Comparative genomics among members of the Streptococcus bovis/Streptococcus equinus complex

Background: Today, only one streptococcal species, i.e. Streptococcus thermophilus is recognized as food-grade. Interestingly, other streptococci like Streptococcus macedonicus and Streptococcus infantarius belonging to the Streptococcus bovis/Streptococcus equinus complex (SBSEC) are also found in food matrices. However, these species are phylogenetically related to Streptococcus gallolyticus and Streptococcus pasteurianus that have been linked to endocarditis, bacteremia and colon cancer. Objectives: To compare the available genomes of the members of the SBSEC in order to shed light onto their evolution and phylogenetic relation and to assess in silico their pathogenic potential. Methods: Comparative genomics analysis including full chromosome and CDS alignments, whole genome phylogeny and evaluation of gene content (e.g. core genome, singletons, etc.) was performed with appropriate bioinformatics tools. Conclusions: Despite the fact that the four species of the SBSEC were found tightly related based on whole genome phylogeny, there were two different patterns of evolution among them. Streptococcus pasteurianus, S. macedonicus and S. infantarius seem to have undergone a reductive evolution process that resulted in significantly diminished genome sizes and increased percentages of potential pseudogenes when compared to S. gallolyticus. In addition, S. pasteurianus, S. macedonicus and S. infantarius seem to have lost several genes previously linked to the ability of S. gallolyticus to survive in the gastrointestinal tract of herbivores and to its pathogenicity. Our findings indicate differences in the ecological niche and the pathogenic potential among the four species

An integrated assessment framework for the analysis of multiple pressures in aquatic ecosystems and the appraisal of management options

The contribution illustrates an integrated assessment framework aimed at evaluating the relationships between multiple pressures and water body status for the purposes of river basin management. The framework includes the following steps. (1) Understanding how the different pressures affect the status of water bodies. This entails the characterization of biophysical state variables and the definition of a causal relationship between pressures and status. Therefore this step involves interaction between experts bearing ecological understanding and experts providing models to represent the effect of pressures. (2) Identifying the relevant pressures to be addressed through appropriate measures to improve the status of water bodies. (3) Evaluating reduction targets for the relevant pressures identified in a river basin, by weighting the effort associated to reducing individual pressures and the potential benefits in terms of water body status. (4) Designing management measures through a creative process and political discussion of alternative options, balancing costs, benefits and effectiveness based on engineering and economic analysis. (5) Simulating scenarios of implementation of a programme of measures in order to check their effectiveness and robustness against climate and land use change. We discuss the five steps of the assessment framework, and particularly the interaction between science and policy at the different stages. We review the assessment tools required at each step and, for setting optimal pressure reduction targets (step 3), we propose and illustrate a simplified multicriteria approach based on semi-quantitative assessment, which produces frontiers of optimal trade-offs between effort spent on measures, and achievements

Properties of contactless and contacted charging in MEMS capacitive switches

The dielectric charging in MEMS capacitive switches is a complex effect. The high electric field during pull-down causes intrinsic free charge migration and dipole orientation as well as charge injection. The macroscopic dipole moment of the first two mechanisms is opposite to the one arising from charge injection. This causes partial compensation hence mitigates the overall charging and increases the device lifetime. The charging due to intrinsic free charge migration and dipole orientation can be monitored under contactless electric field application in the pull-up state. The paper investigates the characteristics of contactless charging and compares them with the ones of contacted charging. The characteristics of the discharging process that follows each charging procedure are also presented

Charging and Discharging Processes in AlN Dielectric Films Deposited by Plasma Assisted Molecular Beam Epitaxy

In the present work the electrical properties of AlN polycrystalline films deposited at low temperatures by plasma-assisted molecular beam epitaxy (PA-MBE) are investigated. The polarization build-up during constant current injection as well as the depolarization process after the current stress have been investigated through monitoring voltage transients in Metal – Insulator – Metal (MIM) capacitors, in temperature range from 300 K to 400 K. Moreover, current – voltage characteristics obtained at different temperatures revealed that charge collection at low fields in these films occurs through variable range hopping

GABRB3 mutations: a new and emerging cause of early infantile epileptic encephalopathy

The gamma-aminobutyric acid type A receptor β3 gene (GABRB3) encodes the β3-subunit of the gamma-aminobutyric acid type A (GABAA ) receptor, which mediates inhibitory signalling within the central nervous system. Recently, GABRB3 mutations have been identified in a few patients with infantile spasms and Lennox-Gastaut syndrome. We report the clinical and electrographic features of a novel case of GABRB3-related early-onset epileptic encephalopathy. Our patient presented with neonatal hypotonia and feeding difficulties, then developed pharmacoresistant epileptic encephalopathy, characterized by multiple seizure types from 3 months of age. Electroencephalography demonstrated ictal generalized and interictal multifocal epileptiform abnormalities. Using a SureSelectXT custom multiple gene panel covering 48 early infantile epileptic encephalopathy/developmental delay genes, a novel de novo GABRB3 heterozygous missense mutation, c.860C>T (p.Thr287Ile), was identified and confirmed on Sanger sequencing. GABRB3 is an emerging cause of early-onset epilepsy. Novel genetic technologies, such as whole-exome/genome sequencing and multiple gene panels, will undoubtedly identify further cases, allowing more detailed electroclinical delineation of the GABRB3-related genotypic and phenotypic spectra

Comparative genomics of Streptococcus macedonicus ACA-DC 198 against related species within the Streptococcus bovis/Streptococcus equinus complex

Apart from Streptococcus thermophilus other streptococci that can be found growing in milk belong to the Streptococcus bovis/Streptococcus equinus complex (SBSEC). Interestingly, Streptococcus macedonicus, which is a member of SBSEC, has been suggested to be adapted to milk and to be nonpathogenic. However, the species is phylogenetically related to Streptococcus gallolyticus and Streptococcus pasteurianus (formerly known as S. bovis biotypes I and II.2, respectively), which in turn are considered pathogenic, since they have been implicated in endocarditis and colon cancer in humans. Comparative analysis of the S. macedonicus genome with the complete genomes of its related streptococci (including that of S. infantarius, which is also a dairy isolate) indicated that a significant portion of the genomic organization has been conserved overall. Following a gene presence/absence strategy, we determined that S. macedonicus shows a reduced capacity to reside in the gastrointestinal tract of ruminants when compared to S. gallolyticus since it misses important genes for metabolizing complex carbohydrates of plant origin and for detoxifying this environment. S. macedonicus also lacks several pathogenicity traits found in S. gallolyticus. For example from the three pilus gene clusters (pil1, pil2, pil3), which may mediate the binding of S. gallolyticus to the extracellular matrix, S. macedonicus carries only one (i.e. the pil3). Gene gain events are also evident in the S. macedonicus genome sometimes originating from dairy bacteria, like the acquisition of the lactococcal plasmid pSMA198. Functional analysis of the S. macedonicus genome is necessary to further assess its pathogenic and technological potential

ρ\rho - nucleus bound states in Walecka model

Possible formation of $\rho$ nucleus bound state is studied in the framework of Walecka model. The bound states are found in different nuclei ranging from $^3He$ to $^{208}Pb$. These bound states may have a direct bearing on the recent experiments on the photoproduction of $\rho$ meson in the nuclear medium.Comment: RevTeX fil