Exploring the larval transcriptome of the common sole (Solea solea L.)

open7noBackground The common sole (Solea solea) is a promising candidate for European aquaculture; however, the limited knowledge of the physiological mechanisms underlying larval development in this species has hampered the establishment of successful flatfish aquaculture. Although the fact that genomic tools and resources are available for some flatfish species, common sole genomics remains a mostly unexplored field. Here, we report, for the first time, the sequencing and characterisation of the transcriptome of S. solea and its application for the study of molecular mechanisms underlying physiological and morphological changes during larval-to-juvenile transition. Results The S. solea transcriptome was generated from whole larvae and adult tissues using the Roche 454 platform. The assembly process produced a set of 22,223 Isotigs with an average size of 726 nt, 29 contigs and a total of 203,692 singletons. Of the assembled sequences, 75.2% were annotated with at least one known transcript/protein; these transcripts were then used to develop a custom oligo-DNA microarray. A total of 14,674 oligonucleotide probes (60 nt), representing 12,836 transcripts, were in situ synthesised onto the array using Agilent non-contact ink-jet technology. The microarray platform was used to investigate the gene expression profiles of sole larvae from hatching to the juvenile form. Genes involved in the ontogenesis of the visual system are up-regulated during the early stages of larval development, while muscle development and anaerobic energy pathways increase in expression over time. The gene expression profiles of key transcripts of the thyroid hormones (TH) cascade and the temporal regulation of the GH/IGF1 (growth hormone/insulin-like growth factor I) system suggest a pivotal role of these pathways in fish growth and initiation of metamorphosis. Pre-metamorphic larvae display a distinctive transcriptomic landscape compared to previous and later stages. Our findings highlighted the up-regulation of gene pathways involved in the development of the gastrointestinal system as well as biological processes related to folic acid and retinol metabolism. Additional evidence led to the formation of the hypothesis that molecular mechanisms of cell motility and ECM adhesion may play a role in tissue rearrangement during common sole metamorphosis. Conclusions Next-generation sequencing provided a good representation of the sole transcriptome, and the combination of different approaches led to the annotation of a high number of transcripts. The construction of a microarray platform for the characterisation of the larval sole transcriptome permitted the definition of the main processes involved in organogenesis and larval growth. Keywords: Solea solea; Flatfish; Larval development; Metamorphosis; Transcriptome; Gene expressionopenSerena Ferraresso; Alessio Bonaldo; Luca Parma; Stefano Cinotti; Paola Massi; Luca Bargelloni; Pier Paolo GattaSerena Ferraresso; Alessio Bonaldo; Luca Parma; Stefano Cinotti; Paola Massi; Luca Bargelloni; Pier Paolo Gatt

Mass Corrections to Flavor-Changing Fermion-Graviton Vertices in the Standard Model

In a previous study, the flavor-changing fermion-graviton interactions have been analyzed in the framework of the standard model, where analytical results for the relevant form factors were obtained at the leading order in the external fermion masses. These interactions arise at one-loop level by the charged electroweak corrections to the fermion-graviton vertex, when the off-diagonal flavor transitions in the corresponding charged weak currents are taken into account. Due to the conservation of the energy-momentum tensor, the corresponding form factors turn out to be finite and gauge invariant when external fermions are on-shell. Here we extend this previous analysis by including the exact dependence on the external fermion masses. Complete analytical results are provided for all the relevant form factors to the flavor-changing fermion-graviton transitions.Comment: 19 pages, 9 figure

IgA anti-Actin antibodies in children with celiac disease: comparison of immunofluorescence with Elisa assay in predicting severe intestinal damage

<p>Abstract</p> <p>Background</p> <p>Previous studies have demonstrated that the presence of serum IgA antibodies against actin filaments (AAA) in patients with celiac disease (CD) is strongly associated with mucosal damage and severe degrees of villous atrophy.</p> <p>The aims of the present study were (1) to verify the effectiveness of IgA-AAA in newly diagnosed CD patients in a clinical setting (2) to compare the immunofluorescence assay with ELISA assay; (3) to compare the correlation of our IgA anti-tissue transglutaminase antibodies (tTG-Ab) class with mucosal intestinal lesions.</p> <p>Methods</p> <p>90 patients underwent endoscopy and multiple biopsies for suspected CD on the basis of symptoms, in presence of positive tTG-Ab tests. Twenty biopsied and 25 not-biopsied subjects with negative tTG-Ab were tested as control groups.</p> <p>IgA-AAA assays were performed by indirect immunofluorescence using rat epithelial intestinal cells, and by ELISA with a commercial kit. tTG-Ab assay was a radio-binding assay.</p> <p>Intestinal specimens were collected by upper endoscopy and the histological study was done according to the Marsh's classification modified by Oberhuber (M/O). Auto-antibodies assays and histological evaluation have been performed blindly by skilled operators.</p> <p>Results</p> <p>CD diagnosis was confirmed in 82 patients (type I M/O in 2 patients, IIIA in 18 patients, IIIB in 29 patients and IIIC in 33 patients). Two patients with type 1 lesion in presence of positive tTG-Ab and abdominal complaints, started a gluten free diet.</p> <p>The rate of IgA-AAA positivity (sensitivity) by IFI and ELISA in histologically proven celiac disease patients, were 5.5% and 25% patients in IIIA, 27.5% and 34.4% patients in IIIB, 78.8% and 75% in IIIC patients, respectively.</p> <p>Patients with normal or nearly normal mucosa, regardless of tTG-Ab status, presented negative IgA-AAA IFI assay. On the other hand, 1 patient with normal mucosa but positive tTG-Ab, also presented positive IgA-AAA ELISA. All healthy non biopsied controls had negative IgA-AAA. tTG-Ab serum concentration was significantly correlated with more severe intestinal lesion (IIIB, IIIC M/O).</p> <p>Conclusions</p> <p>IgA-AAA may be undetectable in presence of severe mucosal damage. Histology is still necessary to diagnose celiac disease and IgA-AAA cannot be included in usual screening tests, because it has little to offer if compared to the well-established tTG-Ab.</p> <p>IgA-AAA could be an adjunctive, very useful tool to support the diagnosis of CD in case of suboptimal histology, when the biopsy is to be avoided for clinical reasons, or in case of negative parents' consensus.</p

Integrated study on production performance and quality traits of European sea bass ( Dicentrarchus labrax ) fed high plant protein diets

In the issue of fishmeal replacement, besides maintaining optimal growth, a key area of investigation for continuing to improve modern aquafeeds includes the evaluation of the effects of plant ingredients on fish quality. It is generally accepted that farmed fish quality can be influenced by the formulation of composition of their feed. Hence, the aim of the present research was to evaluate plant protein inclusion up to 84% of the overall protein content in an integrated study on growth and quality traits of European sea bass. Three diets were formulated to contain increasing plant protein levels (50, 67 and 84%; 50PP, 67PP and 84PP, respectively), with fishmeal dietary levels at 30, 20 and 10%, respectively. No significant differences due to reducing fishmeal content were observed after 118 days in terms of growth (final body weight and specific growth rate) and feed intake, even though a trend towards lower growth performance at higher fishmeal replacement levels was observed. Fish fed diet 50PP showed lower feed conversion rate in comparison to those fed diet 84PP, while no differences were recorded between diet 50PP and 67PP. No significant differences among treatments were found in protein efficiency rate. On the contrary, fish fed diet 84PP showed lower gross protein efficiency in comparison to those fed diet 50PP and 67PP. No significant differences in biometric indices and fillet composition were observed. No significant differences were found in pH, liquid holding capacity and skin colour measurements between treatments, while regarding fillet colour, significant differences were found only for H\ub0ab. In conclusion, our findings demonstrated that dietary plant proteins up to 84% of the overall protein content had no effects on quality traits of European sea bass in comparison with 50% and 67%. All experimental groups showed similar growth even though 84% plant protein inclusion negatively influenced feed and protein utilisation