Molecular evidence for increased regulatory conservation during metamorphosis, and against deleterious cascading effects of hybrid breakdown in Drosophila

<p>Abstract</p> <p>Background</p> <p>Speculation regarding the importance of changes in gene regulation in determining major phylogenetic patterns continues to accrue, despite a lack of broad-scale comparative studies examining how patterns of gene expression vary during development. Comparative transcriptional profiling of adult interspecific hybrids and their parental species has uncovered widespread divergence of the mechanisms controlling gene regulation, revealing incompatibilities that are masked in comparisons between the pure species. However, this has prompted the suggestion that misexpression in adult hybrids results from the downstream cascading effects of a subset of genes improperly regulated in early development.</p> <p>Results</p> <p>We sought to determine how gene expression diverges over development, as well as test the cascade hypothesis, by profiling expression in males of <it>Drosophila melanogaster</it>, <it>D. sechellia</it>, and <it>D. simulans</it>, as well as the <it>D. simulans </it>(♀) × <it>D. sechellia </it>(♂) male F1 hybrids, at four different developmental time points (3rd instar larval, early pupal, late pupal, and newly-emerged adult). Contrary to the cascade model of misexpression, we find that there is considerable stage-specific autonomy of regulatory breakdown in hybrids, with the larval and adult stages showing significantly more hybrid misexpression as compared to the pupal stage. However, comparisons between pure species indicate that genes expressed during earlier stages of development tend to be more conserved in terms of their level of expression than those expressed during later stages, suggesting that while Von Baer's famous law applies at both the level of nucleotide sequence and expression, it may not apply necessarily to the underlying overall regulatory network, which appears to diverge over the course of ontogeny and which can only be ascertained by combining divergent genomes in species hybrids.</p> <p>Conclusion</p> <p>Our results suggest that complex integration of regulatory circuits during morphogenesis may lead to it being more refractory to divergence of underlying gene regulatory mechanisms - more than that suggested by the conservation of gene expression levels between species during earlier stages. This provides support for a 'developmental hourglass' model of divergence of gene expression in <it>Drosophila </it>resulting in a highly conserved pupal stage.</p

riboviz: analysis and visualization of ribosome profiling datasets

Abstract Background Using high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell. Since its introduction in 2009, this technique has played a key role in driving biological discovery, and yet it requires a rigorous computational toolkit for widespread adoption. Description We have developed a database and a browser-based visualization tool, riboviz, that enables exploration and analysis of riboseq datasets. In implementation, riboviz consists of a comprehensive and flexible computational pipeline that allows the user to analyze private, unpublished datasets, along with a web application for comparison with published yeast datasets. Source code and detailed documentation are freely available from https://github.com/shahpr/RiboViz . The web-application is live at www.riboviz.org. Conclusions riboviz provides a comprehensive database and analysis and visualization tool to enable comparative analyses of ribosome-profiling datasets. This toolkit will enable both the community of systems biologists who study genome-wide ribosome profiling data and also research groups focused on individual genes to identify patterns of transcriptional and translational regulation across different organisms and conditions

Ribosome profiling reveals the what, when, where and how of protein synthesis

Ribosome profiling, which involves the deep sequencing of ribosome-protected mRNA fragments, is a powerful tool for globally monitoring translation in vivo. The method has facilitated discovery of the regulation of gene expression underlying diverse and complex biological processes, of important aspects of the mechanism of protein synthesis, and even of new proteins, by providing a systematic approach for experimental annotation of coding regions. Here, we introduce the methodology of ribosome profiling and discuss examples in which this approach has been a key factor in guiding biological discovery, including its prominent role in identifying thousands of novel translated short open reading frames and alternative translation products

Emergenze dal presente, prospettive di futuro. Forum AIS Giovani 2012

Questo volume raccoglie i contributi selezionati in occasione del nono Forum Giovani dell'Associazione Italiana di Sociologia (AIS), che si è tenuto nel 2012 all'Università del Salento. I saggi qui raccolti si confrontano, a partire da diverse prospettive teoriche e approcci metodologici, con le emergenze del presente, in particolare con le conseguenze della crisi economica, sociale e culturale che stiamo vivendo in questi anni. Nel complesso lo spessore dei contributi fa ritenere che la ricerca italiana nel campo della sociologia sia viva, qualificata e tutt'altro che depressa, il che costituisce un incoraggiante segnale di riscatto da parte delle giovani generazioni di studiosi rispetto alla situazione critica in cui si trova a operare la ricerca universitaria nel nostro paese, in particolare nel settore delle scienze sociali

SARS-CoV-2 infection and neonates : a review of evidence and unresolved questions

SARS-CoV-2 infection in the neonatal period poses previously unmet challenges to obstetricians and neonatologists, but several key questions are yet to be answered. Few cases of presumed in utero vertical transmission of the virus from infected mothers to fetuses have been reported, but stronger evidence is needed, from larger datasets with multiple biospecimens rigorously analyzed. Whether acquired before or after birth, SARS-CoV-2 infection in neonates can be symptomatic, but our comprehension of neonatal immune response and the subsequent clinical characteristics of COVID-19 in early life are incomplete. Finally, the pandemic challenged several dogmas regarding the management of mother-infant dyads, and again more robust data are needed to support the formulation of evidence-based guidelines. Here, we briefly summarize existing evidence and key unresolved questions about SARS-CoV-2 infection and COVID-19 in the neonatal period

Mass media and the web in the light of Luhmann’s media system

The aim of the article is to observe the contemporary media system in the light of Luhmann’s media system, namely a specific function system of society which has witnessed ever greater internal complexity vis-a-vis an environment marked by the spread of the web and social network sites. From the viewpoint of sociocybernetics, the question of increased complexity can be addressed through an ecological approach in order to analyse the distinction between the mass media and the web – in its specific 2.0 evolution, characterized by user-generated content and algorithms. This approach allows to observe the reciprocal relations by preserving the autonomy of the two spheres without resorting to explanations that have to do with hybridization or the blur of the boundaries. In this sense the article analyses Facebook – as an example of web 2.0 operational logic – as a social system distinct from that of the mass media, where the first substantial difference depends on the role played by individuals in reproducing communication and on the role of the algorithm. In this sense mass media and the web are treated on the basis of their relationship of structural coupling by observing how they irritate, or disturb, each other and at the same time maintain their autonomy