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.

Design of 1D and 2D molecule-based magnets with the ligand 4,5-dimethyl-1,2-phenylenebis(oxamato)

Three new bimetallic oxamato-based magnets with the proligand 4,5-dimethyl-1,2-phenylenebis-(oxamato) (dmopba) were synthesized using water or dimethylsulfoxide (DMSO) as solvents. Single crystal X-ray diffraction provided structures for two of them: [MnCu(dmopba)(H(2)O)(3)]n center dot 4nH(2)O (1) and [MnCu(dmopba)(DMSO)(3)](n center dot)nDMSO (2). The crystalline structures for both 1 and 2 consist of linearly ordered oxamato-bridged Mn(II)Cu(II) bimetallic chains. The magnetic characterization revealed a typical behaviour of ferrimagnetic chains for 1 and 2. Least-squares fits of the experimental magnetic data performed in the 300-20 K temperature range led to J(MnCu) = -27.9 cm(-1), g(Cu) = 2.09 and g(Mn) = 1.98 for 1 and J(MnCu) = -30.5 cm(-1), g(Cu) = 2.09 and g(Mn) = 2.02 for 2 (H = -J(MnCu)Sigma S(Mn, i)(S(Cu, i) + S(Cu, i-1))). The two-dimensional ferrimagnetic system [Me(4)N](2n){Co(2)[Cu(dmopba)](3)}center dot 4nDMSO center dot nH(2)O (3) was prepared by reaction of Co(II) ions and an excess of [Cu(dmopba)](2-) in DMSO. The study of the temperature dependence of the magnetic susceptibility as well as the temperature and field dependences of the magnetization revealed a cluster glass-like behaviour for 3.

Adenosine binding to low-molecular-weight purine nucleoside phosphorylase: the structural basis for recognition based on its complex with the enzyme from Schistosoma mansoni

Schistosomes are unable to synthesize purines de novo and depend exclusively on the salvage pathway for their purine requirements. It has been suggested that blockage of this pathway could lead to parasite death. The enzyme purine nucleoside phosphorylase (PNP) is one of its key components and molecules designed to inhibit the low-molecular-weight (LMW) PNPs, which include both the human and schistosome enzymes, are typically analogues of the natural substrates inosine and guanosine. Here, it is shown that adenosine both binds to Schistosoma mansoni PNP and behaves as a weak micromolar inhibitor of inosine phosphorolysis. Furthermore, the first crystal structures of complexes of an LMW PNP with adenosine and adenine are reported, together with those with inosine and hypoxanthine. These are used to propose a structural explanation for the selective binding of adenosine to some LMW PNPs but not to others. The results indicate that transition-state analogues based on adenosine or other 6-amino nucleosides should not be discounted as potential starting points for alternative inhibitors.

Antiferromagnetism with spin polarization of GaN-based diluted magnetic semiconductors

The diluted magnetic semiconductors are promising materials for spintronic applications. Usually one intents to find the ferromagnetic state but recently the antiferromagnetism (AFM) was proposed to have some advantages. In this work, we verify the possibility to obtain spin polarization with an AFM state. In particular, we studied GaN 5% double doped with two different transition metals atoms (Mn and Co or Cr and Ni), forming the Mn(x)Co(0.056-x)Ga(0.944)N and Cr(x)Ni(0.056-x)Ga(0.944)N quaternary alloys. In order to simulate these systems in a more realistic way, and take into account composition fluctuations, we adapted the generalized quasichemical approach to diluted alloys, which is used in combination with spin density-functional theory. We find that is possible to obtain an AFM ground state up to 70% spin polarization.