bluuebunny/crossref_metadata_2025 huggingface dataset:
Annexin‐1 peptide Anx‐12–26 protects adult rat cardiac myocytes from cellular injury induced by simulated ischaemia
Authors: Ritchie Rebecca H , Gordon Jennifer M , Woodman Owen L , Cao Anh H , Dusting Gregory J
Published: April 2005

The anti‐inflammatory properties of annexin‐1 peptides have been largely ascribed to their powerful antineutrophil actions in vivo. We have recently reported that the N‐terminal fragment of annexin‐1, Anx‐12–26, preserves contractile function of cardiac muscle in vitro. The aim of the present study was to determine if Anx‐12–26 elicits protective actions specifically on the cardiac myocyte (in the absence of neutrophils), using a model of metabolic inhibition to simulate ischaemia.

Metabolic inhibition of cardiac myocytes (4 h incubation at 37°C in HEPES‐containing buffer supplemented with 2‐deoxy‐D‐glucose, D,L‐lactic acid and pH adjusted to 6.5) followed by 2.5 h recovery in normal medium markedly increased creatine kinase (CK) and lactate dehydrogenase (LDH) levels by 179±39 and 26±7 IU L−1 (both n=40, P<0.001), respectively. However, cellular injury was significantly decreased when Anx‐12–26 (0.3 μM) was present during metabolic inhibition, CK by 74±10% and LDH by 71±6% (both n=31, P<0.001), respectively.

Boc 2 (10 μM), a nonselective formyl peptide receptor antagonist, present during metabolic inhibition, abolished the cardioprotective effect of Anx‐12–26.

Addition of chelerythrine (10 μM), 5‐hydroxydecanoate (500 μM) or SB202190 (1 μM) during metabolic inhibition also abolished Anx‐12–26‐induced cardioprotection.

Cellular injury induced by metabolic inhibition was also largely prevented when myocytes were incubated with Anx‐12–26 for 5 min with 10 min recovery prior to the insult, or when Anx‐12–26 was present only during the recovery period following drug‐free metabolic inhibition.

In conclusion, the annexin‐1 peptide Anx‐12–26 potently prevents cardiac myocyte injury induced by metabolic inhibition, an action that was dependent at least in part on the activation of the formyl peptide receptor family of G‐protein‐coupled receptors, protein kinase C, p38 mitogen‐activated protein kinase and ATP‐sensitive potassium channels.

British Journal of Pharmacology (2005) 145, 495–502. doi:10.1038/sj.bjp.0706211
Activation of cannabinoid CB2 receptor negatively regulates IL‐12p40 production in murine macrophages: role of IL‐10 and ERK1/2 kinase signaling
Authors: Correa Fernando , Mestre Leyre , Docagne Fabian , Guaza Carmen
Published: April 2005

Cannabinoid (CB) receptor agonists have potential utility as anti‐inflammatory drugs for the treatment of many disease conditions. In the present study, we investigated the effects of the synthetic CB2 ligand, JWH‐133 on the production of interleukins (ILs), IL‐12 and IL‐10 by lipopolyssacharide (LPS) or Theiler's virus (TMEV)‐activated macrophages.

JWH‐133 evoked a concentration‐related inhibition (10 nM–5 μM) of LPS/IFN‐γ induced IL‐12p40 release. The effect of JWH‐133 (100 nM) was significantly blocked by the CB2 antagonist SR‐144528 (1 μM). Macrophages infected with TMEV increased IL‐12p40 production and activation of CB2 receptors by JWH‐133 (100 nM) inhibited it.

The inhibitory effect of JWH‐133 (100 nM) on IL‐12p40 production may involve extracellular‐regulated kinase (ERK1/2) signaling: (i) JWH‐133 induced a greater and sustained activation of ERK1/2 kinase in comparison with the level of activation observed following LPS; (ii) the inhibition of ERK1/2 by the specific inhibitor PD98059 increased LPS‐induced IL‐12p40 production in the presence or absence of JWH‐133 suggesting a negative regulation of ERK pathway on IL‐12p40 biosynthesis.

Activation of CB2 receptors by JWH‐133 (10 nM–5 μM) enhanced IL‐10 release by LPS/IFN‐γ‐activated macrophages and addition of SR144558 (1 μM) totally blocked the effect of JWH (100 nM).

Inhibition of ERK by PD98059 significantly suppressed IL‐10 production by LPS‐activated macrophages. Endogenous IL‐10 plays a modulatory role in IL‐12 production. Blocking IL‐10 with neutralizing antibody resulted in increased IL‐12p40 secretion by LPS‐activated macrophages in the absence or presence of JWH‐133. In contrast, the addition of exogenous mIL‐10 reduced the secretion of IL‐12p40 in response to LPS.

British Journal of Pharmacology (2005) 145, 441–448. doi:10.1038/sj.bjp.0706215
Activation of calcineurin in human failing heart ventricle by endothelin‐1, angiotensin II and urotensin II
Authors: Li Joan , Wang Jianchun , Russell Fraser D , Molenaar Peter
Published: April 2005

The calcineurin (CaN) enzyme–transcriptional pathway is critically involved in hypertrophy of heart muscle in some animal models. Currently there is no information concerning the regulation of CaN activation by endogenous agonists in human heart.

Human right ventricular trabeculae from explanted human (14 male/2 female) failing hearts were set up in a tissue bath and electrically paced at 1 Hz and incubated with or without 100 nM endothelin‐1 (ET‐1), 10 μM, angiotensin‐II (Ang II) or 20 nM human urotensin‐II (hUII) for 30 min. Tissues from four patients were incubated with 200 nM tacrolimus (FK506) for 30 min and then incubated in the presence or absence of ET‐1 for a further 30 min.

ET‐1 increased contractile force in all 13 patients (P<0.001). Ang II and hUII increased contractile force in three out of eight and four out of 10 patients but overall nonsignificantly (P>0.1). FK506 had no effect on contractile force (P=0.12).

ET‐1, Ang II and hUII increased calcineurin activity by 32, 71 and 15%, respectively, while FK506 reduced activity by 34%. ET‐1 in the presence of FK506 did not restore calcineurin activity (P=0.1).

There was no relationship between basal CaN activity and expression levels in the right ventricle. Increased levels of free phosphate were detected in ventricular homogenates that were incubated with PKCɛ compared to samples incubated without PKCɛ.

Endogenous cardiostimulants which activate Gαq‐coupled receptors increase the activity of calcineurin in human heart following acute (30 min) exposure. PKC may contribute to this effect by increasing levels of phosphorylated calcineurin substrate.

British Journal of Pharmacology (2005) 145, 432–440. doi:10.1038/sj.bjp.0706217
Isolation and characterization of microsatellite loci in the aphid species, Rhopalosiphum padi
Authors: Simon Jean‐Christophe , Leterme Nathalie , Delmotte François , Martin Olivier , Estoup Arnaud
Published: April 2005

Due to their properties for resolving patterns of population genetic structure, microsatellites are increasingly used in studies of breeding systems. Here, eight polymorphic microsatellite loci were isolated and characterized in the aphid Rhopalosiphum padi, in which populations show a mixture of cyclically and obligatory parthenogenetic lines. These loci were then applied to distinguish between 55 parthenogenetic lines of R. padi collected across France. Interestingly, they allowed to detect several copies of the same genotypes among the sample, confirming the great sensitivity of microsatellites and their usefulness in population genetic studies of parthenogenetic organisms.
Characterization of microsatellite loci in the aphid species Macrosiphoniella tanacetaria (Homoptera, Aphididae)
Authors: Massonnet Blandine , Leterme Nathalie , Simon Jean‐Christophe , Weisser Wolfgang W.
Published: April 2005

Measuring dispersal in small insects can now be achieved through the development of highly polymorphic molecular markers. We isolated eight microsatellites in the aphid species Macrosiphoniella tanacetaria Kaltenbach, feeding on the common Tansy (Tanacetum vulgare L.). For each locus, we observed between three and seven alleles and expected heterozogosities ranged between 0.29 and 0.76 within 45 individuals (five aphids/population × nine populations = 45). First analyses revealed that all individuals had different genotypes, showing a great potential variability within and between populations, facilitating the further study of dispersal in aphids.
Indices of multilocus linkage disequilibrium
Authors: Agapow Paul‐Michael , Burt Austin
Published: April 2005

Linkage disequilibrium is an ubiquitous biological phenomenon. However a common metric for disequilibrium – the index of association or IA– is dependent on sample size. In this paper we present a modification of IA that removes this dependency. This method has been implemented in a software package.
Isolation and characterization of 10 microsatellite loci in poor cod Trisopterus minutus (L)
Authors: Zhang De‐Xing , Smith Julie A. , Rico Ciro , Hewitt Godfrey M.
Published: April 2005

The taxonomic status of the Atlantic and Mediterranean poor cod is a controversial issue. Here we present 10 microsatellite loci from poor cod Trisopterus minutus (L), which have been tested across 10 populations of poor cod. Most loci are highly polymorphic with 7–65 alleles, with one exception, the Tmssr two loci. In poor cod it is a compound microsatellite exhibiting extensive allelic variation. These markers have utility for the two subspecies of poor cod and possible utility for the Trisopterus genus. They may also provide a strong tool for detailed population studies in all gadoids.
New microsatellite loci for suckers (Catostomidae): primer homology in Catostomus, Chasmistes, and Deltistes
Authors: Tranah Gregory J. , Agresti Jeremy J. , May Bernie
Published: April 2005

Herein we describe the development of microsatellite markers for five Catostomid species: Catostomus snyderi, Catostomus rimiculus, Chasmistes brevirostris, Deltistes luxatus, and Catostomus occidentalis. A total of 89 primer pairs were developed from enriched (CA)n and (GATA)n libraries created from the D. luxatus genome. The successful amplification of 82 polymorphic loci across three Catostomid genera indicates that the microsatellite markers described in this study will be broadly applicable.
Isolation and characterization of microsatellite loci from the endangered bagrid catfish,Pseudobagrus ichikawai
Authors: Watanabe K. , Watanabe T. , Nishida M.
Published: April 2005

A total of 20 polymorphic microsatellite loci of the Japanese endangered bagrid catfish,Pseudobagrus ichikawai, are reported. The number of alleles per locus, observed heterozygosity and expected heterozygosity ranged from 2 to 10 (4.8 on average), from 0.03 to 0.82 (0.54), and from 0.05 to 0.81 (0.56), respectively. The microsatellite loci will be useful for studying population structure, genetic diversity and mating systems ofP. ichikawai, as well as related species.
Characterization of microsatellite loci in the endangered species of fern Marsilea strigosa Willd. (Marsileaceae, Pteridophyta)
Authors: Vitalis R. , Dubois M.‐P. , Olivieri I.
Published: April 2005

Absence of enzymatic polymorphism in the endangered species of fern Marsilea strigosa prompted us to develop microsatellite loci in this species. We used an enriched partial genomic library, from which six polymorphic microsatellite loci were obtained. From a previous attempt to develop microsatellite markers with standard techniques, a single long and polymorphic locus was obtained. This highlights the benefits from using enrichment techniques in those species where microsatellite loci may be rare in the genome.
A set of primers for amplification of noncoding regions of chloroplast DNA in the grasses
Authors: Saltonstall Kristin
Published: April 2005

Twelve primer pairs, which amplify noncoding regions of chloroplast DNA, were designed for grass species. Their universality was tested on the six major grass subfamilies, and several were sequenced to examine their variability in Phragmites australis. The primers amplified well for most species tested and the majority showed intraspecific variation.
Isolation and characterization of tri‐ and tetranucleotide microsatellite loci in the Asian elephant, Elephas maximus
Authors: Fernando Prithiviraj , Vidya T. N. C. , Melnick Don J.
Published: April 2005

Asian elephants (Elephas maximus) are an endangered species. Their future survival depends on intensive conservation and management, based on in‐depth knowledge of particular populations. Molecular genetic methods, especially microsatellite analysis through noninvasive sampling, provides an effective means of obtaining such information. The use of tri‐ and tetranucleotide microsatellite markers is advantageous in noninvasive sampling through dung analysis. Here we describe the isolation and characterization of five tri‐ and tetranucleotide markers in the Asian elephant. All five loci were found to be polymorphic in a sample of 20 Asian elephants from Sri Lanka.
Pitfalls in determining size homoplasy of microsatellite loci
Authors: Liepelt S. , Kuhlenkamp V. , Anzidei M. , Vendramin G. G. , Ziegenhagen B.
Published: April 2005

Size homoplasy of microsatellite loci can be detected by single‐strand conformation polymorphism analysis (SSCP) or sequence analysis. The present note demonstrates pitfalls of sequencing microsatellite loci. A complex chloroplast microsatellite locus was polymerase chain reaction (PCR) amplified from 33 Abies alba individuals, and the products cloned and sequenced. After 2–7 clones per individual had been sequenced and aligned, differences in repeat numbers occurred among clones of the same individual. It was concluded that the DNA polymerase slippage during PCR most probably caused this variation. A solution specific to the analysed complex locus was found by splitting it into two new loci.
Isolation and characterization of DNA microsatellite from cotton bollworm (Helicoverpa armigera, Hübner)
Authors: Tan Shengjiang , Chen Xiaofeng , Zhang Aibing , Li Dianmo
Published: April 2005

Five microsatellite loci of Helicoverpa armigera were isolated from a partial genomic library screened by oligonucleotide probes. Primers were designed to detect allelic variability and heterozygosity in 60 individuals collected from different host species. All loci were found to be polymorphic, have 8–11 alleles with expected heterozygosity ranging from 0.81 to 0.88. Our results indicate that the five microsatellite loci could provide valuable markers for population genetic and ecological studies of the cotton bollworm.
Isolation and characterization of microsatellite loci in Piaractus mesopotamicus and their applicability in other Serrasalminae fish
Authors: Calcagnotto D. , Russello M. , DeSalle R.
Published: April 2005

The subfamily Serrasalminae (Characidae, Teleostei) is an endemic Neotropical group of fishes distributed along the Amazon, Paraná‐Paraguay and Orinoco Basins. The pacu (Piaractus mesopotamicus) is found in all major rivers that comprise the Pantanal of Mato Grosso. In order to investigate population genetic structure within the group, an enriched microsatellite library was constructed. Eight polymorphic were loci screened, with an average of 6.5 alleles per locus. Five loci exhibited greater than 60% heterozygosity. Additionally, a high level of cross‐species amplification was obtained.
Large mitochondrial repeats multiplied during the polymerase chain reaction
Authors: Campbell Nick J. H. , Sturm Richard A. , Barker Stephen C.
Published: April 2005

The number of repeats in repetitive DNA like micro‐ and minisatellites is often determined by polymerase chain reaction (PCR). When we counted repeats in an array of mitochondrial repeats in the cattle tick (Boophilus microplus) we found that the number of repeats increased during PCR. Multiplication of the repeats was independent of the primers used to amplify the region, the PCR annealing temperature and the length of the PCR product. The use of PCR to determine the number of repeats in arrays needs to be reassessed. For long repeats, a subset of samples should always be analysed by Southern blot hybridization to confirm the PCR results.
Characterization of nine polymorphic microsatellite loci from the alpine accentorPrunella collaris
Authors: Saito D. , Nishiumi I. , Nakamura M.
Published: April 2005

Nine polymorphic microsatellite loci were isolated and characterized from the alpine accentorPrunella collaris. In analyses of 50 unrelated individuals, allelic diversity ranged from 2 to 7, and observed heterozygosity ranged from 0.08 to 0.70. Except for one locus (Pco2), variability was relatively low even in long repeat loci. This result may be due to the high return rate to the natal population. Primer sets were also tested in Japanese accentorPrunella rubida, and seven out of nine loci were successfully amplified.
Isolation and characterization of microsatellite loci from the orchid Serapias vomeracea (Orchidaceae) and cross‐priming to other Serapias species
Authors: Pellegrino G. , Cafasso D. , Widmer A. , Soliva M. , Musacchio A. , Cozzolino S.
Published: April 2005

In this paper we describe the isolation and characterization of six polymorphic microsatellite loci from the orchid Serapias vomeracea. This species is widely distributed in the Mediterranean region. Microsatellite loci were isolated from an enriched library and primer pairs were designed for 18 loci. Primer pairs for six loci amplified well and were tested on samples from southern Italy. Levels of genetic variability detected at these six loci are high, with numbers of alleles per locus ranging from 3 to 6, and observed heterozygosity (HO) ranging from 0.35 to 0.86. All primer pairs tested amplified DNA from four other Serapias species, indicating that the primers are useful for population genetic studies throughout the genus.
Isolation and characterization of microsatellites in the bryozoan Crisia denticulata
Authors: Craig S. F. , D’Amato M. E. , Harley M. , Bishop J. , Hughes R. , Carvalho G. R.
Published: April 2005

Cyclostomata bryozoa are thought to reproduce via polyembryony, a clonal replication of a fertilized egg. To test this hypothesis and to assess the impact of their reproductive strategy on the structure of populations, we isolated microsatellite markers in Crisia denticulata (Cyclostomata, Stenolemata), using an initial enrichment step with random amplified polymorphic DNA (RAPD) primers. A total of nine microsatellites, one tetra‐ and eight dinucleotides repeats were isolated; seven were found to be polymorphic in a test sample of 30 individuals, with allele numbers/locus varying from 2 to 6. The tetranucleotide locus showed heterozygote deficiency. These primers did not amplify the DNA of Crisia eburnea.
Development of simple sequence repeat (SSR) markers for the assessment of gene flow and genetic diversity in pigeonpea (Cajanus cajan)
Authors: Burns M. J. , Edwards K. J. , Newbury H. J. , Ford‐Lloyd B. V. , Baggott C. D.
Published: April 2005

Pigeonpea (Cajanus cajan) is an important subsistence crop in India where traditional landraces and improved hybrids are grown alongside each other. Gene flow may result in genetic erosion of these landraces and their wild relatives, whilst transgene escape from future genetically engineered varieties is another potential hazard. To assess the impact of these factors gene flow needs to be measured. A set of 10 simple sequence repeat markers have been developed, which exhibit polymorphism across a range of pigeonpea varieties. Use of these markers also offers an efficient system for the assessment of genetic diversity within populations of pigeonpea.
Microsatellite primers for Sorbus torminalis and related species
Authors: Oddou‐Muratorio S. , Aligon C. , Decroocq S. , Plomion C. , Lamant T. , Mush‐Demesure B.
Published: April 2005

This study reports the cloning and characterization of nine microsatellite primer pairs in a scattered woody species (Sorbus torminalis), and shows their potential for further use in 36 species of the Maloideae, a Rosaceae subfamily containing important fruit crop and ornamental species. These primers were designed from a microsatellite library constructed from genomic DNA of S. torminalis and enriched for CA and GA repeats. Genotyping 48 S. torminalis of a natural population with the six best markers yielded a mean of 10.7 alleles per locus, and an expectation of exclusion probability for paternity analysis greater than 0.993.
Polymerase chain reaction primers for microsatellite loci in the Common Toad Bufo bufo
Authors: Brede Edward G. , Rowe Graham , Trojanowski Jan , Beebee Trevor J. C.
Published: April 2005

The Common Toad Bufo bufo is a wide‐ranging species, with a distribution encompassing much of Europe and Asia. Few molecular studies have been undertaken on this species, and only one polymorphic microsatellite locus has been identified. Therefore, little is known about the genetic variability within and between B. bufo populations. The value of such information is essential for monitoring the species and its environment. This paper reports the characterization of 15 B. bufo microsatellite loci using individuals from a Spanish and UK sample.
Patterns of Interaction between Populus Esch5 and Piriformospora indica: A Transition from Mutualism to Antagonism
Authors: Kaldorf M. , Koch B. , Rexer K.‐H. , Kost G. , Varma A.
Published: April 2005

Abstract: Piriformospora indica (Sebacinaceae, Basidiomycota) is an axenically cultivable, plant growth promoting root endophyte with a wide host range, including Populus. Rooting of Populus Esch5 explants started within 6 days after transfer to WPM medium. If such plantlets with roots were inoculated with P. indica, there was an increase in root biomass, and the number of 2nd order roots was increased significantly. A totally different observation was recorded when the explants were placed into WPM with pre‐grown P. indica. The interaction led to complete blocking of root production and severely inhibited plant growth. Additionally, branched aerial roots appeared which did not penetrate the medium. On contact with the fungal colony or the medium, the ends of the aerial roots became inflated. Prolonged incubation stimulated the fungus to colonize aerial parts of the plant (stem and leaves). Mycelium not only spread on the surface of the aerial parts, but also invaded the cortical tissues inter‐ and intracellularly. Detached Populus leaves remained vital for 4 ‐ 5 weeks on sterile agar media or on AspM medium with pre‐grown P. indica. When the fungus was pre‐grown on culture media such as WPM, containing ammonium as the main source of nitrogen, leaves in contact with the cultures turned brownish within 4 ‐ 12 h. Thereafter, the leaves bleached, and about one day later had become whitish. Thus, cultural conditions could alter the behaviour of the fungus drastically: the outcome of the interaction between plant and fungus can be directed from mutualistic to antagonistic, characterized by fungal toxin formation and extension of the colonization to Populus shoots.
Thermal Dissipation of Light Energy is Regulated Differently and by Different Mechanisms in Lichens and Higher Plants
Authors: Kopecky J. , Azarkovich M. , Pfündel E. E. , Shuvalov V. A. , Heber U.
Published: April 2005

Abstract: Modulated chlorophyll fluorescence was used to compare dissipation of light energy as heat in photosystem II of homoiohydric and poikilohydric photosynthetic organisms which were either hydrated or dehydrated. In hydrated chlorolichens with an alga as the photobiont, fluorescence quenching revealed a dominant mechanism of energy dissipation which was based on a protonation reaction when zeaxanthin was present. CO2 was effective as a weak protonating agent and actinic light was not necessary. In a hydrated cyanobacterial lichen, protonation by CO2 was ineffective to initiate energy dissipation. This was also true for leaves of higher plants. Thus, regulation of zeaxanthin‐dependent energy dissipation by protonation was different in leaves and in chlorolichens. A mechanism of energy dissipation different from that based on zeaxanthin became apparent on dehydration of both lichens and leaves. Quenching of maximum or Fm fluorescence increased strongly during dehydration. In lichens, this was also true for so‐called basal or Fo fluorescence. In contrast to zeaxanthin‐dependent quenching, dehydration‐induced quenching could not be inhibited by dithiothreitol. Both zeaxanthin‐dependent and dehydration‐induced quenching cooperated in chlorolichens to increase thermal dissipation of light energy if desiccation occurred in the light. In cyanolichens, which do not possess a zeaxanthin cycle, only desiccation‐induced thermal energy dissipation was active in the dry state. Fluorescence emission spectra of chlorolichens revealed stronger desiccation‐induced suppression of 685‐nm fluorescence than of 720‐nm fluorescence. In agreement with earlier reports of Bilger et al. (1989), fluorescence excitation data showed that desiccation reduced flow of excitation energy from chlorophyll b of the light harvesting complex II to emitting centres more than flow from chlorophyll a of core pigments. The data are discussed in relation to regulation and localization of thermal energy dissipation mechanisms. It is concluded that desiccation‐induced fluorescence quenching of lichens results from the reversible conversion of energy‐conserving to energy‐dissipating photosystem II core complexes.
Reproductive Biology of the Epiphytic Bromeliad Werauhia gladioliflora in a Premontane Tropical Forest
Authors: Cascante‐Marín A. , Oostermeijer J. G. B. , Wolf J. H. D. , den Nijs J. C. M.
Published: April 2005

Abstract: The floral phenology, fruit and seed production, and self‐compatibility of Werauhia gladioliflora, an epiphytic bromeliad with a wide distribution, were studied in a premontane forest in the Monteverde area in Costa Rica. The species presents the pollination syndrome of chiropterophily, and it is visited by the small bats Hylonycteris underwoodi and Glossophaga commissarisi (Glossophaginae). The population flowering period extended from October to early December (end of rainy season) and seed dispersal occurred from February to April (dry season). Most plants opened a single flower per night, either every day or at one‐day intervals during the flowering period. In natural conditions, the average fruit set amounted to almost half of the potential output, but individual fecundity (number of seeds) remained high. Seed number per fruit and germination capacity after artificial selfing and out‐crossing treatments did not differ from natural pollination conditions. Werauhia gladioliflora exhibited high levels of autonomous self‐pollination and self‐compatibility at the individual and population level, characters associated with the epiphytic habitat. These reproductive traits are also associated with early colonizer species, yet life history traits, such as seed dispersal, seedling establishment success, and growth, are likely to have a major role in determining the presence of this species in the successional vegetation patches scattered over the studied premontane area.
Allene and pentatetraene cations as models for intramolecular charge transfer: Vibronic coupling Hamiltonian and conical intersections
Authors: Markmann Andreas , Worth Graham A. , Cederbaum Lorenz S.
Published: April 2005

We consider the vibronic coupling effects involving cationic states with degenerate components that can be represented as charge localized at either end of the short cumulene molecules allene and pentatetraene. Our aim is to simulate dynamically the charge transfer process when one component is artificially depopulated. We model the Jahn–Teller vibronic interaction within these states as well as their pseudo-Jahn–Teller coupling with some neighboring states. For the manifold of these states, we have calculated cross sections of the ab initio adiabatic potential energy surfaces along all nuclear degrees of freedom, including points at large distances from the equilibrium to increase the physical significance of our model. Ab initio calculations for the cationic states of allene and pentatetraene were based on the fourth-order Møller–Plesset method and the outer valence Green’s function method. In some cases we had to go beyond this method and use the more involved third-order algebraic diagrammatic construction method to include intersections with satellite states. The parameters for a five-state, all-mode diabatic vibronic coupling model Hamiltonian were least-square fitted to these potentials. The coupling parameters for the diabatic model Hamiltonian are such that, in comparison to allene, an enhanced preference for indirect charge transfer is predicted for pentatetraene.
Günther’s formalism (k-symplectic formalism) in classical field theory: Skinner–Rusk approach and the evolution operator
Authors: Rey Angel M. , Román-Roy Narciso , Salgado Modesto
Published: April 2005

The first aim of this paper is to extend the Skinner–Rusk formalism on classical mechanics for first-order field theories. The second is to generalize the definition and properties of the evolution K-operator on classical mechanics for first-order field theories using in both cases Günther’s formalism (k-symplectic formalism).
Reactions and clustering of water with silica surface
Authors: Ma Yuchen , Foster A. S. , Nieminen R. M.
Published: April 2005

The interaction between silica surface and water is an important topic in geophysics and materials science, yet little is known about the reaction process. In this study we use first-principles molecular dynamics to simulate the hydrolysis process of silica surface using large cluster models. We find that a single water molecule is stable near the surface but can easily dissociate at three-coordinated silicon atom defect sites in the presence of other water molecules. These extra molecules provide a mechanism for hydrogen transfer from the original water molecule, hence catalyzing the reaction. The two-coordinated silicon atom is inert to the water molecule, and water clusters up to pentamer could be stably adsorbed at this site at room temperature.
A linear-scaling self-consistent generalization of the multistate empirical valence bond method for multiple excess protons in aqueous systems
Authors: Wang Feng , Voth Gregory A.
Published: April 2005

An extension to the multistate empirical valence bond (MS-EVB) method is presented in this paper that is capable of treating multiple excess protons within the context of molecular-dynamics simulation. The computational cost of the method scales linearly with respect to the number of excess protons. Calculations for a 0.44 M HCl systems are carried out to illustrate the multiproton extension of the MS-EVB method. A significant decrease in the Eigen-type H9O4+ cation is observed in the contact ion-pair configuration formed between Cl− and hydronium ions.
Levitation effect: Size-dependent maximum in rotational diffusion in confined systems
Authors: Sharma Manju , Bhide S. Y. , Yashonath S.
Published: April 2005

Molecular dynamics of a model guest tetrahedral molecule AX4 with differing bond lengths lAX for A–X bonds have been carried out in a sphere with different surface roughness. The rotational-diffusion coefficient DR shows a maximum for a particular value of lAX. We show that this corresponds to the distance at which the interaction of the guest with the atoms of the host is most favorable. Although, the intensity of the maximum decreases with increase in the roughness of the confining surface, it is seen that the maximum exists even for a reasonably high degree of roughness. The observed maximum arises from the minimum in the torque on the tetrahedral molecule from its interaction with the confining medium due to mutual cancellation of forces. Activation energy for rotation is seen to be also a minimum for the bond length for which DR is a maximum. These results suggest that there is a maximum in the rotational-diffusion coefficient when the rotating molecule is confined to a sphere of comparable size similar to the maximum in translational diffusion coefficient seen in porous solids (the levitation effect) [Yashonath and Santikary J. Phys. Chem. 98, 6368 (1994)]. On increase in the roughness of the sphere surface, the value of lAX at which the maximum in DR is seen decreases.
Correlations between adhesion hysteresis and friction at molecular scales
Authors: Szoszkiewicz R. , Bhushan B. , Huey B. D. , Kulik A. J. , Gremaud G.
Published: April 2005

Correlations between adhesion hysteresis and local friction are theoretically and experimentally investigated. The model is based on the classical theory of adhesional friction, contact mechanics, capillary hysteresis, and nanoscale roughness. Adhesion hysteresis was found to scale with friction through the scaling factor containing a varying ratio of adhesion energy over the reduced Young’s modulus. Capillary forces can offset the relationship between adhesion hysteresis and friction. Measurements on a wide range of engineering samples with varying adhesive and elastic properties confirm the model. Adhesion hysteresis is investigated under controlled, low humidity atmosphere via ultrasonic force microscopy. Friction is measured by the friction force microscopy.
Analysis of the spectrum generating algebra method for obtaining energy spectra
Authors: Cordero Patricio , Daboul Jamil
Published: April 2005

We analyze and clarify how the SGA (spectrum generating algebra) method has been applied to different potentials. We emphasize that each energy level Eν obtained originally by Morse belongs to a different so(2,1) multiplet. The corresponding wave functions Ψν are eigenfuntions of the compact generators J0ν with the same eigenvalue k0, but with different eigenvalues qν of the Casimir operators Q. We derive a general expression for all effective potentials which have Ψλν,ν+m(r)∝(J+ν)mΨλν,ν(r) as eigenfunctions, without using supersymmetry formalism. The different actions of SGA is further illustrated by two diagrams.
The two NUT-like solutions of Ernst equation
Authors: Wu Yabo , Dong Peng , Deng Xuemei , Zhao Guoming
Published: April 2005

By applying Ehlers transformation to Schwarzschild and Kerr solutions of Ernst equation and choosing the suitable coordinate transformations, the two NUT-like solutions, i.e., the so called NUT–Taub-like and the Kerr–NUT-like solutions are obtained which not only can, respectively, reduce to Schwarzschild and Kerr solutions when the parameter l′=0, but also can also reduce to the NUT–Taub metric and Kerr–NUT metric, respectively, when l′ satisfies the some approximation. Meanwhile it is shown that in the NUT–Taub and Kerr–NUT solutions the range of value for the parameter l interpreted as the gravomagnetic monopole cannot be arbitrary and should be confined by mass of the source to ∣l∣⪡m. Furthermore, the differences in the geometrical structure between the NUT–Taub-like and NUT–Taub solutions are discussed and the physical properties of the horizons on the Kerr–NUT-like space–time are analyzed.
Structural control of self-assembled PbTiO3 nanoislands fabricated by metalorganic chemical vapor deposition
Authors: Nonomura Hajime , Nagata Masaki , Fujisawa Hironori , Shimizu Masaru , Niu Hirohiko , Honda Koichiro
Published: April 2005

Self-assembled PbTiO3 nanoislands of three different shapes with orderly in-plane directions were fabricated on Pt∕SrTiO3 substrates by metalorganic chemical vapor deposition. The shapes of the nanoislands were triangular-shaped (width 50–110nm, height 20–30nm), triangular-prism-shaped (width 50–110nm, length 100–550nm, height 10–30nm) and square-shaped (width 40–130nm, height 4–10nm) on Pt∕SrTiO3(111), (101), and (001), respectively. The PbTiO3 nanoislands were epitaxially grown on the Pt∕SrTiO3 substrates and consisted of {100} and {001} facets irrespective of the orientation of the substrates indicating that structural control of shape and in-plane direction of self-assembled PbTiO3 nanoislands can be achieved through epitaxial relations. The self-assembled PbTiO3 nanoislands with three different shapes were found to be ferroelectric by piezoresponse force microscopy.
Electric field-induced transition from heterojunction to bulk charge recombination in bilayer polymer light-emitting diodes
Authors: Morteani Arne C. , Ho Peter K. H. , Friend Richard H. , Silva Carlos
Published: April 2005

We investigate the photo- and electroluminescence from bilayers of electron- and hole-transporting polyfluorene derivatives at different device temperatures. We show that barrier-free charge capture at the heterojunction is the sole capture mechanism at low driving voltages (below 2.4×105V∕cm2 at room temperature). In this mechanism, which we suggested recently [Morteani et al., Adv. Mater. 15, 1708 (2003)], charge capture produces an interfacial excited state (exciplex) directly and bulk exciton electroluminescence is only achieved through endothermic transfer (activation energy 200meV) from the exciplex. For high driving voltages (above 8.3×105V∕cm2 at 43K), however, we find that charges are injected over the heterojunction barriers and subsequent charge recombination occurs in the polymer bulk.
Lattice distortion of MnAs nanocrystals embedded in GaAs: Effect on the magnetic properties
Authors: Moreno M. , Jenichen B. , Däweritz L. , Ploog K. H.
Published: April 2005

The x-ray coherent scattering in nanosized MnAs crystallites embedded in a GaAs matrix has been detected. The room-temperature interatomic distances along three orthogonal directions of the crystallites are determined. The MnAs nanocrystals are found to exhibit an anisotropically distorted hexagonal structure as compared to unstrained bulk MnAs. Despite the crystallite lattice distortion, the granular GaAs:MnAs material exhibits robust ferromagnetism, with enhanced transition temperature. The observed magnetic behavior is consistently explained by a localized double-exchange model of MnAs ferromagnetism, where magnetic order appears for large enough Mn–As–Mn distances, i.e., for weak enough p-d hybridization.
Ferromagnetism of an all-carbon composite composed of a carbon nanowire inside a single-walled carbon nanotube
Authors: Yang Xiaoping , Dong Jinming
Published: April 2005

Using the first-principles spin density functional approach, we have studied magnetism of a type of all-carbon nanomaterials, i.e., the carbon nanowires inserted into the single-walled carbon nanotubes. It is found that if the one-dimensional (1D) carbon nanowire density is not too higher, the ferromagnetic ground state will be more stable than the antiferromagnetic one, which is caused by weak coupling between the 1D carbon nanowire and the single-walled carbon nanotube. Also, both dimerization of the carbon nanowire and carbon vacancy on the tube wall are found to enhance the magnetic moment of the composite.
Intergranular strain correlation with magnetic behavior in steel
Authors: Hutanu Roxana , Clapham Lynann , Rogge R. B.
Published: April 2005

The correlation between the magnetic behavior and intergranular residual strain was investigated on several mild steel samples which were plastically deformed in the range 0.5%–20% engineering strain followed by unloading. At low deformation levels (0.5%–∼2%) the samples exhibited Luders banding, but after 2% strain the samples appeared uniformly deformed. Magnetic Barkhausen noise (MBN) measurements were used to characterize magnetic behavior and neutron diffraction measurements were used to determine the inter-granular strain. MBN results indicated a high MBN value in the direction transverse to the applied stress. This corresponded to a high strain in the (100) crystallographic direction (the easy magnetization direction), as observed using neutron diffraction. Little correlation was obtained between the MBN result and the (112) strain, which is generally assumed to reflect the macroscopic residual stress. Angular MBN and neutron diffraction results further confirmed the strong correlation between the (100) strain and the MBN result.
Inhomogeneous distribution of dislocations in a SiGe graded layer and its influence on surface morphology and misfit dislocations at the interface of strained Si∕Si0.8Ge0.2
Authors: Yuan X. L. , Sekiguchi T. , Niitsuma J. , Sakuma Y. , Ito S. , Ri S. G.
Published: April 2005

To improve the quality of a strained Si layer on a SiGe virtual substrate, the distribution of dislocations in a graded SiGe layer is characterized using electron beam induced current (EBIC). A crosshatch pattern of dark and bright bands running along the two ⟨110⟩ directions is observed in an EBIC image taken with a 25-keV-electron beam at 80 K. These dark and bright EBIC bands are attributed, respectively, to high- and low-density dislocation regions in the graded SiGe layer, as is confirmed by transmission electron microscopy. The effects of such an inhomogeneous dislocation distribution on the surface morphology and the generation of misfit dislocations (MDs) at the interface of strained Si∕SiGe are investigated. Comparison between the EBIC image and an atomic force microscope image shows that the high-density dislocation regions are correlated with ridges on the surface topography. A chemical etching image shows that most of the MDs lie along the edges of surface ridges. Possible mechanisms of MD generation at the interface of the strained Si∕SiGe are proposed.
Magnetic anisotropy and domain patterning of amorphous films by He-ion irradiation
Authors: McCord Jeffrey , Gemming Thomas , Schultz Ludwig , Fassbender Jürgen , Liedke Maciej Oskar , Frommberger Michael , Quandt Eckhard
Published: April 2005

The magnetic anisotropy in amorphous soft magnetic FeCoSiB films was modified by He-ion irradiation. A rotation of uniaxial anisotropy depending on the applied field direction in the irradiated areas is observed by magnetometry and complementary domain observation by Kerr microscopy. No significant degradation in magnetic properties relative to the as-deposited state is found from the magnetization loops on nonpatterned films. Using irradiation together with photolithography, the films were treated locally, resulting in “anisotropy patterned” structures. Complicated periodic domain patterns form due to the locally varying anisotropy distribution. Overall magnetic properties and domain patterns are adjusted.
Direct observation of copper depletion and potential changes at copper indium gallium diselenide grain boundaries
Authors: Hetzer M. J. , Strzhemechny Y. M. , Gao M. , Contreras M. A. , Zunger A. , Brillson L. J.
Published: April 2005

We have used micro-Auger electron spectroscopy, cathodoluminescence spectroscopy, and work function measurements in copper indium gallium diselenide polycrystalline solar cell films cleaved in ultrahigh vacuum. We establish that, relative to the grain interior, the grain boundary shows (1) a Cu composition decrease, as large as a factor of two, (2) a work function decrease of up to 480 meV, and (3) no additional radiative recombination centers despite a high concentration of grain boundary (GB) defects. These results confirm theoretical predictions that (i) polar GB interfaces are stabilized by massive (∼50%) removal of Cu atoms, leading to (ii) a valence band offset between GB and grain interiors that (iii) repels holes from the GB, thus likely reducing GB electron-hole recombination and improving photovoltaic (and other photonic) device operation.
A Rho family GTPase controls actin dynamics and tip growth via two counteracting downstream pathways in pollen tubes
Authors: Gu Ying , Fu Ying , Dowd Peter , Li Shundai , Vernoud Vanessa , Gilroy Simon , Yang Zhenbiao
Published: April 2005

Tip growth in neuronal cells, plant cells, and fungal hyphae is known to require tip-localized Rho GTPase, calcium, and filamentous actin (F-actin), but how they interact with each other is unclear. The pollen tube is an exciting model to study spatiotemporal regulation of tip growth and F-actin dynamics. An Arabidopsis thaliana Rho family GTPase, ROP1, controls pollen tube growth by regulating apical F-actin dynamics. This paper shows that ROP1 activates two counteracting pathways involving the direct targets of tip-localized ROP1: RIC3 and RIC4. RIC4 promotes F-actin assembly, whereas RIC3 activates Ca2+ signaling that leads to F-actin disassembly. Overproduction or depletion of either RIC4 or RIC3 causes tip growth defects that are rescued by overproduction or depletion of RIC3 or RIC4, respectively. Thus, ROP1 controls actin dynamics and tip growth through a check and balance between the two pathways. The dual and antagonistic roles of this GTPase may provide a unifying mechanism by which Rho modulates various processes dependent on actin dynamics in eukaryotic cells.
Inhibition of the anaphase-promoting complex by the Xnf7 ubiquitin ligase
Authors: Casaletto Jessica B. , Nutt Leta K. , Wu Qiju , Moore Jonathan D. , Etkin Laurence D. , Jackson Peter K. , Hunt Tim , Kornbluth Sally
Published: April 2005

Degradation of specific protein substrates by the anaphase-promoting complex/cyclosome (APC) is critical for mitotic exit. We have identified the protein Xenopus nuclear factor 7 (Xnf7) as a novel APC inhibitor able to regulate the timing of exit from mitosis. Immunodepletion of Xnf7 from Xenopus laevis egg extracts accelerated the degradation of APC substrates cyclin B1, cyclin B2, and securin upon release from cytostatic factor arrest, whereas excess Xnf7 inhibited APC activity. Interestingly, Xnf7 exhibited intrinsic ubiquitin ligase activity, and this activity was required for APC inhibition. Unlike other reported APC inhibitors, Xnf7 did not associate with Cdc20, but rather bound directly to core subunits of the APC. Furthermore, Xnf7 was required for spindle assembly checkpoint function in egg extracts. These data suggest that Xnf7 is an APC inhibitor able to link spindle status to the APC through direct association with APC core components.
An internal GAP domain negatively regulates presynaptic dynamin in vivo
Authors: Narayanan Radhakrishnan , Leonard Marilyn , Song Byeong Doo , Schmid Sandra L. , Ramaswami Mani
Published: April 2005

The mechanism by which the self-assembling GTPase dynamin functions in vesicle formation remains controversial. Point mutations in shibire, the Drosophila dynamin, cause temperature-sensitive (ts) defects in endocytosis. We show that the ts2 mutation, which occurs in the switch 2 region of dynamin's GTPase domain, compromises GTP binding affinity. Three second-site suppressor mutations, one in the switch 1 region of the GTPase domain and two in the GTPase effector domain (GED), dynamin's putative GAP, fully rescue the shits2 defects in synaptic vesicle recycling. The functional rescue in vivo correlates with a reduction in both the basal and assembly-stimulated GTPase activity in vitro. These findings demonstrate that GED is indeed an internal dynamin GAP and establish that, as for other GTPase superfamily members, dynamin's function in vivo is negatively regulated by its GAP activity. Based on these and other observations, we propose a two-step model for dynamin during vesicle formation in which an early regulatory GTPase-like function precedes late, assembly-dependent steps during which GTP hydrolysis is required for vesicle release.
Failure to detect capsule gene bexA in Haemophilus influenzae types e and f by real-time PCR due to sequence variation within probe binding sites
Authors: Sam I.-C , Smith M
Published: April 2005

Detection of the conserved capsule gene bexA is used to distinguish capsulate from non-capsulate Haemophilus influenzae. While developing a real-time PCR assay to detect bexA, it was found that bexA probes produced a detectable signal for H. influenzae types a to d, but failed to do so for H. influenzae types e and f. Sequencing revealed differences compared with H. influenzae types a to d within probe binding sites. To prevent misclassification of strains as non-capsulate, assays must detect all capsular types.