iSPOT: A Web Tool for the Analysis and Recognition of Protein Domain Specificity

Methods that aim at predicting interaction partners are very likely to play an important role in the interpretation of genomic information. iSPOT (iSpecificity Prediction Of Target) is a web tool (accessible at http://cbm.bio.uniroma2.it/iSPOT) developed for the prediction of protein-protein interaction mediated by families of peptide recognition modules. iSPOT accesses a database of position specific residue-residue interaction frequencies for members of the SH3 and PDZ protein domain families. The software utilises this database to provide a score for any potential domain peptide interaction

A serine protease secreted from Bacillus subtilis cleaves human plasma transthyretin to generate an amyloidogenic fragment

Aggregation of human wild-type transthyretin (hTTR), a homo-tetrameric plasma protein, leads to acquired senile systemic amyloidosis (SSA), recently recognised as a major cause of cardiomyopathies in 1-3% older adults. Fragmented hTTR is the standard composition of amyloid deposits in SSA, but the protease(s) responsible for amyloidogenic fragments generation in vivo is(are) still elusive. Here, we show that subtilisin secreted from Bacillus subtilis, a gut microbiota commensal bacterium, translocates across a simulated intestinal epithelium and cleaves hTTR both in solution and human plasma, generating the amyloidogenic fragment hTTR(59-127), which is also found in SSA amyloids in vivo. To the best of our knowledge, these findings highlight a novel pathogenic mechanism for SSA whereby increased permeability of the gut mucosa, as often occurs in elderly people, allows subtilisin (and perhaps other yet unidentified bacterial proteases) to reach the bloodstream and trigger generation of hTTR fragments, acting as seeding nuclei for preferential amyloid fibrils deposition in the heart. Peterle et al. show that a subtilisin like serine protease secreted from gut microbiota Bacillus subtilis cleaves the wild-type human transthyretin (hTTR) to generate an amyloidogenic peptide. High propensity of the hTTR fragment to form pathogenic protein aggregates implicates the serine protease in the pathogenesis of acquired senile systemic amyloidosis

La dinamica del clima nell’ultimo ciclo glaciale-interglaciale

Attraverso questo primo incontro, il Gruppo di Lavoro Dinamica del paleoclima del CNR intende creare ed intensificare la rete tra i ricercatori italiani che si occupano di paleoclima, favorire la collaborazione tra la comunità paleoclimatica e di modellistica climatica ed individuare grandi sfide e temi di ricerca comuni per promuovere la partecipazione congiunta a programmi di ricerca nazionali ed internazionali

Hair-Derived Exposome Exploration of Cardiometabolic Health: Piloting a Bayesian Multitrait Variable Selection Approach.

peer reviewedCardiometabolic health is complex and characterized by an ensemble of correlated and/or co-occurring conditions including obesity, dyslipidemia, hypertension, and diabetes mellitus. It is affected by social, lifestyle, and environmental factors, which in-turn exhibit complex correlation patterns. To account for the complexity of (i) exposure profiles and (ii) health outcomes, we propose to use a multitrait Bayesian variable selection approach and identify a sparse set of exposures jointly explanatory of the complex cardiometabolic health status. Using data from a subset (N = 941 participants) of the nutrition, environment, and cardiovascular health (NESCAV) study, we evaluated the link between measurements of the cumulative exposure to (N = 33) pollutants derived from hair and cardiometabolic health as proxied by up to nine measured traits. Our multitrait analysis showed increased statistical power, compared to single-trait analyses, to detect subtle contributions of exposures to a set of clinical phenotypes, while providing parsimonious results with improved interpretability. We identified six exposures that were jointly explanatory of cardiometabolic health as modeled by six complementary traits, of which, we identified strong associations between hexachlorobenzene and trifluralin exposure and adverse cardiometabolic health, including traits of obesity, dyslipidemia, and hypertension. This supports the use of this type of approach for the joint modeling, in an exposome context, of correlated exposures in relation to complex and multifaceted outcomes

Hair-Derived Exposome Exploration of Cardiometabolic Health: Piloting a Bayesian Multitrait Variable Selection Approach

Cardiometabolic health is complex and characterized by an ensemble of correlated and/or co-occurring conditions including obesity, dyslipidemia, hypertension, and diabetes mellitus. It is affected by social, lifestyle, and environmental factors, which in-turn exhibit complex correlation patterns. To account for the complexity of (i) exposure profiles and (ii) health outcomes, we propose to use a multitrait Bayesian variable selection approach and identify a sparse set of exposures jointly explanatory of the complex cardiometabolic health status. Using data from a subset ( N = 941 participants) of the nutrition, environment, and cardiovascular health (NESCAV) study, we evaluated the link between measurements of the cumulative exposure to ( N = 33) pollutants derived from hair and cardiometabolic health as proxied by up to nine measured traits. Our multitrait analysis showed increased statistical power, compared to single-trait analyses, to detect subtle contributions of exposures to a set of clinical phenotypes, while providing parsimonious results with improved interpretability. We identified six exposures that were jointly explanatory of cardiometabolic health as modeled by six complementary traits, of which, we identified strong associations between hexachlorobenzene and trifluralin exposure and adverse cardiometabolic health, including traits of obesity, dyslipidemia, and hypertension. This supports the use of this type of approach for the joint modeling, in an exposome context, of correlated exposures in relation to complex and multifaceted outcomes

An Extensive Quality Control and Quality Assurance (QC/QA) Program Significantly Improves Inter-Laboratory Concordance Rates of Flow-Cytometric Minimal Residual Disease Assessment in Acute Lymphoblastic Leukemia: An I-BFM-FLOW-Network Report

Monitoring of minimal residual disease (MRD) by flow cytometry (FCM) is a powerful prognostic tool for predicting outcomes in acute lymphoblastic leukemia (ALL). To apply FCM-MRD in large, collaborative trials, dedicated laboratory staff must be educated to concordantly high levels of expertise and their performance quality should be continuously monitored. We sought to install a unique and comprehensive training and quality control (QC) program involving a large number of reference laboratories within the international Berlin-Frankfurt-Münster (I-BFM) consortium, in order to complement the standardization of the methodology with an educational component and persistent quality control measures. Our QC and quality assurance (QA) program is based on four major cornerstones: (i) a twinning maturation program, (ii) obligatory participation in external QA programs (spiked sample send around, United Kingdom National External Quality Assessment Service (UK NEQAS)), (iii) regular participation in list-mode-data (LMD) file ring trials (FCM data file send arounds), and (iv) surveys of independent data derived from trial results. We demonstrate that the training of laboratories using experienced twinning partners, along with continuous educational feedback significantly improves the performance of laboratories in detecting and quantifying MRD in pediatric ALL patients. Overall, our extensive education and quality control program improved inter-laboratory concordance rates of FCM-MRD assessments and ultimately led to a very high conformity of risk estimates in independent patient cohorts

Il Futuro della Cybersecurity in Italia: Ambiti Progettuali Strategici

Il presente volume nasce come continuazione del precedente, con l’obiettivo di delineare un insieme di ambiti progettuali e di azioni che la comunità nazionale della ricerca ritiene essenziali a complemento e a supporto di quelli previsti nel DPCM Gentiloni in materia di sicurezza cibernetica, pubblicato nel febbraio del 2017. La lettura non richiede particolari conoscenze tecniche; il testo è fruibile da chiunque utilizzi strumenti informatici o navighi in rete. Nel volume vengono considerati molteplici aspetti della cybersecurity, che vanno dalla definizione di infrastrutture e centri necessari a organizzare la difesa alle azioni e alle tecnologie da sviluppare per essere protetti al meglio, dall’individuazione delle principali tecnologie da difendere alla proposta di un insieme di azioni orizzontali per la formazione, la sensibilizzazione e la gestione dei rischi. Gli ambiti progettuali e le azioni, che noi speriamo possano svilupparsi nei prossimi anni in Italia, sono poi accompagnate da una serie di raccomandazioni agli organi preposti per affrontare al meglio, e da Paese consapevole, la sfida della trasformazione digitale. Le raccomandazioni non intendono essere esaustive, ma vanno a toccare dei punti che riteniamo essenziali per una corretta implementazione di una politica di sicurezza cibernetica a livello nazionale. Politica che, per sua natura, dovrà necessariamente essere dinamica e in continua evoluzione in base ai cambiamenti tecnologici, normativi, sociali e geopolitici. All’interno del volume, sono riportati dei riquadri con sfondo violetto o grigio; i primi sono usati nel capitolo introduttivo e nelle conclusioni per mettere in evidenza alcuni concetti ritenuti importanti, i secondi sono usati negli altri capitoli per spiegare il significato di alcuni termini tecnici comunemente utilizzati dagli addetti ai lavori. In conclusione, ringraziamo tutti i colleghi che hanno contribuito a questo volume: un gruppo di oltre 120 ricercatori, provenienti da circa 40 tra Enti di Ricerca e Università, unico per numerosità ed eccellenza, che rappresenta il meglio della ricerca in Italia nel settore della cybersecurity. Un grazie speciale va a Gabriella Caramagno e ad Angela Miola che hanno contribuito a tutte le fasi di produzione del libro. Tra i ringraziamenti ci fa piacere aggiungere il supporto ottenuto dai partecipanti al progetto FILIERASICURA