bluuebunny/crossref_metadata_2025 huggingface dataset:
Mass Spectrometry, Nutrition and Protein Turnover
Authors: Affolter Michael
Published: July 2010

Protein turnover is the result of synthesis of new and breakdown of old proteins in the body thereby providing a mechanism for the maintenance of optimally functioning proteins. Quantification of protein turnover rates is essential to understand these fundamental biological processes in all living organisms. Over the last decades, mass spectrometry has greatly contributed to the progress in the analysis of protein synthesis and breakdown and stable-isotope labelled tracers play a key role for the detailed quantitative measurement of protein metabolism. Isotope ratio and atmospheric pressure mass spectrometry enable the precise, accurate, and sensitive determination of isotope enrichments. More recently, methods have been developed to study total protein metabolism and multiplexed protein analysis for a comprehensive profiling at proteome level. Addressing protein turnover dynamics represent some technical challenges for proteome-wide analysis, i.e. the high isotope enrichment needed for proteome-wide studies is still difficult to achieve in animals and humans.

Nutrition plays a key role in the anabolic signalling for the stimulation of skeletal muscle protein synthesis. The combination of physical training and adequate protein intake acts synergistically to enhance muscle mass and performance. Studies in the elderly population confirmed the potential to address sarcopenia, the gradual loss of muscle mass and function with ageing, by adapted nutrition with adequate daily protein intake and resistance-type exercise training, allowing a substantial gain in skeletal muscle mass, strength, and functional performance.
Ecosystem Services and Food Production
Authors: Norris Ken , Potts Simon G. , Mortimer Simon R.
Published: July 2010

By 2030, the world's human population could rise to 8 billion people and world food demand may increase by 50%. Although food production outpaced population growth in the 20th century, it is clear that the environmental costs of these increases cannot be sustained into the future. This challenges us to re-think the way we produce food. We argue that viewing food production systems within an ecosystems context provides the basis for 21st century food production. An ecosystems view recognises that food production systems depend on ecosystem services but also have ecosystem impacts. These dependencies and impacts are often poorly understood by many people and frequently overlooked. We provide an overview of the key ecosystem services involved in different food production systems, including crop and livestock production, aquaculture and the harvesting of wild nature. We highlight the important ecosystem impacts of food production systems, including habitat loss and degradation, changes to water and nutrient cycles across a range of scales, and biodiversity loss. These impacts often undermine the very ecosystem services on which food production systems depend, as well as other ecosystem services unrelated to food. We argue that addressing these impacts requires us to re-design food production systems to recognise and manage the limitations on production imposed by the ecosystems within which they are embedded, and increasingly embrace a more multi-functional view of food production systems and associated ecosystems. In this way, we should be able to produce food more sustainably whilst inflicting less damage on other important ecosystem services.
Natural Capital and Ecosystem Services: The Ecological Foundation of Human Society
Authors: Gómez-Baggethun Erik , Groot Rudolf de
Published: July 2010

Ecosystems provide both the energy and materials needed for the production of economic goods and services and act as a sink of wastes generated by the economic metabolism. Other nature's services benefits are obtained directly from nature, often without passing through transformation processes or the mediation of markets, as in the case of clean air, erosion control, aesthetic benefits, or climate regulation. Economic health in the long term thus depends on the maintenance of the integrity and resilience of the natural ecosystems in which it is embedded. The fact that standard economic theory neglects this aspect has been identified as a main cause of the current environmental problems and ecological crises. Approaches such as ecological and environmental economics attempt to deal with these shortcomings of standard economics through the development of concepts and accounting methods that better reflect the role of nature in the economy and the ecological costs derived from economic growth. Concepts such as natural capital, ecosystem functions and ecosystem services are playing a key role as tools to communicate societal dependence on natural ecosystems and in the articulation of a new form of understanding economics. This paper gives a brief overview of the key concepts for understanding the links between ecosystems and human well-being, and discusses a range of valuation and accounting methods as possible ways to measure the quantities and importance of natural capital and ecosystem services.
Protecting Water Resources and Health by Protecting the Environment: A Case Study
Authors: Vial Luke de , Bowles Fiona , Dennis P. Julian
Published: July 2010

The effluent from growing populations and the increasing use and disposal of chemicals into the environment can overwhelm ecosystems’ natural ability to absorb and treat waste. Historically, the approach to protecting the environment from sewage discharged into it is to collect and treat it. Similarly water taken from sources used for public water supply is treated to protect populations from the effects of untreated or diffuse pollution. Both approaches have proved successful and will continue to play an essential role in protecting ecosystems and public health. However, if the cost of treatment and the associated carbon footprint of these treatment processes are to be controlled, a complementary approach is needed to protecting ecosystems and the water extracted from them for public supply. Catchment management, a means of minimising diffuse pollution, and therefore the need for more complex treatment, is being used by Wessex Water and other water companies to drive down the cost and carbon footprint of more expensive and energy-intensive treatment processes needed to meet the demands of tightening health and environmental standards. The impact of this approach in a number of defined catchments in the Wessex Water region has been studied over the last three years. Whilst the catchment management approach has demonstrated that a reduction in the residual levels of nitrogen in the soil can be achieved without affecting a farm's output, it is not yet clear whether the impact of these changes has reached the water supply aquifer. However, in surface waters where travel times are much faster, immediate impacts have been achieved, particularly a reduction in the detection of pesticides.
Life Cycle Assessment as a Tool for Sustainable Management of Ecosystem Services
Authors: Azapagic Adisa
Published: July 2010

Humanity depends on healthy ecosystems: they support or improve our quality of life, and without them, the Earth would be uninhabitable. However, over the past 50 years, fast-growing demands for food, fuel, water and other natural resources have led to an unprecedented degradation of many ecosystem services so that their ability to sustain future generations can no longer be taken for granted. Therefore, reversing ecosystem degradation is one of the great challenges of sustainable development. This is by no means a trivial task as it requires action by all actors in society, including governments, industry and individuals. One of the difficulties is that, even if there was a universal commitment to sustainable development, it is still unclear what goods, services and activities are sustainable and how they could be identified. In an attempt to contribute towards a better understanding of this complex problem, this paper illustrates how environmentally-sustainable products and activities can be identified using Life Cycle Assessment as a tool. Four industrial sectors and supply chains are discussed: energy, transport, industry and food & agriculture. The examples used within these sectors include, respectively, electricity generation; different transportation options and fuels; chemicals and related products; different food products and packaging. Their impacts on the ecosystem services are examined from ‘cradle to grave’ to help identify more sustainable alternatives. For illustration purposes, the discussion centres on carbon footprint (global warming potential), as one of the major global impacts; however, other impacts are also discussed as appropriate.
The resource‐based view revisited: Comparative firm advantage, willingness‐based isolating mechanisms and competitive heterogeneity
Authors: Madhok Anoop , Li Sali , Priem Richard L.
Published: July 2010

Abstract We take a step beyond the resource‐based view that resource characteristics (i.e., valuable, rare, inimitable and non‐substitutable) are the sole basis for isolating mechanisms. Instead, we apply Ricardo's principle of Comparative Advantage in a two‐firm, two‐product scenario to show how additional isolating mechanisms can result from economic incentives that provide managers with distinct strategic choices. Specifically, our analysis indicates that managers' strategic decisions based on comparative firm advantage (CFA) affect their willingness to imitate competitors, even when their firms are fully capable of such imitation. This willingness, in turn, helps to determine the direction of firm expansion. We discuss how Ricardo's CFA logic can provide specific guidance for managers regarding effective firm strategies in specific comparative advantage situations by factoring in both internal efficiencies and competitive pressures when designing and implementing rent‐seeking strategies.
A generalized coupled Korteweg–de Vries hierarchy, bi-Hamiltonian structure, and Darboux transformation
Authors: Zhaqilao  , Sirendaoreji
Published: July 2010

A new generalized coupled Korteweg–de Vries (KdV) hierarchy is presented starting from a 4×4 matrix spectral problem with four potentials. Its generalized bi-Hamiltonian structure is also investigated by using the trace identity. Most importantly, a new generalized coupled KdV equation is produced. Moreover, a Darboux transformation for the generalized coupled KdV equation is established with the aid of the gauge transformation between the corresponding 4×4 matrix spectral problems, by which some explicit solutions of the generalized coupled KdV equation are obtained. As a reduction, a Darboux transformation of the KdV equation and its explicit solutions are given.
Insights into solid phase epitaxy of ultrahighly doped silicon
Authors: Gouyé A. , Berbezier I. , Favre L. , Aouassa M. , Amiard G. , Ronda A. , Campidelli Y. , Halimaoui A.
Published: July 2010

In this study we investigate the mechanisms of growth and boron (B) incorporation into crystalline silicon (c-Si) during crystallization of amorphous doped silicon (a-Si:B) films. The process developed consists of two steps, first the chemical vapor codeposition at low temperature of Si and B atoms to form a-Si:B layer and second the crystallization of amorphous phase during in situ annealing to incorporate boron atoms on the substitutional sites of c-Si. We find that the crystallization rate linearly increases with the nominal boron concentration (CB) up to a critical CB∗ which corresponds to the maximum concentration of electrically active boron atoms in the crystalline phase. In these conditions, an increase in the crystallization rate by a factor 22 as compared to the intrinsic crystallization rate is obtained. We suggest that this remarkable behavior is attributed to D+ charged defects associated to the activated doping atoms in agreement with the generalized Fermi level shifting model. For larger CB, further boron atoms are incorporated in the amorphous phase in the form of ultrasmall clusters that do not contribute to shift the Fermi level of a-Si. As a consequence, for CB>CB∗ the crystallization rate does not increase any more. We also show that crystallization provides a more complete incorporation of boron atoms already present in a-Si than the codeposition of Si and B atoms in the same experimental conditions (same growth rate and temperature). This result is attributed to the lower kinetic segregation at the amorphous-crystalline (a/c) interface than at the vacuum-crystalline interface. The lower kinetic segregation results from both a higher diffusion barrier of boron atoms at the a/c interface and a lower segregation energy (due to a low a/c interface energy).
Interpretation of recombination at c-Si/SiNx interfaces by surface damage
Authors: Steingrube Silke , Altermatt Pietro P. , Steingrube Daniel S. , Schmidt Jan , Brendel Rolf
Published: July 2010

The measured effective surface recombination velocity Seff at the interface between crystalline p-type silicon (p-Si) and amorphous silicon nitride (SiNx) layers increases with decreasing excess carrier density Δn<1015 cm−3 at dopant densities below 1017 cm−3. If such an interface is incorporated into Si solar cells, it causes their performance to deteriorate under low-injection conditions. With the present knowledge, this effect can neither be experimentally avoided nor fully understood. In this paper, Seff is theoretically reproduced in both p-type and n-type Si at all relevant Δn and all relevant dopant densities. The model incorporates a reduction in the Shockley–Read–Hall lifetime in the Si bulk near the interface, called the surface damage region (SDR). All of the parameters of the model are physically meaningful, and a parametrization is given for numerical device modeling. The model predicts that a ten-fold reduction in the density of defect states within the SDR is sufficient to weaken this undesirable effect to the extent that undiffused surfaces can be incorporated in Si solar cells. This may serve to simplify their fabrication procedures. We further discuss possible causes of the SDR and suggest implications for experiments.
Strain relaxation in highly mismatched hexagonal heterosystems
Authors: Lebedev Vadim
Published: July 2010

In this work, the formation of interfacial misfit dislocations (IMD) along with the elastic strain relaxation have been considered for the case of highly lattice mismatched heterosystems with m:n matched interfaces. It was shown that for the growth stage anticipating the coalescence, the strain relaxation in the nuclei can be described analytically by means of the unified mechanical/thermodynamical (Kern’s/IMD) model using two key parameters–the residual strain in the nuclei and their critical thickness. The general conditions for the rapid coalescence in such systems have been formulated in terms of the macroscopic system parameters: coalescence thickness<mean system length<critical size of the nucleus.
Collective excitations in supercritical fluids: Analytical and molecular dynamics study of “positive” and “negative” dispersion
Authors: Bryk Taras , Mryglod Ihor , Scopigno Tullio , Ruocco Giancarlo , Gorelli Federico , Santoro Mario
Published: July 2010

The approach of generalized collective modes is applied to the study of dispersion curves of collective excitations along isothermal lines of supercritical pure Lennard-Jones fluid. An effect of structural relaxation and other nonhydrodynamic relaxation processes on the dispersion law is discussed. A simple analytical expression for the dispersion law in the long-wavelength region of acoustic excitations is obtained within a three-variable viscoelastic model of generalized hydrodynamics. It is shown that the deviation from the linear dependence in the long-wavelength region can be either “positive” or “negative” depending on the ratio between the high-frequency (elastic) and isothermal speed of sound. An effect of thermal fluctuations on positive and negative dispersion is estimated from the analytical solution of a five-variable thermoviscoelastic model that generalizes the results of the viscoelastic treatment. Numerical results are reported for a Lennard-Jones supercritical fluid along two isothermal lines T∗=1.71,4.78 with different densities and discussed along the theoretical expressions derived.
Elastic constants and anisotropic internal frictions of decagonal Al72Ni18Co8 single quasicrystal at low temperatures
Authors: Tarumi R. , Ledbetter H. , Shiomi S. , Ogi H. , Hirao M. , Tsai A. P.
Published: July 2010

We studied the complete set of elastic constants Cij and internal frictions tensor Qij−1 of anisotropic decagonal Al72Ni18Co8 single quasicrystal by electromagnetic acoustic resonance at low temperatures, to 5 K. Most Cij(T) showed usual stiffening upon cooling and their temperature behaviors are well characterized by an Einstein-lattice-vibration model. The average Grüneisen parameter estimated from the bulk modulus is 2.4, almost identical to crystalline Al. Ambient temperature Qij−1 show a linear relationship to the elastic-constants temperature derivatives |dCij/dT|/Cij with a slope of 1.28 K−1, suggesting that lattice anharmonicity plays a dominant role for Qij−1. The longitudinal modulus for the decagonal axis C33 and corresponding internal friction Q33−1, however, showed significant deviation from such ideal behavior, suggesting additional low-frequency phonon-excitation modes along the decagonal axis.
In-plane optical anisotropy in GaAsN/GaAs single-quantum well investigated by reflectance-difference spectroscopy
Authors: Yu J. L. , Chen Y. H. , Ye X. L. , Jiang C. Y. , Jia C. H.
Published: July 2010

The interface properties of GaNxAs1−x/GaAs single-quantum well is investigated at 80 K by reflectance difference spectroscopy. Strong in-plane optical anisotropies (IPOA) are observed. Numerical calculations based on a 4 band K⋅P Hamiltonian are performed to analyze the origin of the optical anisotropy. It is found that the IPOA can be mainly attributed to anisotropic strain effect, which increases with the concentration of nitrogen. The origin of the strain component ϵxy is also discussed.
Electronic and magnetic structure of bulk cobalt: The α, β, and ε-phases from density functional theory calculations
Authors: de la Peña O’Shea Víctor Antonio , Moreira Iberio de P. R. , Roldán Alberto , Illas Francesc
Published: July 2010

The geometric, electronic and magnetic properties of the three metallic cobalt phases: hcp(α), fcc(β), and epsilon(ε) have been theoretically studied using periodic density functional calculations with generalized gradient approximation (GGA) and plane wave basis set. These results have been compared with those obtained with GGA+U approach which have shown a noticeable improvement with regard to experimental data. For instance, the cohesive energy values predicted by GGA are overestimated by ∼25%, whereas GGA+U underestimate them by 14%–17%. On the other hand, magnetic moment values are underestimated in GGA while are overestimated for GGA+U approach by almost the same amount. Besides, the introduction of U parameter gives rise to an electronic redistribution in the d-band structure, which leads to variations in the magnetic properties. Moreover, a higher attention has been paid in the study of the electronic and magnetic properties of the ε-phase that has not described previously. These studies show that this phase posses special properties that could lead to an unusual behavior in magnetic or catalytic applications.
Electrical properties with relaxation through human blood
Authors: Abdalla S. , Al-ameer S. S. , Al-Magaishi S. H.
Published: July 2010

The present work aims to study the effects of the blood-microstructure on the electrical conduction from two different but correlated properties: Electrical and mechanical (viscosity), and to derive useful parameters for the evaluation of electrical conduction as a function of the blood viscosity. ac-conductivity and dielectric constant of normal and diabetic blood are measured in the frequency range 10 kHz–1 MHz at the room temperature. An empirical relation relating the resistivity and viscosity of the blood has been presented. The results show that a microfluidic device is a viable and simple solution for determination of electrical and rheological behaviors of blood samples.
Interaction between like-charged polyelectrolyte-colloid complexes in electrolyte solutions: A Monte Carlo simulation study in the Debye–Hückel approximation
Authors: Truzzolillo D. , Bordi F. , Sciortino F. , Sennato S.
Published: July 2010

We study the effective interaction between differently charged polyelectrolyte-colloid complexes in electrolyte solutions via Monte Carlo simulations. These complexes are formed when short and flexible polyelectrolyte chains adsorb onto oppositely charged colloidal spheres, dispersed in an electrolyte solution. In our simulations the bending energy between adjacent monomers is small compared to the electrostatic energy, and the chains, once adsorbed, do not exchange with the solution, although they rearrange on the particles surface to accommodate further adsorbing chains or due to the electrostatic interaction with neighbor complexes. Rather unexpectedly, when two interacting particles approach each other, the rearrangement of the surface charge distribution invariably produces antiparallel dipolar doublets that invert their orientation at the isoelectric point. These findings clearly rule out a contribution of dipole-dipole interactions to the observed attractive interaction between the complexes, pointing out that such suspensions cannot be considered dipolar fluids. On varying the ionic strength of the electrolyte, we find that a screening length κ−1, short compared with the size of the colloidal particles, is required in order to observe the attraction between like-charged complexes due to the nonuniform distribution of the electric charge on their surface (“patch attraction”). On the other hand, by changing the polyelectrolyte/particle charge ratio ξs, the interaction between like-charged polyelectrolyte-decorated particles, at short separations, evolves from purely repulsive to strongly attractive. Hence, the effective interaction between the complexes is characterized by a potential barrier, whose height depends on the net charge and on the nonuniformity of their surface charge distribution.
Rapid evolution of ritual architecture in central Polynesia indicated by precise
230
Th/U coral dating
Authors: Sharp Warren D. , Kahn Jennifer G. , Polito Christina M. , Kirch Patrick V.
Published: July 2010

In Polynesia, the complex Society Islands chiefdoms constructed elaborate temples (
marae
), some of which reached monumental proportions and were associated with human sacrifice in the ‘Oro cult. We investigated the development of temples on Mo‘orea Island by
230
Th/U dating of corals used as architectural elements (facing veneers, cut-and-dressed blocks, and offerings). The three largest coastal
marae
(associated with the highest-ranked chiefly lineages) and 19
marae
in the inland ‘Opunohu Valley containing coral architectural elements were dated. Fifteen corals from the coastal temples meet geochemical criteria for accurate
230
Th/U dating, yield reproducible ages for each
marae
, and have a mean uncertainty of 9 y (2σ). Of 41 corals from wetter inland sites, 12 show some diagenesis and may yield unreliable ages; however, the majority (32) of inland dates are considered accurate. We also obtained six
14
C dates on charcoal from four
marae
. The dates indicate that temple architecture on Mo‘orea Island developed rapidly over a period of approximately 140 y (
ca.
AD 1620–1760), with the largest coastal temples constructed immediately before initial European contact (AD 1767). The result of a seriation of architectural features corresponds closely with this chronology.
Acropora
coral veneers were superceded by cut-and-dressed
Porites
coral blocks on altar platforms, followed by development of multitier stepped altar platforms and use of pecked basalt stones associated with the late ‘Oro cult. This example demonstrates that elaboration of ritual architecture in complex societies may be surprisingly rapid.
Genome-wide analysis of DNA binding and transcriptional regulation by the mammalian Doublesex homolog DMRT1 in the juvenile testis
Authors: Murphy Mark W. , Sarver Aaron L. , Rice Daren , Hatzi Katerina , Ye Kenny , Melnick Ari , Heckert Leslie L. , Zarkower David , Bardwell Vivian J.
Published: July 2010

The DM domain proteins Doublesex- and MAB-3–related transcription factors (DMRTs) are widely conserved in metazoan sex determination and sexual differentiation. One of these proteins, DMRT1, plays diverse and essential roles in development of the vertebrate testis. In mammals DMRT1 is expressed and required in both germ cells and their supporting Sertoli cells. Despite its critical role in testicular development, little is known about how DMRT1 functions as a transcription factor or what genes it binds and regulates. We combined ChIP methods with conditional gene targeting and mRNA expression analysis and identified almost 1,400 promoter-proximal regions bound by DMRT1 in the juvenile mouse testis and determined how expression of the associated mRNAs is affected when
Dmrt1
is selectively mutated in germ cells or Sertoli cells. These analyses revealed that DMRT1 is a bifunctional transcriptional regulator, activating some genes and repressing others. ChIP analysis using conditional mutant testes showed that DNA binding and transcriptional regulation of individual target genes can differ between germ cells and Sertoli cells. Genes bound by DMRT1 in vivo were enriched for a motif closely resembling the sequence DMRT1 prefers in vitro. Differential response of genes to loss of DMRT1 corresponded to differences in the enriched motif, suggesting that other transacting factors may modulate DMRT1 activity. DMRT1 bound its own promoter and those of six other
Dmrt
genes, indicating auto- and cross-regulation of these genes. Many of the DMRT1 target genes identified here are known to be important for a variety of functions in testicular development; the others are candidates for further investigation.
Absence of NMDA receptors in dopamine neurons attenuates dopamine release but not conditioned approach during Pavlovian conditioning
Authors: Parker Jones G. , Zweifel Larry S. , Clark Jeremy J. , Evans Scott B. , Phillips Paul E. M. , Palmiter Richard D.
Published: July 2010

During Pavlovian conditioning, phasic dopamine (DA) responses emerge to reward-predictive stimuli as the subject learns to anticipate reward delivery. This observation has led to the hypothesis that phasic dopamine signaling is important for learning. To assess the ability of mice to develop anticipatory behavior and to characterize the contribution of dopamine, we used a food-reinforced Pavlovian conditioning paradigm. As mice learned the cue–reward association, they increased their head entries to the food receptacle in a pattern that was consistent with conditioned anticipatory behavior. D1-receptor knockout (D1R-KO) mice had impaired acquisition, and systemic administration of a D1R antagonist blocked both the acquisition and expression of conditioned approach in wild-type mice. To assess the specific contribution of phasic dopamine transmission, we tested mice lacking NMDA-type glutamate receptors (NMDARs) exclusively in dopamine neurons (NR1-KO mice). Surprisingly, NR1-KO mice learned at the same rate as their littermate controls. To evaluate the contribution of NMDARs to phasic dopamine release in this paradigm, we performed fast-scan cyclic voltammetry in the nucleus accumbens of awake mice. Despite having significantly attenuated phasic dopamine release following reward delivery, KO mice developed cue-evoked dopamine release at the same rate as controls. We conclude that NMDARs in dopamine neurons enhance but are not critical for phasic dopamine release to behaviorally relevant stimuli; furthermore, their contribution to phasic dopamine signaling is not necessary for the development of cue-evoked dopamine or anticipatory activity in a D1R-dependent Pavlovian conditioning paradigm.
Reversal of hyperglycemia in diabetic mouse models using induced-pluripotent stem (iPS)-derived pancreatic β-like cells
Authors: Alipio Zaida , Liao Wenbin , Roemer Elizabeth J. , Waner Milton , Fink Louis M. , Ward David C. , Ma Yupo
Published: July 2010

Diabetes mellitus is characterized by either the inability to produce insulin (type 1 diabetes) or as insensitivity to insulin secreted by the body (type 2 diabetes). In either case, the body is unable to move blood glucose efficiently across cell membranes to be used. This leads to a variety of local and systemic detrimental effects. Current treatments for diabetes focus on exogenous insulin administration and dietary control. Here, we describe a potential cure for diabetes using a cellular therapy to ameliorate symptoms associated with both reduced insulin secretion and insulin sensitivity. Using induced pluripotent stem (iPS) cells, we were able to derive β-like cells similar to the endogenous insulin-secreting cells in mice. These β-like cells secreted insulin in response to glucose and corrected a hyperglycemic phenotype in two mouse models of type 1 and 2 diabetes via an iPS cell transplant. Long-term correction of hyperglycemia was achieved, as determined by blood glucose and hemoglobin A1c levels. These data provide an initial proof of principle for potential clinical applications of reprogrammed somatic cells in the treatment of diabetes type 1 or 2.
The nature of trapping sites and recombination centres in PVK and PVK–PBD electroluminescent matrices seen by spectrally resolved thermoluminescence
Authors: Glowacki Ireneusz , Szamel Zbigniew
Published: July 2010

Two electroluminescent polymer matrices poly(N-vinylcarbazole) (PVK) and PVK with 40 wt% of 2-tert-butylphenyl-5-biphenyl–1,3,4-oxadiazole (PBD) were studied using spectrally resolved thermoluminescence (SRTL) in the temperature range 15–325 K. The comparison of the SRTL results with the electroluminescence (EL) spectra has allowed identification of the localized (trapping) sites and the radiative recombination centres present in the investigated matrices. In the neat PVK films deep traps with a depth about 200 meV, related to triplet excimers dominate, while in the PVK–PBD (40 wt%) blend films the traps that are related to triplet exciplexes formed by the carbazole groups and the PBD molecules dominate. Depth of the traps in the PVK–PBD blend is somewhat lower than that in the neat PVK. An analysis of the EL spectra shows that in the PVK and in the PVK–PBD blend the dominant radiative centres are singlet excimers and singlet exciplexes, respectively. However, in the neat PVK some contributions of the triplet monomer and the triplet excimer states in the EL were also detected.
Bulk-form TiCx/Ti nanocomposites with controlled nanostructure prepared by a new method: selective laser melting
Authors: Gu Dongdong , Meiners Wilhelm , Hagedorn Yves-Christian , Wissenbach Konrad , Poprawe Reinhart
Published: July 2010

A novel selective laser melting method was applied to consolidate the high-energy ball-milled nanostructured TiC
P
/Ti composite powder to prepare TiC
x
/Ti nanocomposites in bulk form. The substoichiometric TiC0.625 with a hexagonal crystal structure acted as the reinforcing phase, having a lamellar nanostructure with an average thickness of ∼48 nm. The nanostructure of TiC0.625 was coarsened and finally disappeared on decreasing the applied linear laser energy density. Reasonable physical mechanisms and conditions for the formation of nanostructured TiC
x
during laser processing were proposed. It was revealed that the formation of nanoscale hexagonal structured TiC0.625 was due to the action of microscopic pressure induced by evaporative recoil and surface tension on (1 1 1) plane of the lamellar TiC
x
crystals. The disappearance of nanostructure of TiC0.625 at a lower laser energy input was ascribed to a decreased microscopic pressure and an elevated carbon activity in the molten pool.
Room temperature stabilized cubic zirconia nanocrystal: a giant dielectric material
Authors: Manna Sujit , Ghoshal Tandra , De S K
Published: July 2010

A giant low-frequency dielectric constant (∼105) has been observed in room temperature stabilized cubic zirconia nanocrystal of size range 4–8 nm. Dielectric constant strongly depends on the crystallite size. Electrical behaviour of nanocrystallites has been described by an equivalent circuit to obtain grain and grain boundary effects. Mixed valency of Zr (Zr4+, Zr3+) ions gives rise to electronic conduction. Giant dielectric constant has been explained by interfacial polarization because of Maxwell–Wagner type relaxation effect.
Chloride Intracellular Channel 4 Is Critical for the Epithelial Morphogenesis of RPE Cells and Retinal Attachment
Authors: Chuang Jen-Zen , Chou Szu-Yi , Sung Ching-Hwa
Published: July 2010

Retinal detachment is a sight-threatening condition. The molecular mechanism underlying the adhesion between the RPE and photoreceptors is poorly understood because the intimate interactions between these two cell types are impossible to model and study in vitro. In this article, we show that chloride intracellular channel 4 (CLIC4) is enriched at apical RPE microvilli, which are interdigitated with the photoreceptor outer segment. We used a novel plasmid-based transfection method to cell-autonomously suppress CLIC4 in RPE in situ. CLIC4 silenced RPE cells exhibited a significant loss of apical microvilli and basal infoldings, reduced retinal adhesion, and epithelial-mesenchymal transition. Ectopically expressing ezrin failed to rescue the morphological changes exerted by CLIC4 silencing. Neural retinas adjacent to the CLIC4-suppressed RPE cells display severe dysplasia. Finally, a high level of aquaporin 1 unexpectedly appeared at the apical surfaces of CLIC4-suppressed RPE cells, together with a concomitant loss of basal surface expression of monocarboxylate transporter MCT3. Our results suggested that CLIC4 plays an important role in RPE-photoreceptor adhesion, perhaps by modulating the activity of cell surface channels/transporters. We propose that these changes may be attributable to subretinal fluid accumulation in our novel retinal detachment animal model.
FIP1/RCP Binding to Golgin-97 Regulates Retrograde Transport from Recycling Endosomes to thetrans-Golgi Network
Authors: Jing Jian , Junutula Jagath R. , Wu Christine , Burden Jemima , Matern Hugo , Peden Andrew A. , Prekeris Rytis
Published: July 2010

Many proteins are retrieved to the trans-Golgi Network (TGN) from the endosomal system through several retrograde transport pathways to maintain the composition and function of the TGN. However, the molecular mechanisms involved in these distinct retrograde pathways remain to be fully understood. Here we have used fluorescence and electron microscopy as well as various functional transport assays to show that Rab11a/b and its binding protein FIP1/RCP are both required for the retrograde delivery of TGN38 and Shiga toxin from early/recycling endosomes to the TGN, but not for the retrieval of mannose-6-phosphate receptor from late endosomes. Furthermore, by proteomic analysis we identified Golgin-97 as a FIP1/RCP-binding protein. The FIP1/RCP-binding domain maps to the C-terminus of Golgin-97, adjacent to its GRIP domain. Binding of FIP1/RCP to Golgin-97 does not affect Golgin-97 recruitment to the TGN, but appears to regulate the targeting of retrograde transport vesicles to the TGN. Thus, we propose that FIP1/RCP binding to Golgin-97 is required for tethering and fusion of recycling endosome-derived retrograde transport vesicles to the TGN.
A system-level investigation into the cellular toxic response mechanism mediated by AhR signal transduction pathway
Authors: Gim Jungsoo , Kim Ho-Shik , Kim Junil , Choi Minsoo , Kim Jeong-Rae , Chung Yeun Jun , Cho Kwang-Hyun
Published: July 2010

Motivation: Viewing a cellular system as a collection of interacting parts can lead to new insights into the complex cellular behavior. In this study, we have investigated aryl hydrocarbon receptor (AhR) signal transduction pathway from such a system-level perspective. AhR detects various xenobiotics, such as drugs or endocrine disruptors (e.g. dioxin), and mediates transcriptional regulation of target genes such as those in the cytochrome P450 (CYP450) family. On binding with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), however, AhR becomes abnormally activated and conveys toxic effects on cells. Despite many related studies on the TCDD-mediated toxicity, quantitative system-level understanding of how TCDD-mediated toxicity generates various toxic responses is still lacking.

Results: Here, we present a manually curated TCDD-mediated AhR signaling pathway including crosstalks with the hypoxia pathway that copes with oxygen deficiency and the p53 pathway that induces a DNA damage response. Based on the integrated pathway, we have constructed a mathematical model and validated it through quantitative experiments. Using the mathematical model, we have investigated: (i) TCDD dose-dependent effects on AhR target genes; (ii) the crosstalk effect between AhR and hypoxia signals; and (iii) p53 inhibition effect of TCDD-liganded AhR. Our results show that cellular intake of TCDD induces AhR signaling pathway to be abnormally up-regulated and thereby interrupts other signaling pathways. Interruption of hypoxia and p53 pathways, in turn, can incur various hazardous effects on cells. Taken together, our study provides a system-level understanding of how AhR signal mediates various TCDD-induced toxicities under the presence of hypoxia and/or DNA damage in cells.

Contact:  ckh@kaist.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
ROAST: rotation gene set tests for complex microarray experiments
Authors: Wu Di , Lim Elgene , Vaillant François , Asselin-Labat Marie-Liesse , Visvader Jane E. , Smyth Gordon K.
Published: July 2010

Motivation: A gene set test is a differential expression analysis in which a P-value is assigned to a set of genes as a unit. Gene set tests are valuable for increasing statistical power, organizing and interpreting results and for relating expression patterns across different experiments. Existing methods are based on permutation. Methods that rely on permutation of probes unrealistically assume independence of genes, while those that rely on permutation of sample are suitable only for two-group comparisons with a good number of replicates in each group.

Results: We present ROAST, a statistically rigorous gene set test that allows for gene-wise correlation while being applicable to almost any experimental design. Instead of permutation, ROAST uses rotation, a Monte Carlo technology for multivariate regression. Since the number of rotations does not depend on sample size, ROAST gives useful results even for experiments with minimal replication. ROAST allows for any experimental design that can be expressed as a linear model, and can also incorporate array weights and correlated samples. ROAST can be tuned for situations in which only a subset of the genes in the set are actively involved in the molecular pathway. ROAST can test for uni- or bi-direction regulation. Probes can also be weighted to allow for prior importance. The power and size of the ROAST procedure is demonstrated in a simulation study, and compared to that of a representative permutation method. Finally, ROAST is used to test the degree of transcriptional conservation between human and mouse mammary stems.

Availability: ROAST is implemented as a function in the Bioconductor package limma available from www.bioconductor.org

Contact:  smyth@wehi.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Phytoalexin Accumulation in the Interaction Between Rice and the Blast Fungus
Authors: Hasegawa Morifumi , Mitsuhara Ichiro , Seo Shigemi , Imai Takuya , Koga Jinichiro , Okada Kazunori , Yamane Hisakazu , Ohashi Yuko
Published: July 2010

Blast fungus–induced accumulations of major rice diterpene phytoalexins (PA), momilactones A and B, and phytocassanes A through E were studied, focusing on their biosynthesis and detoxification. In resistant rice, all PA started to accumulate at 2 days postinoculation (dpi), at which hypersensitive reaction (HR)-specific small lesions became visible and increased 500- to 1,000-fold at 4 dpi, while the accumulation was delayed and several times lower in susceptible rice. Expression of PA biosynthetic genes was transiently induced at 2 dpi only in resistant plants, while it was highly induced in both plants at 4 dpi. Fungal growth was severely suppressed in resistant plants by 2 dpi but considerably increased at 3 to 4 dpi in susceptible plants. Momilactone A treatment suppressed fungal growth in planta and in vitro, and the fungus detoxified the PA in vitro. These results indicate that HR-associated rapid PA biosynthesis induces severe restriction of fungus, allowing higher PA accumulation in resistant rice, while in susceptible rice, failure of PA accumulation at the early infection stage allows fungal growth. Detoxification of PA would be a tactic of fungus to invade the host plant, and prompt induction of PA biosynthesis upon HR would be a trait of resistant rice to restrict blast fungus.
The Basic Leucine Zipper Transcription Factor Moatf1 Mediates Oxidative Stress Responses and Is Necessary for Full Virulence of the Rice Blast Fungus Magnaporthe oryzae
Authors: Guo Min , Guo Wang , Chen Yue , Dong Suomeng , Zhang Xing , Zhang Haifeng , Song Wenwen , Wang Wei , Wang Qi , Lv Ruili , Zhang Zhengguang , Wang Yuanchao , Zheng Xiaobo
Published: July 2010

Magnaporthe oryzae is the causal agent of rice blast disease, leading to enormous losses of rice production. Here, we characterized a basic leucine zipper (bZIP) transcription factor, Moatf1, in M. oryzae, a homolog of Schizosaccharomyces pombe ATF/CREB that regulates the oxidative stress response. Moatf1 deletion caused retarded vegetative growth of mycelia, and the Moatf1 mutant exhibited higher sensitivity to hydrogen peroxide (H2O2) than did the wild-type strain. The mutant showed severely reduced activity of extracellular enzymes and transcription level of laccases and peroxidases and exhibited significantly reduced virulence on rice cultivar CO-39. On rice leaf sheath, most of the infectious hyphae of the mutant became swollen and displayed restricted growth in primary infected cells. Defense response was strongly activated in plants infected by the mutant. Diamino benzidine staining revealed an accumulation of H2O2 around Moatf1 mutant appressoria and rice cells with Moatf1 hyphae that was absent in the wild type. Inhibition of the plant NADPH oxidase by diphenyleneiodonium prevented host-derived H2O2 accumulation and restored infectious hyphal growth of the mutant in rice cells. Thus, we conclude that Moatf1 is necessary for full virulence of M. oryzae by regulating the transcription of laccases and peroxidases to impair reactive oxygen species–mediated plant defense.
A Partial Chromosomal Deletion Caused by Random Plasmid Integration Resulted in a Reduced Virulence Phenotype in Fusarium graminearum
Authors: Baldwin Thomas K. , Gaffoor Iffa , Antoniw John , Andries Corrie , Guenther John , Urban Martin , Hallen-Adams Heather E. , Pitkin John , Hammond-Kosack Kim E. , Trail Frances
Published: July 2010

Fusarium graminearum (teleomorph: Gibberella zeae) is an Ascomycete fungal plant pathogen which infects a range of agriculturally important crops, including wheat, barley, and maize. A random plasmid insertion mutagenesis approach was used to analyze the pathogenicity of the PH-1 strain, for which full genomic information is available. Fungal transformants were initially screened for their ability to infect wheat ears. From a total of 1,170 transformants screened, eight were confirmed to be highly reduced in pathogenicity toward wheat ears and roots. These were designated disease-attenuated F. graminearum (daf) mutants. The in vitro growth rate and appearance of each daf mutant was equivalent to the parental strain. Deoxynivalenol (DON) was not detected in threshed grain recovered from ears inoculated with the daf10 mutant. Plasmid rescue and sequencing of the mutant daf10 revealed a deletion of approximately 350 kb from one end of chromosome 1. This chromosome segment is predicted to contain 146 genes. Microarray analysis of daf10 gene expression during growth in DON-inducing conditions confirmed the large deletion. The identities of the genes deleted and their potential role in DON production, pathogenesis, and other life processes are discussed.
Individual right whales call louder in increased environmental noise
Authors: Parks Susan E. , Johnson Mark , Nowacek Douglas , Tyack Peter L.
Published: July 2010

The ability to modify vocalizations to compensate for environmental noise is critical for successful communication in a dynamic acoustic environment. Many marine species rely on sound for vital life functions including communication, navigation and feeding. The impacts of significant increases in ocean noise levels from human activities are a current area of concern for the conservation of marine mammals. Here, we document changes in calling behaviour by individual endangered North Atlantic right whales (
Eubalaena glacialis
) in increased background noise. Right whales, like several bird and primate species, respond to periods of increased noise by increasing the amplitude of their calls. This behaviour may help maintain the communication range with conspecifics during periods of increased noise. These call modifications have implications for conservation efforts for right whales, affecting both the way whales use sound to communicate and our ability to detect them with passive acoustic monitoring systems.
Endophytic fungi reduce leaf-cutting ant damage to seedlings
Authors: Bittleston L. S. , Brockmann F. , Wcislo W. , Van Bael S. A.
Published: July 2010

Our study examines how the mutualism between
Atta colombica
leaf-cutting ants and their cultivated fungus is influenced by the presence of diverse foliar endophytic fungi (endophytes) at high densities in tropical leaf tissues. We conducted laboratory choice trials in which ant colonies chose between
Cordia alliodora
seedlings with high (
E
high
) or low (
E
low
) densities of endophytes. The
E
high
seedlings contained 5.5 times higher endophyte content and a greater diversity of fungal morphospecies than the
E
low
treatment, and endophyte content was not correlated with leaf toughness or thickness. Leaf-cutting ants cut over 2.5 times the leaf area from
E
low
relative to
E
high
seedlings and had a tendency to recruit more ants to
E
low
plants. Our findings suggest that leaf-cutting ants may incur costs from cutting and processing leaves with high endophyte loads, which could impact Neotropical forests by causing variable damage rates within plant communities.
Immune defence under extreme ambient temperature
Authors: Seppälä Otto , Jokela Jukka
Published: July 2010

Owing to global climate change, the extreme weather conditions are predicted to become more frequent, which is suggested to have an even greater impact on ecological interactions than the gradual increase in average temperatures. Here, we examined whether exposure to high ambient temperature affects immune function of the great pond snail (
Lymnaea stagnalis
). We quantified the levels of several immune traits from snails maintained in a non-stressful temperature (15°C) and in an extreme temperature (30°C) that occurs in small ponds during hot summers. We found that snails exposed to high temperature had weaker immune defence, which potentially predisposes them to infections. However, while phenoloxidase and antibacterial activity of snail haemolymph were reduced at high temperature, haemocyte concentration was not affected. This suggests that the effect of high temperature on snail susceptibility to infections may vary across different pathogens because different components of invertebrate immune defence have different roles in resistance.