CNR personnel: Pesole Graziano, Ceci Luigi, De Leo Francesca, Monica Santamaria, Sgaramella Giuseppe, Armenise Annarita, De Marzo Barbara, Marra Laura, Mirizzi Maria Rosa
Associated personnel: D’Erchia Anna Maria, Picardi Ernesto, Saccone Cecilia, Svelto Maria
Other collaborators: Aiello Italia, Annese Anita, Balech Bachir, Chiara Matteo, Fosso Bruno, Intranuovo Marianna, Leoni Claudia, Lionetti Claudia, Lovero Dominga, Manzari Caterina, Marzano Marinella, Mastropasqua Francesca, Placido Antonio, Tomasino Maria Paola, Zambelli Federico
The advent of high-throughput technologies, particularly next generation sequencing platforms, initiated a major revolution in biomedical research, which has now moved to the larger “omics” scale, and led to the opening of new horizons with unprecedented potential applications. The “omics” research scale, which produces huge amount of data, still exponentially growing with increasingly reduced costs, requires ICT infrastructures and advanced bioinformatic analysis tools. This research activity section is focused on these topics, making use of multidisciplinary expertise, integration of the most advanced experimental and computational resources for the analysis and the interpretation of data and support of major European research infrastructures such as ELIXIR (Bioinformatics) and LIFEWATCH (Molecular Biodiversity).
Main Research Topics
1) Development of bioinformatics methodologies and specialized databases for taxonomic analysis and functional characterization of “omics” data. In particular, bioinformatic methodologies are aimed to: i) assembly and annotation of viral, prokaryotic and eukaryotic genomes; ii) study of the transcriptome in prokaryotes and eukaryotes and of the pattern of alternative splicing of eukaryotic genes; iii) identification and functional characterization of RNA editing events; iv) evolutionary and functional characterization of the mitochondrial genome; v) taxonomic and functional characterization of the microbiome.
2) Structural and functional annotation of the genome and study of the mechanisms of regulation of gene expression in prokaryotic and eukaryotic organisms, viruses and organelles (mitochondria and chloroplasts) through High-Throughput Sequencing (HTS) technology and advanced bioinformatics tools. In particular, the research is focused on assembly and functional annotation of genomes and analysis of transcriptome, eukaryotic genes alternative splicing, RNA editing, other epigenetic features and interactions between nucleic acids and proteins.
3) Taxonomic and functional characterization of the microbiome in environmental (including water, soil, sediments), clinical (including faeces, intestinal mucosa, respired air) and food (including intermediate products of fermentation chains) samples, based on metagenomic approaches through HTS technologies and advanced bioinformatics tools.
The mainly used analysis technologies include:
– Automatic systems and advanced tools for the extraction of nucleic acids (DNA and RNA) from heterogeneous clinical and environmental samples, for the massive sequencing and enzymatic characterization of proteins expressed in heterologous systems;
– Advanced bioinformatic platforms for data storage and analysis, including specialized databases, algorithms and software for bioinformatics analysis.
The main objectives 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 metagenomic analysis, for the taxonomic and functional characterization of microbial biodiversity in food, environmental and clinical samples, aimed at environmental monitoring, at food quality, traceability and safety safeguard and at studying the correlations to specific 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 medical, nutritional and environmental fields. In particular, the analysis of samples from “extreme” environments or habitats hosting specific metabolic activities will be aimed at searching for new molecular functionalities potentially transferable to biotechnological chains.
4) Development and delivery of services and know-how for public and private stakeholders.