La valutazione della ricerca scientifica: Uno studio empirico nelle Scienze umane

Nel corso degli ultimi anni si è assistito ad un ampio dibattito sull’uso della valutazione della ricerca nelle università e nelle strutture di ricerca. Nell’ambito di tale dibattito, nella presente tesi, vengono analizzate le più importanti metodologie per la valutazione della ricerca presenti a livello internazionale, i principali strumenti qualitativi di valutazione della ricerca (in particolare la peer review), gli strumenti quantitativi, quali la bibliometria, e le caratteristiche dei più importanti archivi bibliografici citazionali (es. Scopus, Web of Science), approfondendo i principali indicatori citazionali utilizzati nelle scienze umane e sociali (es. Indice H). Inoltre la tesi affronta il tema dell’impatto socio-economico della ricerca e le principali criticità di questo innovativo strumento, attraverso uno studio di caso realizzato nel Regno Unito. Una successiva analisi empirica riguarda le principali liste di riviste realizzate a livello internazionale e nazionale, nel settore scientifico di Storia e Filosofia della scienza. I risultati degli studi mostrano che le liste internazionali di riviste possono rappresentare, un punto di partenza a cui devono necessariamente essere affiancati altri strumenti di valutazione (peer review, analisi citazionali, etc); mentre le liste nazionali rischiano, invece, di essere uno strumento poco utile ed in alcuni casi inadeguato al fine di una corretta valutazione della ricerca, a causa della scarsa internazionalizzazione dei repertori e dei giudizi generalmente troppo elevati attribuiti alle riviste. Un ulteriore risultato raggiunto nella presente tesi riguarda la valutazione della ricerca nelle diverse discipline scientifiche: nelle Scienze umane e sociali risulta esserci uno scarso grado di presenza di pubblicazioni scientifiche nei principali archivi bibliografici e citazionali internazionali. Questa situazione limita fortemente l’attendibilità delle analisi statistiche basate su indici e indicatori quantitativi, per valutare la produttività scientifica di un ricercatore, oppure di una istituzione di ricerca.

Reconstruction and analysis of the NF-kB pathway interactome: a systems biology approach

Background. One of the phenomena observed in human aging is the progressive increase of a systemic inflammatory state, a condition referred to as “inflammaging”, negatively correlated with longevity. A prominent mediator of inflammation is the transcription factor NF-kB, that acts as key transcriptional regulator of many genes coding for pro-inflammatory cytokines. Many different signaling pathways activated by very diverse stimuli converge on NF-kB, resulting in a regulatory network characterized by high complexity. NF-kB signaling has been proposed to be responsible of inflammaging. Scope of this analysis is to provide a wider, systemic picture of such intricate signaling and interaction network: the NF-kB pathway interactome. Methods. The study has been carried out following a workflow for gathering information from literature as well as from several pathway and protein interactions databases, and for integrating and analyzing existing data and the relative reconstructed representations by using the available computational tools. Strong manual intervention has been necessarily used to integrate data from multiple sources into mathematically analyzable networks. The reconstruction of the NF-kB interactome pursued with this approach provides a starting point for a general view of the architecture and for a deeper analysis and understanding of this complex regulatory system. Results. A “core” and a “wider” NF-kB pathway interactome, consisting of 140 and 3146 proteins respectively, were reconstructed and analyzed through a mathematical, graph-theoretical approach. Among other interesting features, the topological characterization of the interactomes shows that a relevant number of interacting proteins are in turn products of genes that are controlled and regulated in their expression exactly by NF-kB transcription factors. These “feedback loops”, not always well-known, deserve deeper investigation since they may have a role in tuning the response and the output consequent to NF-kB pathway initiation, in regulating the intensity of the response, or its homeostasis and balance in order to make the functioning of such critical system more robust and reliable. This integrated view allows to shed light on the functional structure and on some of the crucial nodes of thet NF-kB transcription factors interactome. Conclusion. Framing structure and dynamics of the NF-kB interactome into a wider, systemic picture would be a significant step toward a better understanding of how NF-kB globally regulates diverse gene programs and phenotypes. This study represents a step towards a more complete and integrated view of the NF-kB signaling system.

New computational biology tools for the systematic analysis of the structure and expression of human genes

From the late 1980s, the automation of sequencing techniques and the computer spread gave rise to a flourishing number of new molecular structures and sequences and to proliferation of new databases in which to store them. Here are presented three computational approaches able to analyse the massive amount of publicly avalilable data in order to answer to important biological questions. The first strategy studies the incorrect assignment of the first AUG codon in a messenger RNA (mRNA), due to the incomplete determination of its 5' end sequence. An extension of the mRNA 5' coding region was identified in 477 in human loci, out of all human known mRNAs analysed, using an automated expressed sequence tag (EST)-based approach. Proof-of-concept confirmation was obtained by in vitro cloning and sequencing for GNB2L1, QARS and TDP2 and the consequences for the functional studies are discussed. The second approach analyses the codon bias, the phenomenon in which distinct synonymous codons are used with different frequencies, and, following integration with a gene expression profile, estimates the total number of codons present across all the expressed mRNAs (named here "codonome value") in a given biological condition. Systematic analyses across different pathological and normal human tissues and multiple species shows a surprisingly tight correlation between the codon bias and the codonome bias. The third approach is useful to studies the expression of human autism spectrum disorder (ASD) implicated genes. ASD implicated genes sharing microRNA response elements (MREs) for the same microRNA are co-expressed in brain samples from healthy and ASD affected individuals. The different expression of a recently identified long non coding RNA which have four MREs for the same microRNA could disrupt the equilibrium in this network, but further analyses and experiments are needed.