15 research outputs found

    A diversity-aware computational framework for systems biology

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    GRAIGH: Gene Regulation accessibility integrating GeneHancer database

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    Single-cell assays for transposase-accessible chromatin sequencing data represent a potent tool for exploring the epigenetic heterogeneity within cell populations. Despite their power, understanding the chromatin accessibility landscape poses challenges. This study introduces Gene Regulation Accessibility Integrating GeneHancer (GRAIGH), a novel approach to interpreting genome accessibility by integrating information from the GeneHancer database, detailing genome-wide enhancer-to-gene associations. Initially, we outline the methods for integrating GeneHancer with scATAC-seq data. This involves creating a new matrix where GeneHancer element IDs replace traditional accessibility peaks as features. Subsequently, the paper assesses the method’s ability to analyze data and detect cellular heterogeneity. Notably, our findings demonstrate the selective accessibility of GeneHancer elements for distinct cell types, with connected genes serving as precise marker genes. Furthermore, we explore the specificity of GeneHancer element accessibility, highlighting their high selectivity against gene activity. This investigation underscores the potential of Gene Regulation Accessibility Integrating GeneHancer in unraveling the complexities of chromatin accessibility, offering insights into the nuanced relationship between accessibility and cellular heterogeneity

    Multi-level and hybrid modelling approaches for systems biology

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    During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The informa- tion collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the dif- ferent parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different sys- tem levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field

    Metodo computerizzato per generare protocolli di coltura per bio-manufacturing

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    La presente invenzione si riferisce generalmente alla predizione delle interazioni di almeno una prima con una seconda cellula all'interno di un sistema biologico e alla generazione di un protocollo di produzione biologica da tale previsione. Gli insegnamenti descritti sono incorporati in sistemi, metodi e prodotti di programmi per computer per prevedere la progressione di un sistema biologico, e per la previsione e l'ottimizzazione della coltura di tale sistema biologico al fine di ottenere un effetto predefinito

    The interaction of SiO2 nanoparticles with the neuronal cell membrane: activation of ionic channels and calcium influx

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    Aim: To clarify the mechanisms of interaction between SiO2 nanoparticles (NPs) and the plasma membrane of GT1\u20137 neuroendocrine cells, with focus on the activation of calcium-permeable channels, responsible for the long lasting calcium influx and modulation of the electrical activity in these cells. Materials & methods: Nontoxic doses of SiO2 NPs were administered to the cells. Calcium imaging and patch clamp techniques were combined with a pharmacological approach. Results: TRPV4, Cx and Panx-like channels are the major components of the NP-induced inward currents. Preincubation with the antioxidant N-acetyl-L-cysteine strongly reduced the [Ca2+]i increase. Conclusion: These findings suggest that SiO2 NPs directly activate a complex set of calcium-permeable channels, possibly by catalyzing free radical production