CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

Recent developments in sequencing technologies have given the opportunity to sequence many bacterial genomes with limited cost and labor, compared to previous techniques. However, a limiting step of genome sequencing is the finishing process, needed to infer the relative position of each contig and close sequencing gaps. An additional degree of complexity is given by bacterial species harboring more than one replicon, which are not contemplated by the currently available programs. The availability of a large number of bacterial genomes allows geneticists to use complete genomes (possibly from the same species) as templates for contigs mapping

Replicon-dependent bacterial genome evolution: the case of Sinorhizobium meliloti

Many bacterial species, such as the alphaproteobacterium Sinorhizobium meliloti, are characterized by open pangenomes and contain multipartite genomes consisting of a chromosome and other large-sized replicons, such as chromids, megaplasmids, and plasmids. The evolutionary forces in both functional and structural aspects that shape the pangenome of species with multipartite genomes are still poorly understood. Therefore, we sequenced the genomes of 10 new S. meliloti strains, analyzed with four publicly available additional genomic sequences. Results indicated that the three main replicons present in these strains (a chromosome, a chromid, and a megaplasmid) partly show replicon-specific behaviors related to strain differentiation. In particular, the p SymB chromid was shown to be a hot spot for positively selected genes, and, unexpectedly, genes resident in the pSymB chromid were also found to be more widespread in distant taxa than those located in the other replicons. Moreover, through the exploitation of a DNA proximity network, a series of conserved "DNA backbones" were found to shape the evolution of the genome structure, with the rest of the genome experiencing rearrangements. The presented data allow depicting a scenario where the pSymB chromid has a distinctive role in intraspecies differentiation and in evolution through positive selection, whereas the pSymA megaplasmid mostly contributes to structural fluidity and to the emergence of new functions, indicating a specific evolutionary role for each replicon in the pangenome evolution. © 2013 The Author(s)

Legislative and ethical aspects on use of canine artificial insemination in the 21st century

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Hierarchichal-segmented AO in order to attain wide field compensation in the visible on an 8m class telescope

We describe the preliminary optimized layout for a partially optimized concept of an optical-8m class VLT-like 2x2 segmented camera where each channel is assisted by an equivalent of an MCAO system where the ground layer correction is commonly employed while the high altitude ones is performed in an open-loop fashion. While we derive the basic relationships among the Field of View and attainable correction with a pre-defined choice for the hardware, we discuss sky coverage and wavefront sensing issues employing natural and artificial references, involving the latest stateof-the-art in the development of wavefront sensing. We show that a flexible approach allow for a compensated Field of View that is variable and can be properly tuned matching the current turbulence situation and the requirement in term of quality of the compensation. A preliminary description of the overall optomechanical package is given as well along with a rough estimates of the efforts required to translates such a concept into reality.Comment: 6 pages, 4 figures, in AO4ELT5 Proceeding

The rational search for selective anticancer derivatives of the peptide Trichogin GA IV: a multi-technique biophysical approach

Peptaibols are peculiar peptides produced by fungi as weapons against other microorganisms. Previous studies showed that peptaibols are promising peptide-based drugs because they act against cell membranes rather than a specific target, thus lowering the possibility of the onset of multi-drug resistance, and they possess non-coded alpha-amino acid residues that confer proteolytic resistance. Trichogin GA IV (TG) is a short peptaibol displaying antimicrobial and cytotoxic activity. In the present work, we studied thirteen TG analogues, adopting a multidisciplinary approach. We showed that the cytotoxicity is tuneable by single amino-acids substitutions. Many analogues maintain the same level of non-selective cytotoxicity of TG and three analogues are completely non-toxic. Two promising lead compounds, characterized by the introduction of a positively charged unnatural amino-acid in the hydrophobic face of the helix, selectively kill T67 cancer cells without affecting healthy cells. To explain the determinants of the cytotoxicity, we investigated the structural parameters of the peptides, their cell-binding properties, cell localization, and dynamics in the membrane, as well as the cell membrane composition. We show that, while cytotoxicity is governed by the fine balance between the amphipathicity and hydrophobicity, the selectivity depends also on the expression of negatively charged phospholipids on the cell surface

Beyond the Weakly Hard Model: Measuring the Performance Cost of Deadline Misses

Most works in schedulability analysis theory are based on the assumption that constraints on the performance of the application can be expressed by a very limited set of timing constraints (often simply hard deadlines) on a task model. This model is insufficient to represent a large number of systems in which deadlines can be missed, or in which late task responses affect the performance, but not the correctness of the application. For systems with a possible temporary overload, models like the m-K deadline have been proposed in the past. However, the m-K model has several limitations since it does not consider the state of the system and is largely unaware of the way in which the performance is affected by deadline misses (except for critical failures). In this paper, we present a state-based representation of the evolution of a system with respect to each deadline hit or miss event. Our representation is much more general (while hopefully concise enough) to represent the evolution in time of the performance of time-sensitive systems with possible time overloads. We provide the theoretical foundations for our model and also show an application to a simple system to give examples of the state representations and their use

Beyond the Weakly Hard Model: Measuring the Performance Cost of Deadline Misses (Artifact)

This document provides a brief description of the artifact material related to the paper "Beyond the Weakly Hard Model: Measuring the Performance Cost of Deadline Misses". The code provided in the artifact implements the algorithms presented in the paper and all the experimental tests

Multiple Spatial Frequencies Pyramid WaveFront Sensing

A modification of the pyramid wavefront sensor is described. In this conceptually new class of devices, the perturbations are split at the level of the focal plane depending upon their spatial frequencies, and then measured separately. The aim of this approach is to increase the accuracy in the determination of some range of spatial frequency perturbations, or a certain classes of modes, disentangling them from the noise associated to the Poissonian fluctuations of the light coming from the perturbations outside of the range of interest or from the background in the pupil planes; the latter case specifically when the pyramid wavefront sensor is used with a large modulation. While the limits and the effectiveness of this approach should be further investigated, a number of variations on the concept are shown, including a generalization of the spatial filtering in the point-diffraction wavefront sensor. The simplest application, a generalization to the pyramid of the well-known spatially filtering in wavefront sensing, is showing promise as a significant limiting magnitude advance. Applications are further speculated in the area of extreme adaptive optics and when serving spectroscopic instrumentation where “light in the bucket” rather than Strehl performance is required