Beryllium abundances along the evolutionary sequence of the open cluster IC 4651-A new test for hydrodynamical stellar models

Context. Previous analyses of lithium abundances in main sequence and red giant stars have revealed the action of mixing mechanisms other than convection in stellar interiors. Beryllium abundances in stars with Li abundance determinations can offer valuable complementary information on the nature of these mechanisms. Aims. Our aim is to derive Be abundances along the whole evolutionary sequence of an open cluster. We focus on the well-studied open cluster IC 4651. These Be abundances are used with previously determined Li abundances, in the same sample stars, to investigate the mixing mechanisms in a range of stellar masses and evolutionary stages. Methods. Atmospheric parameters were adopted from a previous abundance analysis by the same authors. New Be abundances have been determined from high-resolution, high signal-to-noise UVES spectra using spectrum synthesis and model atmospheres. The careful synthetic modeling of the Be lines region is used to calculate reliable abundances in rapidly rotating stars. The observed behavior of Be and Li is compared to theoretical predictions from stellar models including rotation-induced mixing, internal gravity waves, atomic diffusion, and thermohaline mixing. Results. Beryllium is detected in all the main sequence and turn-off sample stars, both slow- and fast-rotating stars, including the Li-dip stars, but is not detected in the red giants. Confirming previous results, we find that the Li dip is also a Be dip, although the depletion of Be is more modest than for Li in the corresponding effective temperature range. For post-main-sequence stars, the Be dilution starts earlier within the Hertzsprung gap than expected from classical predictions, as does the Li dilution. A clear dispersion in the Be abundances is also observed. Theoretical stellar models including the hydrodynamical transport processes mentioned above are able to reproduce all the observed features well. These results show a good theoretical understanding of the Li and Be behavior along the color-magnitude diagram of this intermediate-age cluster for stars more massive than 1.2 M(circle dot).

Phylogenetic position of the acariform mites: sensitivity to homology assessment under total evidence

Background: Mites (Acari) have traditionally been treated as monophyletic, albeit composed of two major lineages: Acariformes and Parasitiformes. Yet recent studies based on morphology, molecular data, or combinations thereof, have increasingly drawn their monophyly into question. Furthermore, the usually basal (molecular) position of one or both mite lineages among the chelicerates is in conflict to their morphology, and to the widely accepted view that mites are close relatives of Ricinulei. Results: The phylogenetic position of the acariform mites is examined through employing SSU, partial LSU sequences, and morphology from 91 chelicerate extant terminals (forty Acariformes). In a static homology framework, molecular sequences were aligned using their secondary structure as guide, whereby regions of ambiguous alignment were discarded, and pre-aligned sequences analyzed under parsimony and different mixed models in a Bayesian inference. Parsimony and Bayesian analyses led to trees largely congruent concerning infraordinal, well-supported branches, but with low support for inter-ordinal relationships. An exception is Solifugae + Acariformes (P. P = 100%, J. = 0.91). In a dynamic homology framework, two analyses were run: a standard POY analysis and an analysis constrained by secondary structure. Both analyses led to largely congruent trees; supporting a (Palpigradi (Solifugae Acariformes)) clade and Ricinulei as sister group of Tetrapulmonata with the topology (Ricinulei (Amblypygi (Uropygi Araneae))). Combined analysis with two different morphological data matrices were run in order to evaluate the impact of constraining the analysis on the recovered topology when employing secondary structure as a guide for homology establishment. The constrained combined analysis yielded two topologies similar to the exclusively molecular analysis for both morphological matrices, except for the recovery of Pedipalpi instead of the (Uropygi Araneae) clade. The standard (direct optimization) POY analysis, however, led to the recovery of trees differing in the absence of the otherwise well-supported group Solifugae + Acariformes. Conclusions: Previous studies combining ribosomal sequences and morphology often recovered topologies similar to purely morphological analyses of Chelicerata. The apparent stability of certain clades not recovered here, like Haplocnemata and Acari, is regarded as a byproduct of the way the molecular homology was previously established using the instrumentalist approach implemented in POY. Constraining the analysis by a priori homology assessment is defended here as a way of maintaining the severity of the test when adding new data to the analysis. Although the strength of the method advocated here is keeping phylogenetic information from regions usually discarded in an exclusively static homology framework; it still has the inconvenience of being uninformative on the effect of alignment ambiguity on resampling methods of clade support estimation. Finally, putative morphological apomorphies of Solifugae + Acariformes are the reduction of the proximal cheliceral podomere, medial abutting of the leg coxae, loss of sperm nuclear membrane, and presence of differentiated germinative and secretory regions in the testis delivering their products into a common lumen.

Normal and defective mariner-like elements in Rhynchosciara species (Sciaridae, Diptera)

Mariner-like elements are widely present in diverse organisms. These elements constitute a large fraction of the eukaryotic genome; they transpose by a ""cut-and-paste"" mechanism with their own transposase protein. We found two groups of mobile elements in the genus Rhynchosciara. PCR using primers designed from R. americana transposons (Ramar1 and Ramar2) were the starting point for this comparative study. Genomic DNA templates of four species: R. hollaenderi, R. millerii, R. baschanti, and Rhynchosciara sp were used and genomic sequences were amplified, sequenced and the molecular structures of the elements characterized as being putative mariner-like elements. The first group included the putative full-length elements. The second group was composed of defective mariner elements that contain a deletion overlapping most of the internal region of the transposase open reading frame. They were named Rmar1 (type 1) and Rmar2 (type 2), respectively. Many conserved amino acid blocks were identified, as well as a specific D,D(34) D signature motif that was defective in some elements. Based on predicted transposase sequences, these elements encode truncated proteins and are phylogenetically very close to mariner-like elements of the mauritiana subfamily. The inverted terminal repeat sequences that flanked the mariner-like elements are responsible for their mobility. These inverted terminal repeat sequences were identified by inverse PCR.

Complete Genome Sequence of Mycoplasma suis and Insights into Its Biology and Adaption to an Erythrocyte Niche

Mycoplasma suis, the causative agent of porcine infectious anemia, has never been cultured in vitro and mechanisms by which it causes disease are poorly understood. Thus, the objective herein was to use whole genome sequencing and analysis of M. suis to define pathogenicity mechanisms and biochemical pathways. M. suis was harvested from the blood of an experimentally infected pig. Following DNA extraction and construction of a paired end library, whole-genome sequencing was performed using GS-FLX (454) and Titanium chemistry. Reads on paired-end constructs were assembled using GS De Novo Assembler and gaps closed by primer walking; assembly was validated by PFGE. Glimmer and Manatee Annotation Engine were used to predict and annotate protein-coding sequences (CDS). The M. suis genome consists of a single, 742,431 bp chromosome with low G+C content of 31.1%. A total of 844 CDS, 3 single copies, unlinked rRNA genes and 32 tRNAs were identified. Gene homologies and GC skew graph show that M. suis has a typical Mollicutes oriC. The predicted metabolic pathway is concise, showing evidence of adaptation to blood environment. M. suis is a glycolytic species, obtaining energy through sugars fermentation and ATP-synthase. The pentose-phosphate pathway, metabolism of cofactors and vitamins, pyruvate dehydrogenase and NAD(+) kinase are missing. Thus, ribose, NADH, NADPH and coenzyme A are possibly essential for its growth. M. suis can generate purines from hypoxanthine, which is secreted by RBCs, and cytidine nucleotides from uracil. Toxins orthologs were not identified. We suggest that M. suis may cause disease by scavenging and competing for host nutrients, leading to decreased life-span of RBCs. In summary, genome analysis shows that M. suis is dependent on host cell metabolism and this characteristic is likely to be linked to its pathogenicity. The prediction of essential nutrients will aid the development of in vitro cultivation systems.

Silica-based cationic bilayers as immunoadjuvants

Background: Silica particles cationized by dioctadecyldimethylammonium bromide (DODAB) bilayer were previously described. This work shows the efficiency of these particulates for antigen adsorption and presentation to the immune system and proves the concept that silica-based cationic bilayers exhibit better performance than alum regarding colloid stability and cellular immune responses for vaccine design. Results: Firstly, the silica/DODAB assembly was characterized at 1 mM NaCl, pH 6.3 or 5 mM Tris. HCl, pH 7.4 and 0.1 mg/ml silica over a range of DODAB concentrations (0.001-1 mM) by means of dynamic light scattering for particle sizing and zeta-potential analysis. 0.05 mM DODAB is enough to produce cationic bilayer-covered particles with good colloid stability. Secondly, conditions for maximal adsorption of bovine serum albumin (BSA) or a recombinant, heat-shock protein from Mycobacterium leprae (18 kDa-hsp) onto DODAB-covered or onto bare silica were determined. At maximal antigen adsorption, cellular immune responses in vivo from delayed-type hypersensitivity reactions determined by foot-pad swelling tests (DTH) and cytokines analysis evidenced the superior performance of the silica/DODAB adjuvant as compared to alum or antigens alone whereas humoral response from IgG in serum was equal to the one elicited by alum as adjuvant. Conclusion: Cationized silica is a biocompatible, inexpensive, easily prepared and possibly general immunoadjuvant for antigen presentation which displays higher colloid stability than alum, better performance regarding cellular immune responses and employs very low, micromolar doses of cationic and toxic synthetic lipid.

Complete Genome Viral Phylogenies Suggests the Concerted Evolution of Regulatory Cores and Accessory Satellites

We consider the concerted evolution of viral genomes in four families of DNA viruses. Given the high rate of horizontal gene transfer among viruses and their hosts, it is an open question as to how representative particular genes are of the evolutionary history of the complete genome. To address the concerted evolution of viral genes, we compared genomic evolution across four distinct, extant viral families. For all four viral families we constructed DNA-dependent DNA polymerase-based (DdDp) phylogenies and in addition, whole genome sequence, as quantitative descriptions of inter-genome relationships. We found that the history of the polymerase gene was highly predictive of the history of the genome as a whole, which we explain in terms of repeated, co-divergence events of the core DdDp gene accompanied by a number of satellite, accessory genetic loci. We also found that the rate of gene gain in baculovirus and poxviruses proceeds significantly more quickly than the rate of gene loss and that there is convergent acquisition of satellite functions promoting contextual adaptation when distinct viral families infect related hosts. The congruence of the genome and polymerase trees suggests that a large set of viral genes, including polymerase, derive from a phylogenetically conserved core of genes of host origin, secondarily reinforced by gene acquisition from common hosts or co-infecting viruses within the host. A single viral genome can be thought of as a mutualistic network, with the core genes acting as an effective host and the satellite genes as effective symbionts. Larger virus genomes show a greater departure from linkage equilibrium between core and satellites functions.

Leishmania-Specific Surface Antigens Show Sub-Genus Sequence Variation and Immune Recognition

Background: A family of hydrophilic acylated surface (HASP) proteins, containing extensive and variant amino acid repeats, is expressed at the plasma membrane in infective extracellular (metacyclic) and intracellular (amastigote) stages of Old World Leishmania species. While HASPs are antigenic in the host and can induce protective immune responses, the biological functions of these Leishmania-specific proteins remain unresolved. Previous genome analysis has suggested that parasites of the sub-genus Leishmania (Viannia) have lost HASP genes from their genomes. Methods/Principal Findings: We have used molecular and cellular methods to analyse HASP expression in New World Leishmania mexicana complex species and show that, unlike in L. major, these proteins are expressed predominantly following differentiation into amastigotes within macrophages. Further genome analysis has revealed that the L. (Viannia) species, L. (V.) braziliensis, does express HASP-like proteins of low amino acid similarity but with similar biochemical characteristics, from genes present on a region of chromosome 23 that is syntenic with the HASP/SHERP locus in Old World Leishmania species and the L. (L.) mexicana complex. A related gene is also present in Leptomonas seymouri and this may represent the ancestral copy of these Leishmania-genus specific sequences. The L. braziliensis HASP-like proteins (named the orthologous (o) HASPs) are predominantly expressed on the plasma membrane in amastigotes and are recognised by immune sera taken from 4 out of 6 leishmaniasis patients tested in an endemic region of Brazil. Analysis of the repetitive domains of the oHASPs has shown considerable genetic variation in parasite isolates taken from the same patients, suggesting that antigenic change may play a role in immune recognition of this protein family. Conclusions/Significance: These findings confirm that antigenic hydrophilic acylated proteins are expressed from genes in the same chromosomal region in species across the genus Leishmania. These proteins are surface-exposed on amastigotes (although L. (L.) major parasites also express HASPB on the metacyclic plasma membrane). The central repetitive domains of the HASPs are highly variant in their amino acid sequences, both within and between species, consistent with a role in immune recognition in the host.

SOME PROPERTIES OF THE MULTIPLICITY SEQUENCE FOR ARBITRARY IDEALS

In this work we prove that the Achilles-Manaresi multiplicity sequence, like the classical Hilbert-Samuel multiplicity, is additive with respect to the exact sequence of modules. We also prove the associativity formula for his mulitplicity sequence. As a consequence, we give new proofs for two results already known. First, the Achilles-Manaresi multiplicity sequence is an invariant up to reduction, a result first proved by Ciuperca. Second, I subset of J is a reduction of (J,M) if and only if c(0)(I(p), M(p)) = c(0)(J(p), M(p)) for all p is an element of Spec(A), a result first proved by Flenner and Manaresi.

Systematic Management of Variability in UML-based Software Product Lines

This paper presents SMarty, a variability management approach for UML-based software product lines (PL). SMarty is supported by a UML profile, the SMartyProfile, and a process for managing variabilities, the SMartyProcess. SMartyProfile aims at representing variabilities, variation points, and variants in UML models by applying a set of stereotypes. SMartyProcess consists of a set of activities that is systematically executed to trace, identify, and control variabilities in a PL based on SMarty. It also identifies variability implementation mechanisms and analyzes specific product configurations. In addition, a more comprehensive application of SMarty is presented using SEI's Arcade Game Maker PL. An evaluation of SMarty and related work are discussed.

A possible role of ground-based microorganisms on cloud formation in the atmosphere

The formation of clouds is an important process for the atmosphere, the hydrological cycle, and climate, but some aspects of it are not completely understood. In this work, we show that microorganisms might affect cloud formation without leaving the Earth's surface by releasing biological surfactants (or biosurfactants) in the environment, that make their way into atmospheric aerosols and could significantly enhance their activation into cloud droplets. In the first part of this work, the cloud-nucleating efficiency of standard biosurfactants was characterized and found to be better than that of any aerosol material studied so far, including inorganic salts. These results identify molecular structures that give organic compounds exceptional cloud-nucleating properties. In the second part, atmospheric aerosols were sampled at different locations: a temperate coastal site, a marine site, a temperate forest, and a tropical forest. Their surface tension was measured and found to be below 30 mN/m, the lowest reported for aerosols, to our knowledge. This very low surface tension was attributed to the presence of biosurfactants, the only natural substances able to reach to such low values. The presence of strong microbial surfactants in aerosols would be consistent with the organic fractions of exceptional cloud-nucleating efficiency recently found in aerosols, and with the correlations between algae bloom and cloud cover reported in the Southern Ocean. The results of this work also suggest that biosurfactants might be common in aerosols and thus of global relevance. If this is confirmed, a new role for microorganisms on the atmosphere and climate could be identified.

Designing real nanotube-based gas sensors

Using a combination of density functional theory and recursive Green's functions techniques, we present a full description of a large scale sensor, accounting for disorder and different coverages. Here, we use this method to demonstrate the functionality of nitrogen-rich carbon nanotubes as ammonia sensors as an example. We show how the molecules one wishes to detect bind to the most relevant defects on the nanotube, describe how these interactions lead to changes in the electronic transport properties of each isolated defect, and demonstrate that there are significative resistance changes even in the presence of disorder, elucidating how a realistic nanosensor works.

Musical genres: beating to the rhythms of different drums

Online music databases have increased significantly as a consequence of the rapid growth of the Internet and digital audio, requiring the development of faster and more efficient tools for music content analysis. Musical genres are widely used to organize music collections. In this paper, the problem of automatic single and multi-label music genre classification is addressed by exploring rhythm-based features obtained from a respective complex network representation. A Markov model is built in order to analyse the temporal sequence of rhythmic notation events. Feature analysis is performed by using two multi-variate statistical approaches: principal components analysis (unsupervised) and linear discriminant analysis (supervised). Similarly, two classifiers are applied in order to identify the category of rhythms: parametric Bayesian classifier under the Gaussian hypothesis (supervised) and agglomerative hierarchical clustering (unsupervised). Qualitative results obtained by using the kappa coefficient and the obtained clusters corroborated the effectiveness of the proposed method.

DNA-based ionic conducting membranes

Deoxyribonucleic acid based gel solid electrolytes were prepared and their electric properties were characterized. Their ionic conductivity is in the range of 10(-4)-10(-5) S/cm at room temperature and increases linearly in function of temperature, obeying an Arrhenius-like relationship. The present study, combined with the literature data, suggests that the electrical conduction mechanism in these membranes involve ion motion and/or charge hopping, promoted most likely by a significant interaction between the membrane components. The good conductivity results, as found here, together with the good transparency and good adhesion to the electrodes show that the DNA-based gel polymer electrolytes are very promising materials for application in various electrochromic devices. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3610951]

Two-dimensional photonic crystals in antimony-based films fabricated by holography

In this work, we demonstrated the fabrication of two-dimensional (2D) photonic crystals layers (2D-PCLs) by combining holographic recording and the evaporation of antimony-based glasses. Such materials present high refractive indices that can be tuned from 1.8 to 2.4, depending on the film composition; thus, they are interesting dielectric materials for fabrication of 2D-PCLs. The good quality of the obtained samples allowed the measurement of their PC properties through the well-defined Fano resonances that appear in the transmittance spectrum measurements at different incidence angles. The experimental results are in good agreement with the calculated band diagram for the hexagonal asymmetric structure. (C) 2008 American Institute of Physics.

Nanostructured Films Based on Carbon Nanotubes and Cobalt for the Electrocatalytic Reduction of H(2)O(2)

This paper presents the fabrication of a nanothick Co-modified film electrochemically synthesized on layer-by-layer (LbL) structures made with dendrimer polyamidoamine/carbon nanotubes (PAMAM/CNT), and its electrocatalytic properties toward H(2)O(2) reduction. Scanning electron microscopy indicated the formation of a homogeneous, 14 nm thick Co film. The porous nature of the PAMAM/CNT LbL film allowed the electrolyte access to the bottom of the electrode, generating a homogenous Co electrodeposit. In addition, the nanostructure based on Co-modified PAMAM/CNT LbL exhibited high electrocatalytic activity for H(2)O(2) reduction when compared to the Co-free PAMAM/CNT LbL film, which demonstrates the suitability of the system studied for biosensing. (C) 2011 The Electrochemical Society. [DOI: 10.1149/1.3602200] All rights reserved.