Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigs

Intramuscular fat content (IMF) is a complex trait influencing the technological and sensorial features of meat products and determining pork quality. Thus, we aimed at analyzing through RNA-sequencing the Semimembranosus muscle transcriptome of Italian Large White pigs to study the gene networks associated with IMF deposition. Two groups of samples were used; each one was composed of six unrelated pigs with extreme and divergent IMF content (0.67 \ub1 0.09% in low IMF vs. 6.81 \ub1 1.17% in high IMF groups) that were chosen from 950 purebred individuals. Paired-end RNA sequences were aligned to Sus scrofa genome assembly 11.1 and gene counts were analyzed using WGCNA and DeSeq2 packages in R environment. Interestingly, among the 58 differentially expressed genes (DEGs), several were related to primary cilia organelles (such as Lebercilin 5 gene), in addition to the genes involved in the regulation of cell differentiation, in the control of RNA-processing, and G-protein and ERK signaling pathways. Together with cilia-related genes, we also found in high IMF pigs an over-expression of the Fibroblast Growth Factor 2 (FGF2) gene, which in other animal species was found to be a regulator of ciliogenesis. Four WGCNA gene modules resulted significantly associated with IMF deposition: grey60 (P = 0.003), darkturquoise (P = 0.022), skyblue1 (P = 0.022), and lavenderblush3 (P = 0.030). The genes in the significant modules confirmed the results obtained for the DEGs, and the analysis with "cyto- Hubba" indicated genes controlling RNA splicing and cell differentiation as hub genes. Among the complex molecular processes affecting muscle fat depots, genes involved in primary cilia may have an important role, and the transcriptional reprogramming observed in high IMF pigs may be related to an FGF-related molecular cascade and to ciliogenesis, which in the literature have been associated with fibro-adipogenic precursor differentiation

Effects of Housing Social Context on Emotional Behaviour and Physiological Responses in Female Mice

In laboratory breeding procedures, mice are usually housed in single-sex unfamiliar groups since weaning,  while individual housing is widely employed in many experimental settings. While there is a considerable  amount of evidence on the behavioural and physiological effects of various social contexts in male mice  and rats, few data are available on female mice. We examined short-term modulation of social context in the  housing environment on exploratory and emotional behaviours in response to novelty (i.e., free-exploratory  open field) and on physiology (i.e. organs and body weight, and basal corticosterone level) of female CD1  mice, taking into account the estrous phase as an additional variable. Living alone or grouped with siblings  or with unfamiliar females for a short period (7 days) did not affect any physiological indexes of stress in  female house mice and had marginal effects on emotional behaviour. When challenged with a free choice  between a novel environment and their home cage, female mice housed with siblings did not differ on any  behavioural parameter from females housed with same-aged unfamiliar mice, while individually housed  females showed higher propensity to enter the novel arena but no differences in activity or in anxiety as  compared to grouped mice. Information about sex specifics under standard housing conditions as well as in  response to common laboratory procedures could be important for the understanding of sex differences in  vulnerability to psychiatric disorders and response to drug treatment.

A gene expression atlas for different kinds of stress in the mouse brain

Stressful experiences are part of everyday life and animals have evolved physiological and behavioral responses aimed at coping with stress and maintaining homeostasis. However, repeated or intense stress can induce maladaptive reactions leading to behavioral disorders. Adaptations in the brain, mediated by changes in gene expression, have a crucial role in the stress response. Recent years have seen a tremendous increase in studies on the transcriptional effects of stress. The input raw data are freely available from public repositories and represent a wealth of information for further global and integrative retrospective analyses. We downloaded from the Sequence Read Archive 751 samples (SRA-experiments), from 18 independent BioProjects studying the effects of different stressors on the brain transcriptome in mice. We performed a massive bioinformatics re-analysis applying a single, standardized pipeline for computing differential gene expression. This data mining allowed the identification of novel candidate stress-related genes and specific signatures associated with different stress conditions. The large amount of computational results produced was systematized in the interactive “Stress Mice Portal”

HPC-REDItools: A novel HPC-aware tool for improved large scale RNA-editing analysis

Background: RNA editing is a widespread co-/post-transcriptional mechanism that alters primary RNA sequences through the modification of specific nucleotides and it can increase both the transcriptome and proteome diversity. The automatic detection of RNA-editing from RNA-seq data is computational intensive and limited to small data sets, thus preventing a reliable genome-wide characterisation of such process. Results: In this work we introduce HPC-REDItools, an upgraded tool for accurate RNA-editing events discovery from large dataset repositories. Availability: https://github.com/BioinfoUNIBA/REDItools2. Conclusions: HPC-REDItools is dramatically faster than the previous version, REDItools, enabling big-data analysis by means of a MPI-based implementation and scaling almost linearly with the number of available cores

An efficient and reproducible method for transformation of genetically recalcitrant bifidobacteria

This study describes an efficient transformation system for the introduction of plasmid DNA into Bifidobacterium bifidum PRL2010 and Bifidobacterium asteroides PRL2011, for which to the best of our knowledge no transformation data have been reported previously. The method is based on electroporation of bifidobacterial cells, which were made competent by an optimized methodology based on varying media and growth conditions. Furthermore, the transformation protocol was applied in order to design a PRL2010-derivative, which carries antibiotic resistance against chloramphenicol and which was used to monitor PRL2010 colonization in a murine model

Bifidobacterium bifidum PRL2010 Modulates the Host Innate Immune Response

Here, we describe data obtained from transcriptome profiling of human cell lines and intestinal cells of a murine model upon exposure and colonization, respectively, with Bifidobacterium bifidum PRL2010. Significant changes were detected in the transcription of genes that are known to be involved in innate immunity. Furthermore, results from enzyme-linked immunosorbent assays (ELISAs) showed that exposure to B. bifidum PRL2010 causes enhanced production of interleukin 6 (IL-6) and IL-8 cytokines, presumably through NFκB activation. The obtained global transcription profiles strongly suggest that Bifidobacterium bifidum PRL2010 modulates the innate immune response of the host. © 2014, american Society for Microbiology. All Rights Reserved.We thank GenProbio srl for financial support of the Laboratory of Probiogenomics. This work was financially supported by Fondazione Cariplo (grant 2010-0678 to S.G. and V.T.) and by a FEMS Jensen Award to F.T. This publication has emanated from research supported in part by a research grant from Science Foundation Ireland (SFI) under grant SFI/12/RC/2273. The grant ILINK2010-0122, funded by CSIC, is also acknowledged.Peer Reviewe

A Trouble Shared Is a Trouble Halved: Social Context and Status Affect Pain in Mouse Dyads

In mice behavioral response to pain is modulated by social status. Recently, social context also has been shown to affect pain sensitivity. In our study, we aimed to investigate the effects of interaction between status and social context in dyads of outbred CD-1 male mice in which the dominance/submission relationship was stable. Mice were assessed for pain response in a formalin (1% concentration) test either alone (individually tested-IT), or in pairs of dominant and subordinate mice. In the latter condition, they could be either both injected (BI) or only one injected (OI) with formalin. We observed a remarkable influence of social context on behavioral response to painful stimuli regardless of the social status of the mice. In the absence of differences between OI and IT conditions, BI mice exhibited half as much Paw-licking behavior than OI group. As expected, subordinates were hypoalgesic in response to the early phase of the formalin effects compared to dominants. Clear cut-differences in coping strategies of dominants and subordinates appeared. The former were more active, whereas the latter were more passive. Finally, analysis of behavior of the non-injected subjects (the observers) in the OI dyads revealed that dominant observers were more often involved in Self-grooming behavior upon observation of their subordinate partner in pain. This was not the case for subordinate mice observing the pain response of their dominant partner. In contrast, subordinate observers Stared at the dominant significantly more frequently compared to observer dominants in other dyads. The observation of a cagemate in pain significantly affected the observer's behavior. Additionally, the quality of observer's response was also modulated by the dominance/submission relationship

CoVaCS : a consensus variant calling system

Background: The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and precision medicine. The body of genome resequencing data is progressively increasing underlining the need for accurate and time-effective bioinformatics systems for genotyping - a crucial prerequisite for identification of candidate causal mutations in diagnostic screens. Results: Here we present CoVaCS, a fully automated, highly accurate system with a web based graphical interface for genotyping and variant annotation. Extensive tests on a gold standard benchmark data-set -the NA12878 Illumina platinum genome- confirm that call-sets based on our consensus strategy are completely in line with those attained by similar command line based approaches, and far more accurate than call-sets from any individual tool. Importantly our system exhibits better sensitivity and higher specificity than equivalent commercial software. Conclusions: CoVaCS offers optimized pipelines integrating state of the art tools for variant calling and annotation for whole genome sequencing (WGS), whole-exome sequencing (WES) and target-gene sequencing (TGS) data. The system is currently hosted at Cineca, and offers the speed of a HPC computing facility, a crucial consideration when large numbers of samples must be analysed. Importantly, all the analyses are performed automatically allowing high reproducibility of the results. As such, we believe that CoVaCS can be a valuable tool for the analysis of human genome resequencing studies. CoVaCS is available at: https://bioinformatics.cineca.it/covacs

Quiste enterogénico de mediastino posterior

Los aparatos respiratorio y digestivo tienen un origen común en el intestino primitivo, motivo por el cual los quistes derivados de aquellos, broncogénicos y entéricos o de duplicación, se denominan conjuntamente quistes enterogénicos. Son malformaciones producidas durante el período de diferenciación y desarrollo embriológico de dicho intestino primitivo. En el tórax, los quistes entéricos representan el 20% de las duplicaciones del tubo digestivo.El 60% de los quistes entéricos se diagnostican en pacientes menores de 1 año. En adultos la incidencia es menor, y la clínica, más solapada. El tratamiento de elección es la exéresis radical de la lesión.Facultad de Ciencias Médica

Quiste enterogénico de mediastino posterior

Los aparatos respiratorio y digestivo tienen un origen común en el intestino primitivo, motivo por el cual los quistes derivados de aquellos, broncogénicos y entéricos o de duplicación, se denominan conjuntamente quistes enterogénicos. Son malformaciones producidas durante el período de diferenciación y desarrollo embriológico de dicho intestino primitivo. En el tórax, los quistes entéricos representan el 20% de las duplicaciones del tubo digestivo.El 60% de los quistes entéricos se diagnostican en pacientes menores de 1 año. En adultos la incidencia es menor, y la clínica, más solapada. El tratamiento de elección es la exéresis radical de la lesión.Facultad de Ciencias Médica