spatial charge formation in glasses and glassy nanocomposites
Authors: Petrov M. I. , Omelchenko A. V. , Lipovskii A. A.
Published: May 2011

This paper concerns to rigorous analysis of the electrodiffusion problem arising during electric field treatment of glasses and glass metal nanocomposites (e.g. glass poling effect). The strict solution of the carrier drift equations for two type ions differing in mobility and diffusion coefficient is obtained. This solution allows finding out the duration of space charge buildup and determining the limits of electroneutrality approximation. The rigorous solution demonstrates a good agreement with experimental data. The results of numerical solution are discussed as well.
Formation and mechanism of ultrahigh density platinum nanoparticles on vertically grown graphene sheets by metal-organic chemical supercritical fluid deposition
Authors: Mase Kota , Kondo Hiroki , Kondo Shingo , Hori Masaru , Hiramatsu Mineo , Kano Hiroyuki
Published: May 2011

An ultrahigh density over 1013 cm−2 of 2 nm diameter Pt nanoparticles was obtained by metal-organic chemical supercritical fluid deposition over the entire surface of vertically standing stacked graphene sheets (carbon nanowalls) on a substrate. The correlation between the surface defect density of graphene sheets and the density of Pt nanoparticles were investigated to clarify the support mechanism. The density of Pt nanoparticles increased with increase in the surface defect density. In addition, the semispherical cross-sectional shape of the nanoparticles indicated nucleation at the surface defects on the graphene sheets (98/100).
Large strain transduction utilizing phase transition in relaxor-ferroelectric Pb(In1/2Nb1/2)O3–Pb(Mg1/3Nb2/3)O3–PbTiO3 single crystals
Authors: Finkel Peter , Benjamin Kim , Amin Ahmed
Published: May 2011

In this work, we present experimental evidence that under relatively low level drive (<0.1 MV/m) the large strain (∼0.5%) associated with ferroelectric rhombohedral FR-ferroelectric orthorhombic FO phase transition in domain engineered relaxor–ferroelectric single crystals under compressive stress and bias electric field can be captured. We have demonstrated this in mechanically confined ternary Pb(In1/2Nb1/2)O3–Pb(Mg1/3Nb2/3)O3–PbTiO3 single crystals poised at the rhombohedral side of the morphotropic phase boundary. Experimental strain-field results, methods of mechanical confinement and drive, and a low frequency, compact, high source level sound projector design are presented. Transducers that operate on a large strain principle as a design rule will benefit from this development.
Cryogenic apparatus for study of near-field heat transfer
Authors: Kralik T. , Hanzelka P. , Musilova V. , Srnka A. , Zobac M.
Published: May 2011

For bodies spaced in vacuum at distances shorter than the wavelength of the thermal radiation, radiative heat transfer substantially increases due to the contribution of evanescent electromagnetic waves. Experimental data on heat transfer in near-field regime are scarce. We have designed a cryogenic apparatus for the study of heat transfer over microscopic distances between metallic and non-metallic surfaces. Using a mechanical positioning system, a planeparallel gap between the samples, concentric disks, each 35 mm in diameter, is set and varied from 100 to 103 μm. The heat transferred from the hot (10 – 100 K) to the cold sample (∼5 K) sinks into a liquid helium bath through a thermal resistor, serving as a heat flux meter. Transferred heat power within ∼2 nW/cm2 and ∼30 μW/cm2 is derived from the temperature drop along the thermal resistor. For tungsten samples, the distance of the near-field effect onset was inversely proportional to temperature and the heat power increase was observed up to three orders of magnitude greater than the power of far-field radiative heat transfer.
Role of anisotropic thermal conductivity in the reversed-field pinch dynamics
Authors: Onofri M. , Malara F. , Veltri P.
Published: May 2011

Two compressible magnetohydrodynamics simulations of the reversed-field pinch are performed, with isotropic and anisotropic thermal conductivity. We describe in detail the numerical method we use to reproduce the effect of a large parallel thermal conductivity, which makes magnetic field lines almost isothermal. We compare the results of the two simulations, showing that the anisotropic thermal conductivity causes the formation of a hot island when closed magnetic surfaces exist, while temperature becomes almost uniform when the magnetic field is chaotic. After a transient single-helicity state that is formed in the initial phase, a stationary state is reached where the RFP configuration exists in a multiple helicity state, even though the Hartmann number is below the threshold found in previous simulations for the formation of multiple helicity states.
Chemical and topological short-range order evolution of Mg65Cu25Gd10 alloy in the process of rapid solidification
Authors: Liu D. , Pan S. P. , Qin J. Y. , Gu T. K.
Published: May 2011

The structural evolution of Mg65Cu25Gd10 alloy from liquid to glass state was investigated by ab initio molecular dynamics simulations. From 500 K, the splitting of the second peaks of the three partial pair correlation functions related to Mg has been perceived which implicates that short-range order is strengthened owing to the atomic rearrangement during the quenching process; medium-range order up to 7.59 Å has been observed from gcc(r) curves. The Gd-centered Voronoi polyhedron with index of 〈 0, 1, 10, 5 〉 was observed to increase drastically to an extraordinary level as the melt transformed to glass at 500 K, suggesting that it plays important role to keep the amorphous system stable. The variation of diffusion coefficients indicates that the solidification occurred at the temperature between 750 and 500 K.
Molecular weight distributions of irradiated siloxane-based elastomers: A complementary study by statistical modeling and multiple quantum nuclear magnetic resonance
Authors: Dinh L. N. , Mayer B. P. , Maiti A. , Chinn S. C. , Maxwell R. S.
Published: May 2011

The statistical methodology of population balance (PB) has been applied in order to predict the effects of cross-linking and chain-scissioning induced by ionizing radiation on the distribution of molecular weight between cross-links (MWBC) of a siloxane-based elastomer. Effective molecular weight distributions were extracted from the quantification of residual dipolar couplings via multiple quantum nuclear magnetic resonance (MQ-NMR) measurements and are taken to reflect actual MWBC distributions. The PB methodology is then applied to the unirradiated MWBC distribution and considers both chain-scissioning and the possibility of the formation of three types of cross-links: random recombination of scissioned-chain ends (end-linking), random covalent bonds of free radicals on scissioned-chain ends (Y-cross-linking), and the formation of random cross-links from free radicals on side groups (H-cross-linking). The qualitative agreement between the statistical modeling approach and the NMR data confirms that it is possible to predict trends for the evolution of the distribution of MWBC of polymers under irradiation. The approach described herein can also discern heterogeneities in radiation effects in different structural motifs in the polymer network.
Large peak-to-valley ratio of negative-differential-conductance in graphene p-n junctions
Authors: Hung Nguyen V. , Bournel A. , Dollfus P.
Published: May 2011

We investigate the transport characteristics of monolayer graphene p-n junctions by means of the nonequilibrium Green’s function technique. It is shown that due to the high interband tunneling of chiral fermions and a finite bandgap opening when the inversion symmetry of the graphene plane is broken, a strong negative-differential-conductance behavior with a peak-to-valley ratio as large as a few tens can be achieved even at room temperature. The dependence of this behavior on the device parameters such as the Fermi energy, the barrier height, and the transition length is then discussed.
Measurement of optical-beat frequency in a photoconductive terahertz-wave generator using microwave higher harmonics
Authors: Murasawa Kengo , Sato Koki , Hidaka Takehiko
Published: May 2011

A new method for measuring optical-beat frequencies in the terahertz (THz) region using microwave higher harmonics is presented. A microwave signal was applied to the antenna gap of a photoconductive (PC) device emitting a continuous electromagnetic wave at about 1 THz by the photomixing technique. The microwave higher harmonics with THz frequencies are generated in the PC device owing to the nonlinearity of the biased photoconductance, which is briefly described in this article. Thirteen nearly periodic peaks in the photocurrent were observed when the microwave was swept from 16 to 20 GHz at a power of −48 dBm. The nearly periodic peaks are generated by the homodyne detection of the optical beat with the microwave higher harmonics when the frequency of the harmonics coincides with the optical-beat frequency. Each peak frequency and its peak width were determined by fitting a Gaussian function, and the order of microwave harmonics was determined using a coarse (i.e., lower resolution) measurement of the optical-beat frequency. By applying the Kalman algorithm to the peak frequencies of the higher harmonics and their standard deviations, the optical-beat frequency near 1 THz was estimated to be 1029.81 GHz with the standard deviation of 0.82 GHz. The proposed method is applicable to a conventional THz-wave generator with a photomixer.
Atomic level micromagnetic model of recording media switching at elevated temperatures
Authors: Mercer J. I. , Plumer M. L. , Whitehead J. P. , van Ek J.
Published: May 2011

An atomic level micromagnetic model of granular recording media is developed and applied to examine external field-induced grain switching at elevated temperatures which captures nonuniform reversal modes. The results are compared with traditional methods which employ the Landau–Lifshitz–Gilbert equations based on uniformly magnetized grains with assigned intrinsic temperature profiles for M(T) and K(T). Using nominal parameters corresponding to high-anisotropy FePt-type media envisioned for energy assisted magnetic recording, our results demonstrate that atomic-level reversal slightly reduces the field required to switch grains at elevated temperatures, but results in larger fluctuations, when compared to a uniformly magnetized grain model.
Memory characteristics of ordered Co/Al2O3 core-shell nanocrystal arrays assembled by diblock copolymer process
Authors: Zhou Huimei , Dorman James A. , Perng Ya-Chuan , Gachot Stephanie , Zheng Jian-Guo , Chang Jane P. , Liu Jianlin
Published: May 2011

An ordered Co/Al2O3 core-shell nanocrystal (NC) nonvolatile memory device was fabricated. Self-assembled diblock copolymer process aligned the NCs with uniform size. Co/Al2O3 core-shell NCs were formed using atomic layer deposition of Al2O3 before and after the ordered Co NC formation. Compared to Co NC memory, Co/Al2O3 core-shell NC memory shows improved retention performance without sacrificing writing and erasing speeds.
Coherent-feedback control strategy to suppress spontaneous switching in ultralow power optical bistability
Authors: Mabuchi Hideo
Published: May 2011

An optical resonator with intracavity Kerr nonlinearity can exhibit dispersive bistability suitable for all-optical switching. With nanophotonic elements it may be possible to achieve attojoule switching energies, which would be very attractive for ultralow power operation but potentially problematic because of quantum fluctuation-induced spontaneous switching. In this letter I derive a quantum-optical model of two Kerr-nonlinear ring resonators connected in a coherent-feedback loop and show via numerical simulation that a properly designed “controller” cavity can significantly reduce the spontaneous switching rate of a bistable “plant” cavity in a completely embedded and autonomous manner.
Thermal transport in nanoclusters
Authors: Desai Tapan G.
Published: May 2011

Nonequilibrium and equilibrium molecular dynamics simulations are employed to study the thermal transport in sintered silicon nanoclusters made of 15 nm diameter nanoparticles arranged on a simple cubic lattice. Both simulation techniques indicate a reduction in the thermal conductivity from ∼120 W/m K (bulk) to 1.5 W/m K (nanoclusters) at 500 K. This dramatic reduction is attributed to the reduced thermal conductivity of nanoparticle (15 W/m K) and most prominently to the nanosized constriction resistance due to necking between the two nanoparticles. Comparison with the existing models, radial distribution function and vibrational analysis show that the phonon transport in the nanosized neck region is ballistic rather than diffusive.
Electrokinetic trapping at the one nanometer limit
Authors: Fields Alexander P. , Cohen Adam E.
Published: May 2011

Anti-Brownian electrokinetic traps have been used to trap and study the free-solution dynamics of large protein complexes and long chains of DNA. Small molecules in solution have thus far proved too mobile to trap by any means. Here we explore the ultimate limits on trapping single molecules. We developed a feedback-based anti-Brownian electrokinetic trap in which classical thermal noise is compensated to the maximal extent allowed by quantum measurement noise. We trapped single fluorophores with a molecular weight of < 1 kDa and a hydrodynamic radius of 6.7 Å for longer than one second, in aqueous buffer at room temperature. This achievement represents an 800-fold decrease in the mass of objects trapped in solution, and opens the possibility to trap and manipulate any soluble molecule that can be fluorescently labeled. To illustrate the use of this trap, we studied the binding of unlabeled RecA to fluorescently labeled single-stranded DNA. Binding of RecA induced changes in the DNA diffusion coefficient, electrophoretic mobility, and brightness, all of which were measured simultaneously and on a molecule-by-molecule basis. This device greatly extends the size range of molecules that can be studied by room temperature feedback trapping, and opens the door to further studies of the binding of unmodified proteins to DNA in free solution.
Systematic identification of immunodominant CD8+T-cell responses to influenza A virus in HLA-A2 individuals
Authors: Wu Chao , Zanker Damien , Valkenburg Sophie , Tan Bee , Kedzierska Katherine , Zou Quan Ming , Doherty Peter C. , Chen Weisan
Published: May 2011

Immunodominant T-cell responses are important for virus clearance. However, the identification of immunodominant T-cell peptide + HLA glycoprotein epitopes has been hindered by the extent of HLA polymorphism and the limitations of predictive algorithms. A simple, systematic approach has been used here to screen for immunodominant CD8+T-cell specificities. The analysis targeted healthy HLA-A2+donors to allow comparison with responses to the well-studied influenza matrix protein 1 epitope. Although influenza matrix protein 1 was consistently detected in all individual samples in our study, the response to this epitope was only immunodominant in three of eight, whereas for the other five, prominent CD8+T-cell responses tended to focus on various peptides from the influenza nucleoprotein that were not presented by HLA-A2. Importantly, with the four immunodominant T-cell epitopes identified here, only one would have been detected by the current prediction programs. The other three peptides would have been either considered too long or classified as not containing typical HLA binding motifs. Our data stress the importance of systematic analysis for discovering HLA-dependent, immunodominant CD8+T-cell epitopes derived from viruses and tumors. Focusing on HLA-A2 and predictive algorithms may be too limiting as we seek to develop targeted immunotherapy and vaccine strategies that depend on T cell-mediated immunity.
Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion
Authors: Meinhold Derrick W. , Wright Peter E.
Published: May 2011

Detailed understanding of protein function and malfunction hinges on the ability to characterize transiently populated states and the transitions between them. Here, we use
15
N,

, and
13
CO NMR
R
2
relaxation dispersion to investigate spontaneous unfolding and refolding events of native apomyoglobin. Above pH 5.0, dispersion is dominated by processes involving fluctuations of the F-helix region, which is invisible in NMR spectra. Measurements of
R
2
dispersion for residues contacted by the F-helix region in the native (N) structure reveal a transient state formed by local unfolding of helix F and undocking from the protein core. A similar state was detected at pH 4.75–4.95 and determined to be an on-pathway intermediate (I1) in a linear three-state unfolding scheme (N⇆I1⇆MG) leading to a transiently populated molten globule (MG) state. The slowest steps in unfolding and refolding are N → I1 (36 s
-1
) and MG → I1 (26 s
-1
), respectively. Differences in chemical shift between N and I1 are very small, except in regions adjacent to helix F, showing that their core structures are similar. Chemical shift changes between the N and MG states, obtained from
R
2
dispersion, reveal that the transient MG state is structurally similar to the equilibrium MG observed previously at high temperature and low pH. Analysis of MG state chemical shifts shows the location of residual helical structure in the transient intermediate and identifies regions that unfold or rearrange into nonnative structure during the N → MG transition. The experiments also identify regions of energetic frustration that “crack” during unfolding and impede the refolding process.
Helicobacter pylori
cytotoxin-associated gene A (CagA) subverts the apoptosis-stimulating protein of p53 (ASPP2) tumor suppressor pathway of the host
Authors: Buti Ludovico , Spooner Eric , Van der Veen Annemarthe G. , Rappuoli Rino , Covacci Antonello , Ploegh Hidde L.
Published: May 2011

Type I strains of
Helicobacter pylori
(Hp) possess a pathogenicity island,
cag
, that encodes the effector protein cytotoxin-associated gene A (CagA) and a type four secretion system. After translocation into the host cell, CagA affects cell shape, increases cell motility, abrogates junctional activity, and promotes an epithelial to mesenchymal transition-like phenotype. Transgenic expression of CagA enhances gastrointestinal and intestinal carcinomas as well as myeloid and B-cell lymphomas in mice, but the mechanism of the induced cancer formation is not fully understood. Here, we show that CagA subverts the tumor suppressor function of apoptosis-stimulating protein of p53 (ASPP2). Delivery of CagA inside the host results in its association with ASPP2. After this interaction, ASPP2 recruits its natural target p53 and inhibits its apoptotic function. CagA leads to enhanced degradation of p53 and thereby, down-regulates its activity in an ASPP2-dependent manner. Finally, Hp-infected cells treated with the p53-activating drug Doxorubicin are more resistant to apoptosis than uninfected cells, an effect that requires ASPP2. The interaction between CagA and ASPP2 and the consequent degradation of p53 are examples of a bacterial protein that subverts the p53 tumor suppressor pathway in a manner similar to DNA tumor viruses. This finding may contribute to the understanding of the increased risk of gastric cancer in patients infected with Hp
CagA+
strains.
Two-point functions in (loop) quantum cosmology
Authors: Calcagni Gianluca , Gielen Steffen , Oriti Daniele
Published: May 2011

The path-integral formulation of quantum cosmology with a massless scalar field as a sum-over-histories of volume transitions is discussed, with particular but non-exclusive reference to loop quantum cosmology. Exploiting the analogy with the relativistic particle, we give a complete overview of the possible two-point functions, pointing out the choices involved in their definitions, deriving their vertex expansions and the composition laws they satisfy. We clarify the origin and relations of different quantities previously defined in the literature, in particular the tie between definitions using a group averaging procedure and those in a deparametrized framework. Finally, we draw some conclusions about the physics of a single quantum universe (where there exist superselection rules on positive- and negative-frequency sectors and different choices of inner product are physically equivalent) and multiverse field theories where the role of these sectors and the inner product are reinterpreted.
First Principles Study of Electronic Structure and Half-metallicity of Molecule-based Ferromagnet Cr[N(CN)2]2
Authors: Huang Hai-ming , Luo Shi-jun , Liu Guo-ying , Yao Kai-lun
Published: May 2011

The electronic structure and half-metallicity of molecule-based ferromagnet Cr[N(CN)2]2 have been investigated using first-principles with generalized gradient approximation. The total energy, spin-polarized electronic band structure, density of states (DOSs) and spin magnetic moments were all calculated. The calculations reveal that the compound Cr[N(CN)2]2 is a really half-metallic ferromagnet with a integral magnetic moment of 2.0000 μB per molecule in the optimized lattice constant. Based on the spin distribution and the DOS, it is found that the total magnetic moment is mainly from the Cr2+ with relative small contribution from C and N atoms. The sensitivity of the half-metallicity to small change in lattice constant is also discussed.
Synthesis of Multishell Carbon Nanotube Composites via Template Method
Authors: Li Wen-bo , Zhai Dong-yuan , Pan Li-jia , Pu Lin , Xu Jian-bin , Shi Yi
Published: May 2011

Multishell nanotubes of polyaniline and carbon were synthesized via a template approach. A thin layer of MnO2 coated on carbon nanotubes acts as a reactive template for the consequent formation of the polyaniline coating. The polyaniline-carbon nanotubes show enhanced dispersibility in water and can be possibly used as a functional material of electrochemical capacitors with improved performance. The general method operates by coating carbon nanotubes on functional materials such as poly (3,4-ethylenedioxythiophene), polypyrrole, silica, and carbon.
Hydrogen Production by Low-temperature Steam Reforming of Bio-oil over Ni/HZSM-5 Catalyst
Authors: Qiu Song-bai , Gong Lu , Liu Lu , Hong Cheng-gui , Yuan Li-xia , Li Quan-xin
Published: May 2011

We investigated high catalytic activity of Ni/HZSM-5 catalysts synthesized by the impregnation method, which was successfully applied for low-temperature steam reforming of bio-oil. The influences of the catalyst composition, reforming temperature and the molar ratio of steam to carbon fed on the stream reforming process of bio-oil over the Ni/HZSM-5 catalysts were investigated in the reforming reactor. The promoting effects of current passing through the catalyst on the bio-oil reforming were also studied using the electrochemical catalytic reforming approach. By comparing Ni/HZSM-5 with commonly used Ni/Al2O3 catalysts, the Ni20/ZSM catalyst with Ni-loading content of about 20% on the HZSM-5 support showed the highest catalytic activity. Even at 450 °C, the hydrogen yield of about 90% with a near complete conversion of bio-oil was obtained using the Ni20/ZSM catalyst. It was found that the performance of the bio-oil reforming was remarkably enhanced by the HZSM-5 supporter and the current through the catalyst. The features of the Ni/HZSM-5 catalysts were also investigated via X-ray diffraction, inductively coupled plasma and atomic emission spectroscopy, hydrogen temperature-programmed reduction, and Brunauer-Emmett-Teller methods.
Smooth muscle modeling and experimental identification: application to bladder isometric contraction
Authors: Laforêt Jérémy , Guiraud David , Andreu David , Taillades Hubert , Azevedo Coste Christine
Published: May 2011

This paper presents an original smooth muscle model based on the Huxley microscopic approach. This model is the main part of a comprehensive lower urinary track model. The latter is used for simulation studies and is assessed through experiments on rabbits, for which a subset of parameters is estimated, using intravesical pressure measurements in isometric conditions. Bladder contraction is induced by electrical stimulation that determines the onset and thus synchronizes simulation and experimental data. Model sensitivity versus parameter accuracy is discussed and allows the definition of a subset of four parameters that must be accurately identified in order to obtain good fitting between experimental and acquired data. Preliminary experimental data are presented as well as model identification results. They show that the model is able to follow the pressure changes induced by an artificial stimulus in isometric contractions. Moreover, the model gives an insight into the internal changes in calcium concentration and the ratio of the different chemical species present in the muscle cells, in particular the bounded and unbounded actin and myosin and the normalized concentration of intracellular calcium.
A new asymptotic behavior of solutions to the Camassa-Holm equation
Authors: Ni Lidiao , Zhou Yong
Published: May 2011

The present work is mainly concerned with an algebraic decay rate of the strong solution to the Camassa-Holm equation in

L

∞

L^{\infty }

-space. In particular, it is proved that the solution decays algebraically with the same exponent as that of the initial datum.
Vimentin intermediate filaments modulate the motility of mitochondria
Authors: Nekrasova Oxana E. , Mendez Melissa G. , Chernoivanenko Ivan S. , Tyurin-Kuzmin Pyotr A. , Kuczmarski Edward R. , Gelfand Vladimir I. , Goldman Robert D. , Minin Alexander A.
Published: May 2011

Interactions with vimentin intermediate filaments (VimIFs) affect the motility, distribution, and anchorage of mitochondria. In cells lacking VimIFs or in which VimIF organization is disrupted, the motility of mitochondria is increased relative to control cells that express normal VimIF networks. Expression of wild-type VimIF in vimentin-null cells causes mitochondrial motility to return to normal (slower) rates. In contrast, expressing vimentin with mutations in the mid-region of the N-terminal non–α-helical domain (deletions of residues 41–96 or 45–70, or substitution of Pro-57 with Arg) did not inhibit mitochondrial motility even though these mutants retain their ability to assemble into VimIFs in vivo. It was also found that a vimentin peptide consisting of residues 41–94 localizes to mitochondria. Taken together, these data suggest that VimIFs bind directly or indirectly to mitochondria and anchor them within the cytoplasm.
Budding yeast Dma1 and Dma2 participate in regulation of Swe1 levels and localization
Authors: Raspelli Erica , Cassani Corinne , Lucchini Giovanna , Fraschini Roberta
Published: May 2011

Timely down-regulation of the evolutionarily conserved protein kinase Swe1 plays an important role in cell cycle control, as Swe1 can block nuclear division through inhibitory phosphorylation of the catalytic subunit of cyclin-dependent kinase. In particular, Swe1 degradation is important for budding yeast cell survival in case of DNA replication stress, whereas it is inhibited by the morphogenesis checkpoint in response to alterations in actin cytoskeleton or septin structure. We show that the lack of the Dma1 and Dma2 ubiquitin ligases, which moderately affects Swe1 localization and degradation during an unperturbed cell cycle with no apparent phenotypic effects, is toxic for cells that are partially defective in Swe1 down-regulation. Moreover, Swe1 is stabilized, restrained at the bud neck, and hyperphosphorylated in dma1Δ dma2Δ cells subjected to DNA replication stress, indicating that the mechanism stabilizing Swe1 under these conditions is different from the one triggered by the morphogenesis checkpoint. Finally, the Dma proteins are required for proper Swe1 ubiquitylation. Taken together, the data highlight a previously unknown role of these proteins in the complex regulation of Swe1 and suggest that they might contribute to control, directly or indirectly, Swe1 ubiquitylation.
The two domains of centrin have distinct basal body functions inTetrahymena
Authors: Vonderfecht Tyson , Stemm-Wolf Alexander J. , Hendershott Melissa , Giddings Thomas H. , Meehl Janet B. , Winey Mark
Published: May 2011

The basal body is a microtubule-organizing center responsible for organizing the cilium, a structure important for cell locomotion and sensing of the surrounding environment. A widely conserved basal body component is the Ca2+-binding protein centrin. Analyses of centrin function suggest a role in basal body assembly and stability; however, its molecular mechanisms remain unclear. Here we describe a mutagenic strategy to study the function and essential nature of the various structural features of Cen1 in the ciliate Tetrahymena. We find that the two domains of Cen1 are both essential, and examination of strains containing mutant CEN1 alleles indicates that there are two predominant basal body phenotypes: misorientation of newly assembled basal bodies and stability defects. The results also show that the two domains of Cen1 are able to bind Ca2+and that perturbation of Ca2+binding affects Cen1 function. In all, the data suggest that the two domains of Cen1 have distinct functions.
Modular model of TNFα cytotoxicity
Authors: Chignola Roberto , Vyshemirsky Vladislav , Farina Marcello , Del Fabbro Alessio , Milotti Edoardo
Published: May 2011

Motivation: Tumour Necrosis Factor alpha (TNF) initiates a complex series of biochemical events in the cell upon binding to its type R1 receptor (TNF-R1). Recent experimental work has unravelled the molecular regulation of the signalling complexes that lead either to cell survival or death. Survival signals are activated by direct binding of TNF to TNF-R1 at the cell membrane whereas apoptotic signals by endocytosed TNF/TNF-R1 complexes. Here we describe a reduced, effective model with few free parameters, where we group some intricate mechanisms into effective modules, that successfully describes this complex set of actions. We study the parameter space to show that the model is structurally stable and robust over a broad range of parameter values.

Results: We use state-of-the-art Bayesian methods (a Sequential Monte Carlo sampler) to perform inference of plausible values of the model parameters from experimental data. As a result, we obtain a robust model that can provide a solid basis for further modelling of TNF signalling. The model is also suitable for inclusion in multi-scale simulation programs that are presently under development to study the behaviour of large tumour cell populations.

Availability: We provide supplementary material that includes all mathematical details and all algorithms (Matlab code) and models (SBML descriptions).

Contact:  edoardo.milotti@ts.infn.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Long-term changes in trophic patterns of Iceland cod and linkages to main prey stock sizes
Authors: Pálsson Ólafur K. , Björnsson Höskuldur
Published: May 2011

Pálsson, Ó. K., and Björnsson, H. 2011. Long-term changes in trophic patterns of Iceland cod and linkages to main prey stock sizes. – ICES Journal of Marine Science, 68: 1488–1499. Data on the diet composition of Iceland cod (Gadus morhua) were collected in March of the years 1981–2010 and in autumn of the years 1988–2010. Capelin, northern shrimp, and euphausiids dominate the diet in all years and may be classified as the stable food of Iceland cod. Overall, total consumption by the smallest cod (20–29 cm) remained stable over the three decades, whereas that of larger fish has declined since the mid-1990s. This decline may explain the reduced growth rate of cod in recent years. Long-term, prey-specific patterns were identified in consumption, and significant trophic links were found between cod consumption and stock sizes of capelin and northern shrimp. In March, the correlation between cod consumption on capelin and capelin stock size was highly significant, a type I functional feeding response, but not significant in autumn. The correlation deteriorated in the early to mid-1990s and in the early 2000s. Increased inflow of Atlantic water into north Icelandic waters, and associated changes in capelin distribution, may have contributed to this trend. The interaction between cod consumption on northern shrimp and shrimp stock size showed a highly significant type I functional feeding response in both seasons.
Cucumber mosaic virus satellite RNAs that induce similar symptoms in melon plants show large differences in fitness
Authors: Betancourt Mónica , Fraile Aurora , García-Arenal Fernando
Published: May 2011

Two groups of Cucumber mosaic virus (CMV) satellite RNAs (satRNAs), necrogenic and non-necrogenic, can be differentiated according to the symptoms they cause in tomato plants, a host in which they also differ in fitness. In most other CMV hosts these CMV-satRNA cause similar symptoms. Here, we analyse whether they differ in traits determining their relative fitness in melon plants, in which the two groups of CMV-satRNAs cause similar symptoms. For this, ten necrogenic and ten non-necrogenic field satRNA genotypes were assayed with Fny-CMV as a helper virus. Neither type of CMV-satRNA modified Fny-CMV symptoms, and both types increased Fny-CMV virulence similarly, as measured by decreases in plant biomass and lifespan. Necrogenic and non-necrogenic satRNAs differed in their ability to multiply in melon tissues; necrogenic satRNAs accumulated to higher levels both in single infection and in competition with non-necrogenic satRNAs. Indeed, multiplication of some non-necrogenic satRNAs was undetectable. Transmission between hosts by aphids was less efficient for necrogenic satRNAs as a consequence of a more severe reduction of CMV accumulation in leaves. The effect of CMV accumulation on aphid transmission was not compensated for by differences in satRNA encapsidation efficiency or transmissibility to CMV progeny. Thus, necrogenic and non-necrogenic satRNAs differ in their relative fitness in melon, and trade-offs are apparent between the within-host and between-host components of satRNA fitness. Hence, CMV-satRNAs could have different evolutionary dynamics in CMV host-plant species in which they do not differ in pathogenicity.
Receptor-Like Activity Evoked by Extracellular ADP in Arabidopsis Root Epidermal Plasma Membrane
Authors: Demidchik Vadim , Shang Zhonglin , Shin Ryoung , Colaço Renato , Laohavisit Anuphon , Shabala Sergey , Davies Julia M.
Published: May 2011

Extracellular purine nucleotides are implicated in the control of plant development and stress responses. While extracellular ATP is known to activate transcriptional pathways via plasma membrane (PM) NADPH oxidase and calcium channel activation, very little is known about signal transduction by extracellular ADP. Here, extracellular ADP was found to activate net Ca2+ influx in roots of Arabidopsis (Arabidopsis thaliana) and transiently elevate cytosolic free Ca2+ in root epidermal protoplasts. An inward Ca2+-permeable conductance in root epidermal PM was activated within 1 s of ADP application and repeated application evoked a smaller current. Such response speed and densitization are consistent with operation of equivalents to animal ionotropic purine receptors, although to date no equivalent genes for such receptors have been identified in higher plants. In contrast to ATP, extracellular ADP did not evoke accumulation of intracellular reactive oxygen species. While high concentrations of ATP caused net Ca2+ efflux from roots, equivalent concentrations of ADP caused net influx. Overall the results point to a discrete ADP signaling pathway, reliant on receptor-like activity at the PM.