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Mazza T.,Mendel Institute | Ballarini P.,Ecole Centrale Paris | Guido R.,University of Calabria | Prandi D.,Center for Integrative Biology
IEEE/ACM Transactions on Computational Biology and Bioinformatics | Year: 2012

Important achievements in traditional biology have deepened the knowledge about living systems leading to an extensive identification of parts-list of the cell as well as of the interactions among biochemical species responsible for cell's regulation. Such an expanding knowledge also introduces new issues. For example, the increasing comprehension of the interdependencies between pathways (pathways cross-talk) has resulted, on one hand, in the growth of informational complexity, on the other, in a strong lack of information coherence. The overall grand challenge remains unchanged: to be able to assemble the knowledge of every "piece of a system in order to figure out the behavior of the whole (integrative approach). In light of these considerations, high performance computing plays a fundamental role in the context of in-silico biology. Stochastic simulation is a renowned analysis tool, which, although widely used, is subject to stringent computational requirements, in particular when dealing with heterogeneous and high dimensional systems. Here, we introduce and discuss a methodology aimed at alleviating the burden of simulating complex biological networks. Such a method, which springs from graph theory, is based on the principle of fragmenting the computational space of a simulation trace and delegating the computation of fragments to a number of parallel processes. © 2012 IEEE.

Xu Z.,New York University | Chen H.,New York University | Chen H.,Princeton University | Ling J.,New York University | And 5 more authors.
Genes and Development | Year: 2014

In vivo cross-linking studies suggest that the Drosophila transcription factor Bicoid (Bcd) binds to several thousand sites during early embryogenesis, but it is not clear how many of these binding events are functionally important. In contrast, reporter gene studies have identified >60 Bcd-dependent enhancers, all of which contain clusters of the consensus binding sequence TAATCC. These studies also identified clusters of TAATCC motifs (inactive fragments) that failed to drive Bcd-dependent activation. In general, active fragments showed higher levels of Bcd binding in vivo and were enriched in predicted binding sites for the ubiquitous maternal protein Zelda (Zld). Here we tested the role of Zld in Bcd-mediated binding and transcription. Removal of Zld function and mutations in Zld sites caused significant reductions in Bcd binding to known enhancers and variable effects on the activation and spatial positioning of Bcd-dependent expression patterns. Also, insertion of Zld sites converted one of six inactive fragments into a Bcd-responsive enhancer. Genome-wide binding experiments in zld mutants showed variable effects on Bcd-binding peaks, ranging from strong reductions to significantly enhanced levels of binding. Increases in Bcd binding caused the precocious Bcd-dependent activation of genes that are normally not expressed in early embryos, suggesting that Zld controls the genome-wide binding profile of Bcd at the qualitative level and is critical for selecting target genes for activation in the early embryo. These results underscore the importance of combinatorial binding in enhancer function and provide data that will help predict regulatory activities based on DNA sequence. © 2014 Xu et al.

Cereseto A.,Center for Integrative Biology | Giacca M.,International Center for Genetic Engineering and Biotechnology
Methods in Molecular Biology | Year: 2014

Advancements in fluorescent microscopy techniques now permit investigation of HIV-1 biology exploiting tools alternative to conventional molecular biology. Here we describe a novel, fluorescence-based method to visualize HIV-1 viral particles within intact nuclei of infected cells. This method allows investigating the localization of pre-integration complexes within the nuclear compartment with respect to the nuclear envelope and the chromatin territories. © 2014 Springer Science+Business Media, LLC.

Ellen A.F.,Center for Integrative Biology | Ellen A.F.,University of Groningen | Zolghadr B.,University of Groningen | Zolghadr B.,Max Planck Institute for Terrestrial Microbiology | And 2 more authors.
Archaea | Year: 2010

Although archaea have a similar cellular organization as other prokaryotes, the lipid composition of their membranes and their cell surface is unique. Here we discuss recent developments in our understanding of the archaeal protein secretion mechanisms, the assembly of macromolecular cell surface structures, and the release of S-layer-coated vesicles from the archaeal membrane. © 2010 Albert F. Ellen et al.

Bernabo P.,CNR Institute of Neuroscience | Bernabo P.,Center for Integrative Biology | Lunelli L.,Fondazione Bruno Kessler | Quattrone A.,Center for Integrative Biology | And 3 more authors.
Journal of Insect Physiology | Year: 2015

In stressed organisms, strategic proteins are selectively translated even if the global process of protein synthesis is compromised. The determination of protein concentrations in tissues of non-model organisms (thus with limited genomic information) is challenging due to the absence of specific antibodies. Moreover, estimating protein levels quantifying transcriptional responses may be misleading, because translational control mechanisms uncouple protein and mRNAs abundances. Translational control is increasingly recognized as a hub where regulation of gene expression converges to shape proteomes, but it is almost completely overlooked in molecular ecology studies. An interesting approach to study translation and its control mechanisms is the analysis of variations of gene-specific translational efficiencies by quantifying mRNAs associated to ribosomes. In this paper, we propose a robust and streamlined pipeline for purifying ribosome-associated mRNAs and calculating global and gene-specific translation efficiencies from non-model insect's species. This method might found applications in molecular ecology to study responses to environmental stressors in non-model organisms. © 2015 Elsevier Ltd.

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