DEVELOPMENT OF A WEBTOOL FOR INTERACTOME­SEQUENCING DATA ANALYSIS AND IDENTIFICATION OF H. PYLORI EPITOPES RESPONSIBLE FOR HOST IMMUNO­RESPONSE MODULATION.

To elucidate the molecular mechanisms involved in persistency/latency of the H. pylori infection or in its progression towards serious diseases, it is necessary to analyse the host pathogen interaction in vivo. The circulating antibody repertoire represents an important source of diagnostic information, serving as biomarker to provide a \u201cdisease signature\u201d. The aim of this work is the identification of H. pylori epitopes responsible for host immuno\uadresponse modulation through: a discovery\uaddriven approach that couples \u201cphage display\u201d and deep sequencing (interactome-sequencing) and the development of a specific webtool for interactome-sequencing data analysis. We used this approach to identify novel antigens by screening gDNA libraries created from the pathogen\u2019s genome, directly with sera from infected patients. Two genomic phage display libraries from 26695 and B128 H. pylori strains have been constructed by using f\uadlactamase ORF selection vector. Genomic DNA was sonicated, fragments cloned into the filtering vector, after transformation libraries of 1x106 clones were obtained and sequenced by Illumina technology. More than 93% of Hp CDSs were represented in the phage genomic libraries therefore being representative of the whole H. pylori antigenic ORFeome. A webtool for interactome-sequencing data analysis was developed and used to identify the H. pylori antigens/epitopes which could be considered specific for infection progression towards three different pathological outcomes. Putative antigens were selected from libraries using sera from patients affected by: i) gastric adenocarcinoma; ii) autoimmune gastritis; iii) MALT lymphoma. The results, obtained thanks to the new interactome sequencing pipeline developed, show that the diversity of the libraries after selection is significantly reduced. Furthermore, individual ranks, for each infection condition, have been compared highlighting the pattern of putative antigens, shared by all the conditions, and some that can distinguish the different stages of infection. One of this new antigens, that seems to be specific for infection progression towards more serious diseases, has been successfully validated through ELISA assay on a wide number of sera from patients. Other more specific antigens identified by our approach and by the application of the new data analysis pipeline here described are in validation

Visuo-spatial attention deficit in children with reading difficulties

Although developmental reading disorders (developmental dyslexia) have been mainly associated with auditory-phonological deficits, recent longitudinal and training studies have shown a possible causal role of visuo-attentional skills in reading acquisition. Indeed, visuo-attentional mechanisms could be involved in the orthographic processing of the letter string and the graphemic parsing that precede the grapheme-to-phoneme mapping. Here, we used a simple paper-and-pencil task composed of three labyrinths to measure visuo-spatial attention in a large sample of primary school children (n = 398). In comparison to visual search tasks requiring visual working memory, our labyrinth task mainly measures distributed and focused visuo-spatial attention, also controlling for sensorimotor learning. Compared to typical readers (n = 340), children with reading difficulties (n = 58) showed clear visuo-spatial attention impairments that appear not linked to motor coordination and procedural learning skills implicated in this paper and pencil task. Since visual attention is dysfunctional in about 40% of the children with reading difficulties, an efficient reading remediation program should integrate both auditory-phonological and visuo-attentional interventions

ELVIS - ELectromagnetic Vector Information Sensor

The ELVIS instrument was recently proposed by the authors for the Indian Chandrayaan-1 mission to the Moon and is presently under consideration by the Indian Space Research Organisation (ISRO). The scientific objective of ELVIS is to explore the electromagnetic environment of the moon. ELVIS samples the full three-dimensional (3D) electric field vector, E(x,t), up to 18 MHz, with selective Nyqvist frequency bandwidths down to 5 kHz, and one component of the magnetic field vector, B(x,t), from a few Hz up to 100 kHz.As a transient detector, ELVIS is capable of detecting pulses with a minimum pulse width of 5 ns. The instrument comprises three orthogonal electric dipole antennas, one magnetic search coil antenna and a four-channel digital sampling system, utilising flexible digital down conversion and filtering together with state-of-the-art onboard digital signal processing.Comment: 8 pages, 3 figures. Submitted to the DGLR Int. Symposium "To Moon and Beyond", Bremen, Germany, 2005. Companion paper to arXiv:astro-ph/050921

Exploring the genetic landscape of nitrogen uptake in durum wheat: genome-wide characterization and expression profiling of NPF and NRT2 gene families

Nitrate uptake by plants primarily relies on two gene families: Nitrate transporter 1/peptide transporter (NPF) and Nitrate transporter 2 (NRT2). Here, we extensively characterized the NPF and NRT2 families in the durum wheat genome, revealing 211 NPF and 20 NRT2 genes. The two families share many Cis Regulatory Elements (CREs) and Transcription Factor binding sites, highlighting a partially overlapping regulatory system and suggesting a coordinated response for nitrate transport and utilization. Analyzing RNA-seq data from 9 tissues and 20 cultivars, we explored expression profiles and co-expression relationships of both gene families. We observed a strong correlation between nucleotide variation and gene expression within the NRT2 gene family, implicating a shared selection mechanism operating on both coding and regulatory regions. Furthermore, NPF genes showed highly tissue-specific expression profiles, while NRT2s were mainly divided in two co-expression modules, one expressed in roots (NAR2/NRT3 dependent) and the other induced in anthers and/ovaries during maturation. Our evidences confirmed that the majority of these genes were retained after small-scale duplication events, suggesting a neo- or sub-functionalization of many NPFs and NRT2s. Altogether, these findings indicate that the expansion of these gene families in durum wheat could provide valuable genetic variability useful to identify NUE-related and candidate genes for future breeding programs in the context of low-impact and sustainable agriculture

EUROMEDITERRANEAN BIOMEDICAL JOURNAL: THE RENEWED MANUSCRIPT LAYOUT AND WEB RENDERING FORESHADOW FURTHER JOURNAL IMPROVEMENT

In January 2006, a new journal, Capsula Eburnea, was born into the Italian scientific publishing scene with the initial goal of creating, at the same time, \u201can open scientific forum and a blog\u201d, based on the premise that \u201cin medicine, nothing should be considered stable, immutable or unsusceptible to critical review at any time, by any scientist\u201d. The Editorial Team progressively sought to improve the quality of the manuscripts published, introducing the requirement for all articles to be written in English, and changed the Journal\u2019s name to EuroMediterranean Biomedical Journal in 2012. Over the last five years, approximately 125 articles by young doctors (including original articles, reviews, commentaries, notes, and abstract books) have been published. The editorial board are confident that the new publishing layout and the renewed web-portal of the journal, introduced in this editorial, represent an essential upgrade after over 10 years of editorial activity, and that these improvements will be appreciated by our authors and, especially, our readers

Genomic and transcriptomic comparison between Staphylococcus aureus strains associated with high and low within herd prevalence of intra-mammary infection

Background: Staphylococcus aureus (Staph. aureus) is one of the major pathogens causing mastitis in dairy ruminants worldwide. The chronic nature of Staph. aureus infection enhances the contagiousness risk and diffusion in herds. In order to identify the factors involved in intra-mammary infection (IMI) and diffusion in dairy cows, we investigated the molecular characteristics of two groups of Staph. aureus strains belonging to ST8 and ST398, differing in clinical properties, through comparison of whole genome and whole transcriptome sequencing. Results: The two groups of strains, one originated from high IMI prevalence herds and the other from low IMI prevalence herds, present a peculiar set of genes and polymorphisms related to phenotypic features, such as bacterial invasion of mammary epithelial cells and host adaptation. Transcriptomic analysis supports the high propensity of ST8 strain to chronicity of infection and to a higher potential cytotoxicity. Conclusions: Our data are consistent with the invasiveness and host adaptation feature for the strains GTB/ST8 associated to high within-herd prevalence of mastitis. Variation in genes coding for surface exposed proteins and those associated to virulence and defence could constitute good targets for further research

Behavior of four main dairy pathogenic bacteria during manufacturing and ripening of pecorino siciliano cheese

Background: Consumption of raw cheese may be associated with different diseases. This study aimed to evaluate behavior of four pathogenic bacteria during manufacture and ripening of Protected Designation of Origin (PDO) Pecorino Siciliano cheese. Methods: The experimental cheese groups were inoculated with pathogenic bacteria, including Escherichia coli O157, Listeria monocytogenes, Salmonella Enteritidis, and Staphylococcus aureus. The cheese making processes were monitored from milk curdling until 3 months ripened cheeses and the levels of Lactic Acid Bacteria (LAB) and the four dairy pathogens were evaluated by plate counts. Randomly Amplified Polymorphic DNA (RAPD)-Polymerase Chain Reaction (PCR) analysis was applied to confirm that the colonies isolated during the several steps of production were the same strains added in milk. Statistical analysis was done using XLStat software. Results: The levels of mesophilic and thermophilic coccus and rod LAB in curd were comparable in both trials and reached values between 8-9 log10 Colony Forming Unit (CFU)/g in cheeses at 90 days of ripening. The four pathogenic bacteria were found in experimental curd at levels higher than those inoculated in milk and completely disappeared after 60 days of ripening. The RAPD analysis clearly demonstrated the presence of the added strain during production and confirmed the results of plate counts. Conclusion: This work showed that the production conditions of PDO Pecorino Siciliano cheese decreased growth of E. coli O157, L. monocytogenes, S. Enteritidis, and S. aureus

Transcriptome changes induced by Arbuscular mycorrhizal symbiosis in leaves of durum wheat (Triticum durum Desf.) promote higher salt tolerance

The salinity of soil is a relevant environmental problem around the world, with climate change raising its relevance, particularly in arid and semiarid areas. Arbuscular Mycorrhizal Fungi (AMF) positively affect plant growth and health by mitigating biotic and abiotic stresses, including salt stress. The mechanisms through which these benefits manifest are, however, still unclear. This work aimed to identify key genes involved in the response to salt stress induced by AMF using RNA-Seq analysis on durum wheat (Triticum turgidum L. subsp. durum Desf. Husn.). Five hundred sixty-three differentially expressed genes (DEGs), many of which involved in pathways related to plant stress responses, were identified. The expression of genes involved in trehalose metabolism, RNA processing, vesicle trafficking, cell wall organization, and signal transduction was significantly enhanced by the AMF symbiosis. A downregulation of genes involved in both enzymatic and non-enzymatic oxidative stress responses as well as amino acids, lipids, and carbohydrates metabolisms was also detected, suggesting a lower oxidative stress condition in the AMF inoculated plants. Interestingly, many transcription factor families, including WRKY, NAC, and MYB, already known for their key role in plant abiotic stress response, were found differentially expressed between treatments. This study provides valuable insights on AMF-induced gene expression modulation and the beneficial effects of plant-AMF interaction in durum wheat under salt stress

Beta-synemin expression in cardiotoxin-injected rat skeletal muscle

Background: β-synemin was originally identified in humans as an α-dystrobrevin-binding protein through a yeast two-hybrid screen using an amino acid sequence derived from exons 1 through 16 of α-dystrobrevin, a region common to both α-dystrobrevin-1 and -2. α-Dystrobrevin-1 and -2 are both expressed in muscle and co-localization experiments have determined which isoform preferentially functions with β-synemin in vivo. The aim of our study is to show whether each α-dystrobrevin isoform has the same affinity for β-synemin or whether one of the isoforms preferentially functions with β-synemin in muscle. Methods: The two α-dystrobrevin isoforms (-1 and -2) and β-synemin were localized in regenerating rat tibialis anterior muscle using immunoprecipitation, immunohistochemical and immunoblot analyses. Immunoprecipitation and co-localization studies for α-dystrobrevin and β-synemin were performed in regenerating muscle following cardiotoxin injection. Protein expression was then compared to that of developing rat muscle using immunoblot analysis.Results: With an anti-α-dystrobrevin antibody, β-synemin co-immunoprecipitated with α-dystrobrevin whereas with an anti-β-synemin antibody, α-dystrobrevin-1 (rather than the -2 isoform) preferentially co-immunoprecipitated with β-synemin. Immunohistochemical experiments show that β-synemin and α-dystrobrevin co-localize in rat skeletal muscle. In regenerating muscle, β-synemin is first expressed at the sarcolemma and in the cytoplasm at day 5 following cardiotoxin injection. Similarly, β-synemin and α-dystrobrevin-1 are detected by immunoblot analysis as weak bands by day 7. In contrast, immunoblot analysis shows that α-dystrobrevin-2 is expressed as early as 1 day post-injection in regenerating muscle. These results are similar to that of developing muscle. For example, in embryonic rats, immunoblot analysis shows that β-synemin and α-dystrobevin-1 are weakly expressed in developing lower limb muscle at 5 days post-birth, while α-dystrobrevin-2 is detectable before birth in 20-day post-fertilization embryos. Conclusion: Our results clearly show that β-synemin expression correlates with that of α-dystrobrevin-1, suggesting that β-synemin preferentially functions with α-dystrobrevin-1 in vivo and that these proteins are likely to function coordinately to play a vital role in developing and regenerating muscle