Highlights CNR 2008-2009

Selezione ragionata degli oltre 14.000 articoli scientifici che i ricercatori del CNR hanno pubblicato nel corso del biennio 2008-2009 sulle principali riviste o volumi di riferimento della propria attività. I temi sono divisi per comodità in 4 grandi settori: Habitat e Vita, Materia e Energia, Informazione e Comunicazione, Cultura e Societ

Activity Report in “Highlights 2010/2011”

Abstract (MCSI 1000) La conoscenza si consolida e progredisce se, pubblicamente, si condividono idee, risultati, metodi, lavori. Per farlo occorre comunicare, raccontare, descrivere, giustificare, difendere il proprio lavoro di ricercatore. Highlights del Consiglio Nazionale delle Ricerche, giunta ormai alla terza edizione: una raccolta ragionata di lavori, notizie e attività funzionali a descrivere la ricchezza e la poliedricità scientifica dell’Ente che è, e resta, patrimonio della collettività. Gli Highlights di quest’anno assumono come riferimento temporale il biennio 2010-2011 e confermano l’impostazione dei contenuti in due sezioni, così come proposta nelle passate edizioni, raccontando, senza cedere alle lusinghe dell’autocelebrazione e dell’autoreferenzialità, lo svolgersi delle attività scientifiche nel più grande ente di ricerca italiano. I temi sono divisi per comodità in 4 grandi settori: Habitat e Vita, Materia e Energia, Informazione e Comunicazione, Cultura e Societ

Highlights CNR 2010-2011

La conoscenza si consolida e progredisce se, pubblicamente, si condividono idee, risultati, metodi, lavori. Per farlo occorre comunicare, raccontare, descrivere, giustificare, difendere il proprio lavoro di ricercatore.Highlights del Consiglio Nazionale delle Ricerche, giunta ormai alla terza edizione: una raccolta ragionata di lavori, notizie e attività funzionali a descrivere la ricchezza e la poliedricità scientifica dell’Ente che è, e resta, patrimonio della collettività. Gli Highlights di quest’anno assumono come riferimento temporale il biennio 2010-2011 e confermano l’impostazione dei contenuti in due sezioni, così come proposta nelle passate edizioni, raccontando, senza cedere alle lusinghe dell’autocelebrazione e dell’autoreferenzialità, lo svolgersi delle attività scientifiche nel più grande ente di ricerca italiano. I temi sono divisi per comodità in 4 grandi settori: Habitat e Vita, Materia e Energia, Informazione e Comunicazione, Cultura e Societ

Caratterizzazione di geni di Arabidopsis thaliana inducibili in anossia

Dai risultati di uno studio compiuto sul trascrittoma di Arabidopsis thaliana in condizioni anossiche sono stati identificati alcuni geni che mostrano una rapida e significativa induzione in seguito all’abbassamento delle concentrazioni dell’ossigeno disponibile nell’ambiente (Loreti et al 2005, Gonzali et al. 2005) Al fine di comprendere quali strategie di tolleranza vengano attuate dalla pianta in condizioni anossiche tali geni sono stati raggruppati in classi funzionali; tuttavia una larga parte delle sequenze è rimasta esclusa in quanto non le è ancora stata assegnata una funzione. Nel contempo anche per geni la cui funzione biochimica è già nota non è sempre chiaro il ruolo assunto nel processo di tolleranza dello stress. Inoltre un quadro complessivo delle strategie di tolleranza non può essere delineato senza prima comprendere i meccanismi regolativi che sovrintendono a tale fenomeno. Il presente lavoro è consistito, dunque, una preliminare caratterizzazione di dieci tra i geni risultati essere maggiormente espressi nella precedente analisi trascrittomica. Lo studio di tali geni è proceduto contemporaneamente su due livelli, uno maggiormente improntato sulla ricerca bioinformatica e l’altro basato prettamente sull’approccio sperimentale. Innanzitutto sono stati selezionati mutanti omozigoti di Arabidopsis per i geni precedentemente individuati ed è stato verificato che tali mutazioni determinassero realmente la perdita dell’espressione dei geni di interesse. Inizialmente è stata portata avanti una ricerca in banche dati di elementi, caratteristici delle sequenze selezionate, che potessero costituire utili linee guida nella progettazione dell’approccio sperimentale. E’ stata perciò presa in esame sia la sequenza nucleotidica dei geni che la relativa sequenza peptidica e, sulla base di queste, sono state svolte ricerche di similarità ed omologia sia globali che locali. Contemporaneamente sono state compiute analisi sia di tipo molecolare (localizzazione dell’espressione del gene di interesse e analisi dell’espressione di geni noti marcatori di condizioni anossiche) che fisiologiche (valutazione della tolleranza allo stress anossico ed ipossico, osservazione di alterazioni morfo-fisiologiche in aria ed in anossia) per caratterizzare il fenotipo di tali mutanti

Utilizzo di Nanoporous Silica Chip nello studio del profilo peptidico plasmatico: applicazione nello sviluppo e progressione del cancro colorettale

Background: To date single tumour molecule identification approach for the protein biomarkers discovery is unabled to unequivocally recognize the cancer, because current tumor biomarkers are also expressed in normal cells. The protein profiling identify a specific pattern of hundred of protein in numerous specimens. Low molecular weight (LMW) proteins/peptides, the fraction less abundant of the biological fluids, seem to contain disease-specific information and correlate to the tissue pathological status. The detection by MS-analysis of low abundant fraction and LMW peptides remains a critical challenge. Aim: A Nanoporous Silica Chip (NSC) was used to select and purify LMW plasma peptides in samples of colorectal cancer (CRC) patients to study the peptide profiling in association to development and progression of tumour. Materials and Methods: NSC is a patented prototype of Prof. M Ferrari Labs (Dept. of Nanomedicine of The Methodist Hospital Research Institute, Houston TX). It is a disc of 10 cm of diameter with a superficial nanoporous silica thin film. A standardized, fast and simple protocol was validated to perform the selection of plasma LMW peptides. 34 health subjects, 27 patients with pre-cancer lesion (adenoma ), 33 patients with early stage of CRC (stage I-II) and 34 patients with late stage of CRC (stage III-IV) was enrolled for this study. MS-analysis by MALDI-TOF instrument was performed on fractionated LMW plasma samples. Data were calibrated, aligned and normalized, and then they were undergone to accurate univariate and multivariate statistical analysis to highlight and identify difference of plasma peptide profile intensity comparing the 4 study group. Results: Good classification of control group was obtained regard patient group, but poor discrimination was observed between adenoma, early stage CRC and late stage CRC. Consequently, 29 ionic species was differentially expressed in study groups. MALDI-TOF/TOF analysis was identified the aminoacid sequence of several ionic species. All of them were fragment peptide of plasma protein arising to inflammatory response and system of complement. Moreover, peptide fragments of C3f and C4-A/B could be generated from precursor peptide by endopreotease and exoprotease cleavage. A peptide fragment was originated from propeptide of ITIH4 (Inter-?-trypsin inhibitor heavy chain H4). ITIH4 was secreted to liver and it belongs to phase acute proteins involved in inflammatory responses. It may also play a role in liver development and regeneration. Some studies were identified some ITIH4 peptide fragments involved in several pathological status as ischemic stroke, breast, ovarian and prostate cancer. Conclusions: A fast and simple method was set to perform study with NSC. NSC is a new tool with wide potential application. A deep study of obtained peptide proteolytic pattern was necessary suggesting a colorectal cancer specific proteases and exoprotease activity

GENOTIPIZZAZIONE MOLECOLARE E ANALISI CLINICA DI PAZIENTI CON TUBERCOLOSI MULTIRESISTENTE NELL¿HINTERLAND MILANESE

Abstract Keywords: tuberculosis, multi-drug-resistance, exogenous reinfection, relapse, fingerprinting, lineage Mycobacterium tuberculosis. Background Tuberculosis (TB) remains a major global health issue. In 2012, an estimated 8.6 million people developed TB and 1.3 million died from the disease (including 320,000 deaths among HIV-positive people). Considering the preventable nature of TB, the number of deaths due to Mycobacterium tuberculosis is unacceptably high. Based on global TB surveillance programs, in 2012 multi-drug resistance was identified among 3.6% of the new TB cases and among 20.0% of previously treated TB cases. The prevalence of MDR TB was particularly worrisome in Eastern Europe and Central Asia: in these areas MDR-TB accounted for more than 20.0% of the new TB cases and more than half of the previously treated TB cases. On the contrary, in Italy in the period 2004-2008 MDR strains represented less than 5% of all TB cases. Objective In this epidemiological retrospective cohort study we aimed to address the phenomenon of MDR-TB in the metropolitan area of Milan in the period 1993-2010. The main objectives of our study were the following: i) to compare epidemiological, microbiological, and clinical features of patients diagnosed with MDR-TB vs. patients diagnosed with non-MDR TB; ii) to evaluate the tendency of M. tuberculosis strains to form clusters and the role played in this setting by MDR-TB; iii) to assess the diffusion of MDR-TB among specific M. tuberculosis lineages; iv) and finally to analyzed the influence of MDR-TB in the recurrence of TB (specifically in the development of relapse vs. exogenous reinfections). Subjects This study was based on the TB dataset maintained at the Infectious Diseases Laboratory at Luigi Sacco Hospital (Milan, Italy), which contains data among TB cases diagnosed in the metropolitan area of Milan. The patients included in the study satisfied the following criteria: i) culture-proven TB; ii) availability of the causative M. tuberculosis strain; iii) presence of antimicrobial in vitro susceptibility data. Material and methods M. tuberculosis DNA was extracted from mycobacterial colonies growing on Lowenstein-Jensen medium according to standard laboratory procedures. Three methods were used to genotype M. tuberculosis strains: the gold standard technique Restriction Fragment Length Polymorphism designed by van Soolingen et al., the Spacer Oligonucleotide Typing (Spoligotyping) as described by Kamerbeek et al., and the Mycobacterial Interspersed Repetitive Unit of Variable Number of Tandem Repeats (MIRU-VNTR) 12-loci genotyping as illustrated by Supply et al. Logistic regression analysis (conducted with SAS Enterprise Guide -Version 5.1, Institute Inc, Cary North Carolina, USA and SPSS Version 20.0, Chicago, Illinois, USA) was used to assess risk factors associated with MDRTB, clustering, TB lineages and recurrent episodes. Results 4,237 TB cases were included in the study. Based on logistic regression analyses, MDR TB cases, were independently associated with presence of comorbidities (aOR 2,5; 95% CI 1,1-5,7), pulmonary TB (aOR 5,2; 95% CI 1,6-16,5), and TB recurrence (aOR 5,2; 95% CI 3,0-9,1). European nationality was associated to a reduced risk of developing MDR-TB (aOR 0,3; 95% CI 0,2-0,6). TB clustered strains were associated to positive microscopic smear exam (aOR 1,9; CI 95% 1,1-3,4). On the contrary there was an inverse correlation between East-European origin of the patient and the tendency of M. tuberculosis strains to clusterize (aOR 0,09; CI 95% 0,01-0,7). Moreover, we showed that East-Asian lineage was independently linked with MDR-TB (aOR 3,4; CI 95% 1,5-7,6). Finally, MDR-TB was more frequently observed in recurrent TB episodes due to relapse; when compared to TB relapse, exogenous TB reinfection were characterized by a reduced risk of MDR (aOR 0,1 CI 95% 0,01-0,9; p 0,04). Conclusions Based on our observations in the metropolitan area of Milan, MDR-TB was associated with foreign origin of the patients, presence of the Beijing lineage of M. tuberculosis and recurrence of TB (specifically, TB relapse). This study highlights the key-role of molecular genotyping in TB epidemiology. Our findings may improve current MDR-TB control strategies. Keywords: tuberculosis, multi-drug-resistance, exogenous reinfection, relapse, fingerprinting, lineage Mycobacterium tuberculosis

Identificazione di nuovi marcatori tumorali nelle neoplasie mammarie del cane: applicazione di tecnologie molecolari innovative

Canine mammary tumors (CMT) are the most common neoplasms in female dogs and the discovery of diagnostic, prognostic, and therapeutic markers is essential for improving the disease outcomes and the animal welfare. The aims of this study were to investigate the role of the Receptor tyrosine-kinase ErbB-2 (HER2) and to discover new potential tumor markers in CMT using innovative proteomic approaches. HER2 protein and RNA expressions were determined by immunohistochemistry (IHC) with an antibody extensively used in veterinary medicine and by real-time quantitative RT-PCR (qRT-PCR) as well as by Western Immunoblotting (WB) and Reverse-Phase Protein Arrays (RPPA). An orthogonal validation of HER2 protein expression was carried out using high-resolution mass spectrometry (MS). A diffuse cytoplasmic staining related to antibody lack of specificity was observed by IHC and further confirmed by WB. No differences between benign and malignant neoplasms were noted at mRNA level and the MS technique failed to detect HER2 peptides in the CMT. These results indicate a minor role of HER2 in CMT. Further, 40 proteins were found to be differentially expressed in normal mammary gland and in CMT by MS. Proteins related to glucose and to mitochondrial function as Transketolase, Transketolase like 1, and Prohibitin 2 were also investigate by IHC. The differences observed in hyperplasic and neoplastic lesions compared to normal mammary gland suggest these proteins as new potential markers for CMT

Cross-Talk tra Bifidobacterium e intestino umano: impatto sulle attività health promoting

Bifidobacteria constitute up to 3% of the total microbiota and represent one of the most important healthpromoting bacterial groups of the human intestinal microflora. The presence of Bifidobacterium in the human gastrointestinal tract has been directly related to several health-promoting activities; however, to date, no information about the specific mechanisms of interaction with the host is available. The first health-promoting activities studied in these job was the oxalate-degrading activity. Oxalic acid occurs extensively in nature and plays diverse roles, especially in pathological processes. Due to its highly oxidizing effects, hyper absorption or abnormal synthesis of oxalate can cause serious acute disorders in mammals and be lethal in extreme cases. Intestinal oxalate-degrading bacteria could therefore be pivotal in maintaining oxalate homeostasis, reducing the risk of kidney stone development. In this study, the oxalate-degrading activity of 14 bifidobacterial strains was measured by a capillary electrophoresis technique. The oxc gene, encoding oxalyl-CoA decarboxylase, a key enzyme in oxalate catabolism, was isolated by probing a genomic library of B. animalis subsp. lactis BI07, which was one of the most active strains in the preliminary screening. The genetic and transcriptional organization of oxc flanking regions was determined, unravelling the presence of other two independently transcribed open reading frames, potentially responsible for B. animalis subsp. lactis ability to degrade oxalate. Transcriptional analysis, using real-time quantitative reverse transcription PCR, revealed that these genes were highly induced in cells first adapted to subinhibitory concentrations of oxalate and then exposed to pH 4.5. Acidic conditions were also a prerequisite for a significant oxalate degradation rate, which dramatically increased in oxalate pre-adapted cells, as demonstrated in fermentation experiments with different pH-controlled batch cultures. These findings provide new insights in the characterization of oxalate-degrading probiotic bacteria and may support the use of B. animalis subsp. lactis as a promising adjunct for the prophylaxis and management of oxalate-related kidney disease. In order to provide some insight into the molecular mechanisms involved in the interaction with the host, in the second part of the job, we investigated whether Bifidobacterium was able to capture human plasminogen on the cell surface. The binding of human plasminogen to Bifidobacterium was dependent on lysine residues of surface protein receptors. By using a proteomic approach, we identified six putative plasminogen-binding proteins in the cell wall fraction of three strain of Bifidobacterium. The data suggest that plasminogen binding to Bifidobactrium is due to the concerted action of a number of proteins located on the bacterial cell surface, some of which are highly conserved cytoplasmic proteins which have other essential cellular functions. Our findings represent a step forward in understanding the mechanisms involved in the Bifidobacterium-host interaction. In these job w studied a new approach based on to MALDI-TOF MS to measure the interaction between entire bacterial cells and host molecular target. MALDI-TOF (Matrix Assisted Laser Desorption Ionization-Time of Flight)—mass spectrometry has been applied, for the first time, in the investigation of whole Bifidobacterium cells-host target proteins interaction. In particular, by means of this technique, a dose dependent human plasminogen-binding activity has been shown for Bifidobacterium. The involvement of lysine binding sites on the bacterial cell surface has been proved. The obtained result was found to be consistent with that from well-established standard methodologies, thus the proposed MALDI-TOF approach has the potential to enter as a fast alternative method in the field of biorecognition studies involving in bacterial cells and proteins of human origin

Bio-Augmented Materiality. Una visione strategica per la progettazione bio-digitale

Oggi il design si ritrova al centro di una straordinaria doppia convergenza – tecnologica e culturale – tra la natura e l’artificio. Da un punto di vista tecnologico, tecnologie sempre più sofisticate e digitalizzate, nano e biosintetiche permettono di analizzare e riprodurre i processi generativi, chimici, fisici e molecolari alla base dei meccanismi naturali, rendendo l’artificio sempre più simile al biologico e la natura sempre più manipolabile fin dentro le sue fibre più profonde. Da un punto di vista culturale, si diffonde una rinnovata consapevolezza per la biologia e l’ecosistema, catalizzata da nuovi approcci alla comprensione ecologica e dal proliferare di filosofie post-antropocentriche. La tesi si propone come indagine delle implicazioni e del significato che questa convergenza apporta nella cultura del progetto, sia negli scenari e nelle opportunità di innovazione che si aprono alla disciplina; sia nel mutamento degli approcci (obiettivi e metodologie); sia nell’evoluzione del modo di progettare e immaginare nuovi artefatti. Il risultato di questa analisi è confluito nel concetto di “Bio-Augmented Materiality”, quale visione strategica esperienziale e rizomatica, ispirata alle dinamiche della crescita biologica, che si riappropria della dimensione spaziale dell’interconnessione e di quella temporale del presente per il progetto di futuri di co-evoluzione tra uomo e natura, tecnologia ed ecologia. Come una delle strade percorribili, la tesi si addentra poi nel campo della biostampa, quale manifattura ibrida in grado di stimolare processualità ed estetiche relazionali, frutto di modelli collaborativi e scambi informazionali, per una progettualità bio-avanzata sempre più allineata alle logiche della vita.Today, design is central to an extraordinary double technological and cultural convergence between nature and artifice. From a technological point of view, increasingly sophisticated and digitalised, nano and biosynthetic technologies make it possible to analyse and reproduce the generative, chemical, physical and molecular processes underlying natural mechanisms, making the artifice increasingly similar to biological and nature increasingly more manipulable till its deepest fibres. From a cultural point of view, a renewed awareness of biology and the ecosystem is spreading, catalysed by new approaches to ecological understanding and the proliferation of post-anthropocentric philosophies. The thesis is an investigation of the implications and meaning that this convergence brings to the design culture, both in the scenarios and in the innovation opportunities that open up to the discipline, both in the change of approaches (objectives and methodologies); and in the evolution of the way of designing and imagining new artefacts. The result of this analysis converged into the concept of “Bio-Augmented Materiality” as an experiential and rhizomatic strategic vision inspired by the dynamics of biological growth, which re-appropriates the spatial dimension of interconnection and the temporal dimension of the present for the project of co-evolution futures between man and nature, technology and ecology. As one of the possible paths, the thesis explores the field of bioprinting as a hybrid manufacturing able to stimulate relational aesthetics and processes, the result of collaborative models and informational exchanges, for a bio-advanced design increasingly aligned with the logic of life

Guida dello studente per la Facoltà di Ingegneria. Anno accademico 1994-1995

La Guida delinea il complesso dell’offerta formativa della Facoltà di Ingegneria, in diversi anni accademici, indicando le modalità di accesso ai Corsi di studio, i piani didattici e i programmi degli insegnamenti