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For the first time, the University of Pisa is the leader of a study whose goal is to sequence the genome of a superior plant, the fig. The team of researchers from Pisa, coordinated by Associate Professor Lucia Natali, includes plant geneticists and bioinformatic specialists from the University, assisted by a number of researchers from the Sant’Anna School, the University of Perugia and the British research centre, Rothamsted Research, with the collaboration of the Consorzio Associazione Produttori Fichi Secchi in Carmignano (Prato). The first authors of the study, published in ‘The Plant Journal’, are two young academics, Gabriele Usai, who is about to complete his doctoral studies, and the researcher Flavia Mascagni. The research project was funded by the Department of Agriculture, Food and Agro-Environmental Sciences (DAFE) and, in part, by funds linked to one of the University’s PRA projects. 

"The fig tree is one of the oldest and most evocative species cultivated by man,” explains Lucia Natali. “According to some Bible specialists, Adam and Eve’s tree of knowledge in paradise was not an apple tree but a fig tree. Italy was the world’s biggest producer until the decline from the 1970s onwards. The availability of the entire genome sequence provides the opportunity to apply different innovative methodologies offering a genetic improvement to fig trees such as molecular marker assisted selection and genome editing. This could re-launch the cultivated species, characterized by its capacity to adapt to adverse environmental conditions such as those foreseen following climate change and whose fruit has a high nutritional and nutraceutical value. As one of the main problems with this crop is its rapid perishability, it would be auspicable to intervene on the genes that control this characteristic in order to obtain plants which produce fruit with a much slower ripening process, hence more suitable for a global rather than simply local market.”

The researchers from Pisa, authors of the work (from the left Alberto Vangelisti, Gabriele Usai, Lucia Natali, Flavia Mascagni, Andrea Cavallini, Tommaso Giordani).

“The new genome sequence of the fig was identified using the new sequencing technique called Pacific Biosciences,” says Flavio Mascagni, “which offers the possibility to evaluate different sequencing between paternal and maternal chromosomes and to analyze the epigenetic modifications found in the DNA. In this sense, the results of our study also have a more general significance for researchers interested in the structural and functional genomics of eukaryotes.”

Schematic representation of the 13 chromosomes of Ficus carica.

È stato uno dei primi iscritti al curriculum di Intelligenza artificiale del corso di laurea magistrale in Informatica all’Università di Pisa e pochi giorni fa si è laureato con 110 e lode discutendo una tesi sviluppata congiuntamente con l’Università di Stanford. Alessio Gravina, 24 anni, originario di Lucca, ha trascorso oltre tre mesi presso il Dipartimento di Chimica e Biologia dei Sistemi dell’università americana, dove ha sviluppato una tesi che tratta di Intelligenza artificiale per la previsione dell’efficacia di composti chimici nel trattamento della schizofrenia, dal titolo “Machine Learning prediction of compounds impact on Schizophrenia treatment”. Suoi relatori sono stati Davide Bacciu e Corrado Priami del Dipartimento di Informatica dell’Università di Pisa e Kevin V. Grimes del Department of Chemical and Systems Biology Operations della Stanford University.
La tesi è stata svolta grazie a una collaborazione tra i due dipartimenti: Stanford ha messo a disposizione competenze in ambito bio-medico e studi sperimentali sull’efficacia di oltre 1000 composti chimici, a diversi dosaggi, nel ridurre fenomeni di fagocitosi delle sinapsi che si pensano essere alla base dell’insorgenza di disturbi schizofrenici. Pisa ha contribuito con competenze e modelli di Machine Learning allo stato dell’arte per il trattamento di grafi molecolari, su cui il gruppo di ricerca “Computational Intelligence & Machine Learning” ha svolto studi pionieristici sin dagli anni ’90. L’unione delle competenze del gruppo di Stanford con quello dell’Università di Pisa ha permesso di costruire un modello predittivo che potrebbe facilitare la ricerca di nuovi farmaci per contrastare la schizofrenia, permettendo di prioritizzare la sperimentazione sui composti più promettenti selezionati dal modello intelligente.
La tesi congiunta è stata resa possibile grazie al progetto SPARK PISA, coordinato da Corrado Priami e nato da un accordo tra l'Università di Pisa e l’Università di Stanford, nel contesto della rete internazionale "SPARK GLOBAL", che riunisce prestigiosi centri di ricerca, al fine di promuovere collaborazioni e finanziare progetti di ricerca con ricadute in ambito bio-medico e farmacologico.
Alessio Gravina è stato tra i primi immatricolati al curriculum di Intelligenza artificiale della laurea magistrale in Informatica nell’anno accademico 2017-2018. Alessio aveva già svolto una tesi riguardante l’applicazione di tecniche di Machine Learning in ambito biomedico per la sua laurea triennale in Informatica (sotto la supervisione di Davide Bacciu e Alessio Micheli dell’Università di Pisa e di Luigi Gagliardi, primario di Pediatria e Neonatologia dell’Ospedale della Versilia). Da studente aveva anche già dato prova delle proprie capacità vincendo, insieme ai colleghi Silvia Severini e Federico Rossetto e sotto la supervisione di Giuseppe Attardi, la competizione internazionale indetta nel 2018 dalla Fujitsu sulla comprensione del linguaggio naturale mediante tecniche di Machine Learning.

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The University of Pisa promptly implements the measures of the Presidential Decree of the Council of Ministers (DPCM) dated 9 March 2020. It includes the suspension of curricular training, the closure of libraries and study rooms and the rescheduling of all the meetings and workshops.
The Rector Paolo Mancarella issued a new Decree dated 10 March 2020 updating the former one (8 March 2020). It includes new stricter measures to contrast and contain the epidemiological emergency caused by COVID -19.

In order to help students, the Board of Directors of the University of Pisa, which met online for the first time on 13 March 2020, has approved a number of concessions with regard to the university fees.

In addition, by Rector’s Decree, which came into effect on Friday 13 March, the University of Pisa has now enabled the completion of final degree exams online. Following the new regulations, not only the candidates but also the president and secretary of the commission need not be present in person at the degree session.

These new measures – the Rector explains – raise the level of protection for our community. They require a sacrifice, I understand, but it is crucial now that we all do our part.
"A few of these measures concern the everyday life of our students - concludes the Rector – to whom I forward my message: do not meet to study or attend e-learning together. At this moment, it is important to minimize everyday contacts to contain the spread".
The new measures implemented by the Rector's decree and valid up to 3 April are the following:

• all in-presence teaching activities in all degree Programmes of the University of Pisa (Bachelor's degrees, Master's degrees, Post- vocational courses, postgraduate vocational Programmes, PhD Programmes, and Specialization Schools (excluding those in Healthcare area) are suspended;
• all curricular training, including those at external institutions or companies, are suspended;
• in-presence laboratory activities are suspended;
• Erasmus+ mobility is suspended with specific rules for curricular or extracurricular training;
• Libraries and book lending are closed;
• Study rooms and reference rooms are closed
• All meetings, workshops, events, organized by the University of Pisa are suspended within the territory of the city of Pisa and in every other national region.

Graduation sessions, exams sessions and their registration shall be assured only by telematic facilities, as stated in the Rector's decree.

New necessary measures for administrative and technical staff. The Rector's decree provides a new work organization to promote and support, upon staff request, the usage of vacation days, days-off or hours' recovery time, on condition it causes no prejudice for the institutional activities linked to didactics and research.
A General Director’s provision will introduce Smart working.
All kind of front-office services will be assured remotely only.
All meetings, events or workshops will be suspended until 3 April 2020.