Area 1 – Technologies
Genomic sequencing (Bargelloni, Campanaro, Comin, Pizzi, Treu, Valle, Cimetta)
The target is the development and application of new strategies for de novo genomic sequencing, on two main research lines. The first one (Bargelloni e Valle) is related to de novo sequencing of complex genomes and will be focused in particular on the development of strategies to facilitate the scaffolding process. One of the prospects is the possibility to resolve the haplotypes. The second line of research (Campanaro Comin, Pizzi and Treu) aims to optimize the analysis of metagenomic data using next-gen sequencing (including single molecule).
Transcriptomics (Cagnin, Di Camillo, Elvassore, Lanfranchi, Valle, Romualdi, Sales, Bagno, Cimetta, Giomo, Pavan)
The project aims to implement and optimize methods for transcriptome analysis, including "single cell transcriptomics". Another target is the development and implementation of bioinformatics tools useful for data analysis.
Systems biology (Bortoluzzi, Romualdi, Sales, Sissi, Taccioli, Toppo, Vandin, Bagno, Cimetta)
This project is aimed at the development of methods for the integration of complex data, related to the molecular regulation of cellular processes.
Analisi delle varianti (Navarin, Pagani, Pegoraro, Sperduti, Valle)
This project proposes several objectives, all aimed at the problem of improving the efficiency of the methods of prioritization of variants that cause particular phenotypes in humans:
1. Further development of the QueryOR data integration system, based on Fuzzy logic (Valle);
2. Further development of the Scuba program, for the functional association of heterogeneous data (Sperduti, Navarin);
3. Integration of GWAS data with exomatic data (Pegoraro); - Integration of population genetics data (Pagani)
Genome editing (Argenton, Bonaldo, Braghetta, Tiso, Tranotti, Varotto)
Development and implementation of innovative genome editing methods. Several model organisms will be used such as topo (Bonaldo, Braghetta), zebrafish (Argenton, Tiso) and plant organisms (Trainoti, Varotto).
Analysis of biomolecules (Spolaore, Arrigoni, De Filippis, Dettin, Marin, Miotto, Negro, Papini, Polverino de Laureto, Spolaore, Tavano, Toppo)
The project aims to implement and optimize methods for the analysis of native or recombinant-engineered proteins, lipids and other biomolecules or drugs.
Specific areas of application concern:
1. analytical methods for the quantitative large-scale analysis of proteins, peptides, lipids and metabolites by LC-MS/MS approaches (Arrigoni, Miotto);
2. nutritional peptidomics: identification and validation of bioactive food peptides (Marin, Miotto, Arrigoni);
3. analysis of the mechanism of molecular recognition in ligand-receptor and antigen-antibody (epitope mapping) interacting systems using spectroscopic techniques (steady state fluorescence and circular dichroism), Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry (ITC), along with advanced techniques of Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) (De Filippis, Polverino, Spolaore);
4. nanomedicine: understanding and designing host biomolecules’ interaction with nanobiointerfaces on nanosystems for medical applications, to obtain biocompatible and pharmacological fit coatings (Papini, Tavano, Negro);
5. biomaterials: design and study of the interaction between cells and surfaces or materials functionalized with bioactive sequences for regenerative medicine and tissue engineering (Dettin).
Area 2 – Technological application fields
Human genetics (Anglani, Pagani, Pegoraro, Rampazzo)
People involved in the project are active in human genetics research. In addition to considering possible interactions and collaborations, it is proposed to evaluate the strengths and weaknesses to identify development strategies for technologies of common interest.
Cancer (Bortoluzzi, Fassan, Morpurgo, Romualdi, Rosato, Cimetta, Dettin, Giomo)
The project participants are involved in several research oncological interest. In addition to considering possible interactions and collaborations, it is proposed to evaluate the strengths and weaknesses to identify development strategies for technologies of common interest. Development of drug delivery solutions and 'intelligent' formulations to improve the transport of cancer drugs and their metastases and the overcoming of drug resistance.
Animal genomics (Bargelloni, Negrisolo, Taccioli)
The target of the project is to evaluate the strengths and weaknesses of the animal genomics field in Padova to identify possible development strategies for the sector. Bargelloni will mainly deal with the problems of genomic sequencing and population genetics; Taccioli will cover several aspects related to the comparative genomics of transposons and non-coding RNAs; Negrisolo will treat various problems related to the evolution of the mitochondrial genome in relation to animal phylogeny.
Plant genomics (Bonghi, Botton, Trainotti, Varotto)
Project participants are involved in various plant genomics research. In addition to considering possible interactions and collaborations, it is proposed to evaluate the strengths and weaknesses to identify development strategies for technologies of common interest.
Metagenomics (Barzon, Campanaro, Cardazzo, Dettin, Favaron, Savarino, Squartini, Treu)
People associated to the “metagenomics” project are involved in many different projects, with particular focus on human gut microbiome, soil, anaerobic digestion, food and plant associated microbes. More specifically the main projects are described as follows:
1. Analysis of human microbiome, mainly intestinal and esophageal, is mainly associated with gut chronic inflammatory diseases such as colorectal cancer, eosinophilic esophagitis, diverticular disease and irritable bowel syndrome (Savarino).
2. Study of the microbiota and of the microbial community dynamics in food production lines (including animal microbiota and food microbiota) using DNA/RNA metabarcoding and metagenomics (Cardazzo).
3. Taxonomic metabarcoding in bacterial and fungal microbial communities (Squartini). The project is focused on identification of indexes useful for determining the degree of genetic diversification within each taxon.
4. Combined transcriptome analysis of plants and phytopathogenic microorganisms (Favaron); studies are focused on the infection step and after treatment with specific substances. Analysis of the biocontrol agents and fungicide performed using metabarcoding analysis of the fungi present in the phyllosphere of cultivars.
5. Analysis of the anaerobic digestion microbiome involved in biogas production in industrial reactors (Treu/Campanaro). Analyses are focused on characterization of the microbiome using 16S rRNA sequencing and genome-centric metagenomics and are centered on reactors fed with different feedstocks.
Bioremediation (Bertucco, Filippini, Alboresi, Bergantino, Bertucco, Cendron)
The target is the application of biological strategies to remove pollutants from environment (i.e. bioremediation). Besides the biological treatment using aerobic activated sludge process, which has been in practice for well over a century, advanced biological treatment processes in recent years have been implemented due to the increasing pressure to meet more stringent discharge standards or treat specific effluents. One example of emerging pollutant is represented by the PFAS, a class of molecules among the most difficult contaminants to deal with conventional wastewater treatment processes. The approach that will be used is represented by bioaugmentation, defined as the introduction of new metabolic pathways into a microbial community, in order to improve the pollutants removal, and the abatement of recalcitrant compounds. A cross multicompetence team is required, endowed with established expertise ranging from synthetic biology, computational design, molecular and cellular biology, NGS, metagenomics and comparative genomics (“Molecule based track”), analytical chemistry, biochemistry and structural biology, agricultural microbiology, application of microalgae and cyanobacteria in real wastewater (“Organism based track”), as well competences in the wastewater treatment process and plants design (“Bioprocess engineering track”).
Data warehousing, web services and interactive visualization (Sales, Toppo)
The target of the project is to develop databases and analysis tools for omic measurements accessible via web interfaces. The activity will focus on software development for dynamic querying of large amounts of data and interactive visualization using recent HTML5 technologies. The services will be made publicly available through the HPC resources available to the Center.
Area 3 – Infrastructures and services
NGS – Next generation sequencing (Valle)
The target is to provide an efficient service of next generation sequencing.
Real time PCR and Digital PCR (Cagnin, Lanfranchi)
The target is to provide an efficient service of real time PCR, digital PCR and NGS sequencing.
HPC – High performance computing (Toppo, Valle, Sales)
The main target of HPC service is to promote and facilitate the use of HPC system at CRIBI and to integrate the different informatics platforms available at Padova University.
Peptidi ed anticorpi PEPT-AB (Marin, Rosato)
The target is to provide an efficient service of peptide synthesis and antibodies production.
Proteomics (Arrigoni, De Filippis, Marin, Miotto, Spolaore, Polverino de Laureto, Toppo )
The project aims to offer an adequate proteomic service that will use the following instrumentation: – Xevo G2-XS Q-TOF connected to an ACQUITY UPLC H-Class System (Waters) in operation at the Department of Pharmaceutical and Pharmacological Sciences. – LTQ-Orbitrap XL (Thermo Fisher Scientific) connected to a Ultimate 3000 nano-HPLC system (Dionex-Thermo Fisher Scientific) in operation at the "Pietro d’Abano" Biomedical Campus. – 6520 Q-TOF (Agilent Technologies) connected to a nano-HPLC 1200 series via a CHIP-Cube module (Agilent Technologies) in operation at the Biomedical Campus "Pietro d’Abano". – MALDI-TOF / TOF 4800 (AB Sciex) in operation at the Biomedical Campus "Pietro d’Abano".