CNR staff: Ceci Luigi, De Leo Francesca, Tullo Apollonia, Balech Bachir, Caratozzolo Mariano Francesco, L’Abbate Alberto, Leoni Claudia, Marzano Flaviana, Marzano Marinella, Placido Antonio, Tangaro Marco Antonio, Armenise Annarita, De Marzo Barbara, Marra Laura , Mirizzi Maria Rosa
Associated personnel: Pesole Graziano, Picardi Ernesto, D’Erchia Anna Maria, Gissi Carmela, Horner David Stephen, Federico Zambelli, Chiara Matteo, Pavesi Giulio
Other collaborators: Fosso Bruno, Manzari Caterina, Amendolare Alessandra, Notario Elisabetta, Mandreoli Pietro, Ferrandi Erika, Bonomo Michela, Lorusso Erika, Quaglia Federica, Visci Grazia, Longo Giovanna, Mazzacuva Pietro.
The advent of high-throughput technologies, particularly next-generation sequencing platforms, has triggered a profound revolution in biomedical research both for the scale, which has now reached an “omic” dimension, and for the opening of new horizons with applications that were unimaginable until some time ago. Research on an “omic” scale, which produces huge volumes of data still growing exponentially and at increasingly low costs, requires ICT infrastructures and advanced bioinformatics analysis systems. The research lines of this com are placed in this scenario, which make use of multidisciplinary skills, the integration of the most advanced experimental activities and computational resources for the analysis and interpretation of data and the support of large European research infrastructures. such as ELISIR (Bioinformatics) and LIFEWATCH (Molecular Biodiversity).
Main research topics:
1) Development of bioinformatics methodologies and specialized databases for phylogenetic analysis and the characterization of functional “omics” data in line with international standards of interoperability and “open science”. In particular, the bioinformatics methodologies, also developed using technologies in the Cloud environment and Artificial Intelligence approaches, include: i) assembly and annotation of viral, prokaryotic and eukaryotic genomes; ii) study of the transcriptome in prokaryotes and eukaryotes and of the alternative splicing pattern of eukaryotic genes; iii) identification and functional characterization of RNA editing events; iv) evolution and functional characterization of the mitochondrial genome; v) taxonomic and functional characterization of the microbiome.
2) Structural and functional annotation of the genome and of the mechanisms of gene expression regulation of prokaryotic and eukaryotic organisms, viruses and organelles (mitochondria and chloroplastics) on the basis of data produced by second and third generation massive sequencing technologies. In particular, the research activity is aimed at the assembly and functional annotation of genomes, the analysis of the transcriptome and the studies on the alternative splicing pattern of eukaryotic genes, the study of RNA editing, other epigenetic characters and of nucleic acid-protein interactions.
3) Taxonomic and functional characterization of the microbiome of environmental samples (including waters, soils, sediments, marine algae), clinical (including faeces, intestinal mucosa, endometrium and ovary) and agri-food (including intermediate products of fermentation chains ) based on metagenomic approaches with high-throughput sequencing technologies and advanced bioinformatics tools.
4) Role of genes belonging to the p53 oncosuppressor gene family (p53 – p63 – p73) in the control of normal and tumor cell proliferation and strategies to reactivate the p53 oncosuppressor in therapy resistant tumors.
5) Study of the structural variability of the human and primate genome and impact in the predisposition to genomic disorders and evolution
Investigation technologies:
Investigation technologies include:
– extraction of nucleic acids (DNA and RNA), using standard and automated technologies, from cells and heterogeneous clinical, animal and environmental samples, for the massive sequencing of genomes, exomes, transcriptomes of single organisms and microbial communities of different origins, using NGS (Next Generation Sequencing) platforms;
– cell and bacterial cultures, cloning in protein vectors, mutagenesis, transfections, bacterial transformations, characterization of recombinants, chromatin immunoprecipitation (ChIp), reporter assays, cell proliferation assays, flow cytometry, Western Blotting, qPCR, dPCR
– advanced bioinformatics platforms for data storage and analysis, including specialized databases, algorithms and software for bioinformatics analysis.
Research goals:
The main goals of the research include:
1) characterization of specific molecular processes in aging, neurodegenerative diseases and tumors and identification of specific biomarkers of the pathological condition and its progression.
2) Development of innovative experimental and bioinformatic methodologies for genomic, epigenomic, epitranscriptomic and metagenomic analysis, for the taxonomic and functional characterization of microbial and animal biodiversity of food, environmental and clinical samples, aimed at environmental monitoring, quality protection, the traceability and safety of food and the study of correlations with respect to specific environmental, physiological and pathological conditions.
3) Identification and characterization of new microbial strains and gene products for the development of innovative processes for biotechnological applications in the medical, agri-food and environmental fields. In particular, the analysis of samples from “extreme” environments or in any case the site of specific metabolic activities will be aimed at the search for new molecular functions potentially transferable to biotechnological chains.
4) p53-dependent role of TRIM8 in the regulation of genes involved in the autophagic process and in the transport of chemotherapeutic agents.
5) Development and provision of services and consultancy to public and private entities.
