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1. Metaproteomics reveals diet-induced changes in gut microbiome function according to Crohn’s disease location

Author

Levi Mortera, Stefano, Marzano, Valeria, Rapisarda, Federica, Marangelo, Chiara, Pirona, Ilaria, Vernocchi, Pamela, Di Michele, Marta, Del Chierico, Federica, Quintero, Maria A., Fernandez, Irina, Hazime, Hajar, Killian, Rose M., Solis, Norma, Ortega, Mailenys, Damas, Oriana M., Proksell, Siobhan, Kerman, David H., Deshpande, Amar R., Garces, Luis, Scaldaferri, Franco, Gasbarrini, Antonio, Abreu, Maria T., and Putignani, Lorenza

Published
2024
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3. Williams–Beuren syndrome shapes the gut microbiota metaproteome

Author

Marzano, Valeria, Levi Mortera, Stefano, Vernocchi, Pamela, Del Chierico, Federica, Marangelo, Chiara, Guarrasi, Valerio, Gardini, Simone, Dentici, Maria Lisa, Capolino, Rossella, Digilio, Maria Cristina, Di Donato, Maddalena, Spasari, Iolanda, Abreu, Maria Teresa, Dallapiccola, Bruno, and Putignani, Lorenza

Published
2023
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5. A Layer Correlation technique for pion energy calibration at the 2004 ATLAS Combined Beam Test

Author

Abat, E., Abdallah, J. M., Addy, T. N., Adragna, P., Aharrouche, M., Ahmad, A., Akesson, T. P. A., Aleksa, M., Alexa, C., Anderson, K., Andreazza, A., Anghinolfi, F., Antonaki, A., Arabidze, G., Arik, E., Atkinson, T., Baines, J., Baker, O. K., Banfi, D., Baron, S., Barr, A. J., Beccherle, R., Beck, H. P., Belhorma, B., Bell, P. J., Benchekroun, D., Benjamin, D. P., Benslama, K., Kuutmann, E. Bergeaas, Bernabeu, J., Bertelsen, H., Binet, S., Biscarat, C., Boldea, V., Bondarenko, V. G., Boonekamp, M., Bosman, M., Bourdarios, C., Broklova, Z., Chromek, D. Burckhart, Bychkov, V., Callahan, J., Calvet, D., Canneri, M., Garrido, M. Capeáns, Caprini, M., Sas, L. Cardiel, Carli, T., Carminati, L., Carvalho, J., Cascella, M., Castillo, M. V., Catinaccio, A., Cauz, D., Cavalli, D., Sforza, M. Cavalli, Cavasinni, V., Cetin, S. A., Chen, H., Cherkaoui, R., Chevalier, L., Chevallier, F., Chouridou, S., Ciobotaru, M., Citterio, M., Clark, A., Cleland, B., Cobal, M., Cogneras, E., Muino, P. Conde, Consonni, M., Constantinescu, S., Cornelissen, T., Correard, S., Radu, A. Corso, Costa, G., Costa, M. J., Costanzo, D., Cuneo, S., Cwetanski, P., Da Silva, D., Dam, M., Dameri, M., Danielsson, H. O., Dannheim, D., Darbo, G., Davidek, T., De, K., Defay, P. O., Dekhissi, B., Del Peso, J., Del Prete, T., Delmastro, M., Derue, F., Di Ciaccio, L., Di Girolamo, B., Dita, S., Dittus, F., Djama, F., Djobava, T., Dobos, D., Dobson, M., Dolgoshein, B. A., Dotti, A., Drake, G., Drasal, Z., Dressnandt, N., Driouchi, C., Drohan, J., Ebenstein, W. L., Eerola, P., Efthymiopoulos, I., Egorov, K., Eifert, T. F., Einsweiler, K., Kacimi, M. El, Elsing, M., Emelyanov, D., Escobar, C., Etienvre, A. I., Fabich, A., Facius, K., Fakhr-Edine, A. I., Fanti, M., Farbin, A., Farthouat, P., Fassouliotis, D., Fayard, L., Febbraro, R., Fedin, O. L., Fenyuk, A., Fergusson, D., Ferrari, P., Ferrari, R., Ferreira, B. C., Ferrer, A., Ferrere, D., Filippini, G., Flick, T., Fournier, D., Francavilla, P., Francis, D., Froeschl, R., Froidevaux, D., Fullana, E., Gadomski, S., Gagliardi, G., Gagnon, P., Gallas, M., Gallop, B. J., Gameiro, S., Gan, K. K., Garcia, R., Garcia, C., Gavrilenko, I. L., Gemme, C., Gerlach, P., Ghodbane, N., Giakoumopoulou, V., Giangiobbe, V., Giokaris, N., Glonti, G., Goettfert, T., Golling, T., Gollub, N., Gomes, A., Gomez, M. D., Gonzalez-Sevilla, S., Goodrick, M. J., Gorfine, G., Gorini, B., Goujdami, D., Grahn, K-J., Grenier, P., Grigalashvili, N., Grishkevich, Y., Grosse-Knetter, J., Gruwe, M., Guicheney, C., Gupta, A., Haeberli, C., Haertel, R., Hajduk, Z., Hakobyan, H., Hance, M., Hansen, J. D., Hansen, P. H., Hara, K., Harvey Jr., A., Hawkings, R. J., Heinemann, F. E. W., Correia, A. Henriques, Henss, T., Hervas, L., Higon, E., Hill, J. C., Hoffman, J., Hostachy, J. Y., Hruska, I., Hubaut, F., Huegging, F., Hulsbergen, W., Hurwitz, M., Iconomidou-Fayard, L., Jansen, E., Plante, I. Jen-La, Johansson, P. D. C., Jon-And, K., Joos, M., Jorgensen, S., Joseph, J., Kaczmarska, A., Kado, M., Karyukhin, A., Kataoka, M., Kayumov, F., Kazarov, A., Keener, P. T., Kekelidze, G. D., Kerschen, N., Kersten, S., Khomich, A., Khoriauli, G., Khramov, E., Khristachev, A., Khubua, J., Kittelmann, T. H., Klingenberg, R., Klinkby, E. B., Kodys, P., Koffas, T., Kolos, S., Konovalov, S. P., Konstantinidis, N., Kopikov, S., Korolkov, I., Kostyukhin, V., Kovalenko, S., Kowalski, T. Z., Krüger, K., Kramarenko, V., Kudin, L. G., Kulchitsky, Y., Lacasta, C., Lafaye, R., Laforge, B., Lampl, W., Lanni, F., Laplace, S., Lari, T., Bihan, A-C. Le, Lechowski, M., Ledroit-Guillon, F., Lehmann, G., Leitner, R., Lelas, D., Lester, C. G., Liang, Z., Lichard, P., Liebig, W., Lipniacka, A., Lokajicek, M., Louchard, L., Lourerio, K. F., Lucotte, A., Luehring, F., Lund-Jensen, B., Lundberg, B., Ma, H., Mackeprang, R., Maio, A., Maleev, V. P., Malek, F., Mandelli, L., Maneira, J., Mangin-Brinet, M., Manousakis, A., Mapelli, L., Marques, C., Garcia, S. Marti i, Martin, F., Mathes, M., Mazzanti, M., McFarlane, K. W., McPherson, R., Mchedlidze, G., Mehlhase, S., Meirosu, C., Meng, Z., Meroni, C., Mialkovski, V., Mikulec, B., Milstead, D., Minashvili, I., Mindur, B., Mitsou, V. A., Moed, S., Monnier, E., Moorhead, G., Morettini, P., Morozov, S. V., Mosidze, M., Mouraviev, S. V., Moyse, E. W. J., Munar, A., Myagkov, A., Nadtochi, A. V., Nakamura, K., Nechaeva, P., Negri, A., Nemecek, S., Nessi, M., Nesterov, S. Y., Newcomer, F. M., Nikitine, I., Nikolaev, K., Nikolic-Audit, I., Ogren, H., Oh, S. H., Oleshko, S. B., Olszowska, J., Onofre, A., Aranda, C. Padilla, Paganis, S., Pallin, D., Pantea, D., Paolone, V., Parodi, F., Parsons, J., Parzhitskiy, S., Pasqualucci, E., Passmored, S. M., Pater, J., Patrichev, S., Peez, M., Reale, V. Perez, Perini, L., Peshekhonov, V. D., Petersen, J., Petersen, T. C., Petti, R., Phillips, P. W., Pina, J., Pinto, B., Podlyski, F., Poggioli, L., Poppleton, A., Poveda, J., Pralavorio, P., Pribyl, L., Price, M. J., Prieur, D., Puigdengoles, C., Puzo, P., Røhne, O., Ragusa, F., Rajagopalan, S., Reeves, K., Reisinger, I., Rembser, C., Renstrom, P. A. Bruckman. de., Reznicek, P., Ridel, M., Risso, P., Riu, I., Robinson, D., Roda, C., Roe, S., Rohne, O., Romaniouk, A., Rousseau, D., Rozanov, A., Ruiz, A., Rusakovich, N., Rust, D., Ryabov, Y. F., Ryjov, V., Salto, O., Salvachua, B., Salzburger, A., Sandaker, H., Rios, C. Santamarina, Santi, L., Santoni, C., Saraiva, J. G., Sarri, F., Sauvage, G., Says, L. P., Schaefer, M., Schegelsky, V. A., Schiavi, C., Schieck, J., Schlager, G., Schlereth, J., Schmitt, C., Schultes, J., Schwemling, P., Schwindling, J., Seixas, J. M., Seliverstov, D. M., Serin, L., Sfyrla, A., Shalanda, N., Shaw, C., Shin, T., Shmeleva, A., Silva, J., Simion, S., Simonyan, M., Sloper, J. E., Smirnov, S. Yu., Smirnova, L., Solans, C., Solodkov, A., Solovianov, O., Soloviev, I., Sosnovtsev, V. V., Spanó, F., Speckmayer, P., Stancu, S., Stanek, R., Starchenko, E., Straessner, A., Suchkov, S. I., Suk, M., Szczygiel, R., Tarrade, F., Tartarelli, F., Tas, P., Tayalati, Y., Tegenfeldt, F., Teuscher, R., Thioye, M., Tikhomirov, V. O., Timmermans, C. J. W. P., Tisserant, S., Toczek, B., Tremblet, L., Troncon, C., Tsiareshka, P., Tyndel, M., Unel, M. Karagoez., Unal, G., Unel, G., Usai, G., Van Berg, R., Valero, A., Valkar, S., Valls, J. A., Vandelli, W., Vannucci, F., Vartapetian, A., Vassilakopoulos, V. I., Vasilyeva, L., Vazeille, F., Vernocchi, F., Vetter-Cole, Y., Vichou, I., Vinogradov, V., Virzi, J., Vivarelli, I., Vivie, J. B. de., Volpi, M., Anh, T. Vu, Wang, C., Warren, M., Weber, J., Weber, M., Weidberg, A. R., Weingarten, J., Wells, P. S., Werner, P., Wheeler, S., Wiessmann, M., Wilkens, H., Williams, H. H., Wingerter-Seez, I., Yasu, Y., Zaitsev, A., Zenin, A., Zenis, T., Zenonos, Z., Zhang, H., Zhelezko, A., and Zhou, N.

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment
Abstract

A new method for calibrating the hadron response of a segmented calorimeter is developed and successfully applied to beam test data. It is based on a principal component analysis of energy deposits in the calorimeter layers, exploiting longitudinal shower development information to improve the measured energy resolution. Corrections for invisible hadronic energy and energy lost in dead material in front of and between the calorimeters of the ATLAS experiment were calculated with simulated Geant4 Monte Carlo events and used to reconstruct the energy of pions impinging on the calorimeters during the 2004 Barrel Combined Beam Test at the CERN H8 area. For pion beams with energies between 20 GeV and 180 GeV, the particle energy is reconstructed within 3% and the energy resolution is improved by between 11% and 25% compared to the resolution at the electromagnetic scale., Comment: 36 pages, 12 figures, accepted by JINST

Published
2010
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6. Alignment of the Pixel and SCT Modules for the 2004 ATLAS Combined Test Beam

Author

Ahmad, A., Andreazza, A., Atkinson, T., Baines, J., Barr, A. J., Beccherle, R., Bell, P. J., Bernabeu, J., Broklova, Z., de Renstrom, P. A. Bruckman, Cauz, D., Chevalier, L., Chouridou, S., Citterio, M., Clark, A., Cobal, M., Cornelissen, T., Correard, S., Costa, M. J., Costanzo, D., Cuneo, S., Dameri, M., Darbo, G., de Vivie, J. B., Di Girolamo, B., Dobos, D., Drasal, Z., Drohan, J., Einsweiler, K., Elsing, M., Emelyanov, D., Escobar, C., Facius, K., Ferrari, P., Fergusson, D., Ferrere, D., Flick, T., Froidevaux, D., Gagliardi, G., Gallas, M., Gallop, B. J., Gan, K. K., Garcia, C., Gavrilenko, I. L., Gemme, C., Gerlach, P., Golling, T., Gonzalez-Sevilla, S., Goodrick, M. J., Gorfine, G., Goettfert, T., Grosse-Knetter, J., Hansen, P. H., Hara, K., Hartel, R., Harvey, A., Hawkings, R. J., Heinemann, F. E. W., Henns, T., Hill, J. C., Huegging, F., Jansen, E., Joseph, J., Unel, M. Karagoz, Kataoka, M., Kersten, S., Khomich, A., Klingenberg, R., Kodys, P., Koffas, T., Konstantinidis, N., Kostyukhin, V., Lacasta, C., Lari, T., Latorre, S., Lester, C. G., Liebig, W., Lipniacka, A., Lourerio, K. F., Mangin-Brinet, M., Garcia, S. Marti i, Mathes, M., Meroni, C., Mikulec, B., Mindur, B., Moed, S., Moorhead, G., Morettini, P., Moyse, E. W. J., Nakamura, K., Nechaeva, P., Nikolaev, K., Parodi, F., Parzhitski, S., Pater, J., Petti, R., Phillips, P. W., Pinto, B., Poppleton, A., Reeves, K., Reisinger, I., Reznicek, P., Risso, P., Robinson, D., Roe, S., Rozanov, A., Salzburger, A., Sandaker, H., Santi, L., Schiavi, C., Schieck, J., Schultes, J., Sfyrla, A., Shaw, C., Tegenfeldt, F., Timmermans, C. J. W. P., Toczek, B., Troncon, C., Tyndel, M., Vernocchi, F., Virzi, J., Anh, T. Vu, Warren, M., Weber, J., Weber, M., Weidberg, A. R., Weingarten, J., Wells, P. S., and Zhelezko, A.

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment
Abstract

A small set of final prototypes of the ATLAS Inner Detector silicon tracker (Pixel and SCT) were used to take data during the 2004 Combined Test Beam. Data were collected from runs with beams of different flavour (electrons, pions, muons and photons) with a momentum range of 2 to 180 GeV/c. Four independent methods were used to align the silicon modules. The corrections obtained were validated using the known momenta of the beam particles and were shown to yield consistent results among the different alignment approaches. From the residual distributions, it is concluded that the precision attained in the alignment of the silicon modules is of the order of 5 micrometers in their most precise coordinate., Comment: 22 pages, submitted to JINST, 129 authors

Published
2008
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15. Characterization of the gut-liver-muscle axis in cirrhotic patients with sarcopenia

Author

Ponziani, Francesca Romana, Picca, A., Marzetti, Emanuele, Calvani, Riccardo, Conta, G., Del Chierico, F., Capuani, G., Faccia, M., Fianchi, Francesca, Funaro, B., Jose Coelho-Junior, H., Petito, Valentina, Rinninella, Emanuele, Paroni Sterbini, F., Reddel, S., Vernocchi, P., Cristina Mele, M., Miccheli, A., Putignani, Lorenza, Sanguinetti, Maurizio, Pompili, Maurizio, Gasbarrini, Antonio, Ponziani F. R. (ORCID:0000-0002-5924-6238), Marzetti E. (ORCID:0000-0001-9567-6983), Calvani R. (ORCID:0000-0001-5472-2365), Fianchi F., Petito V., Rinninella E. (ORCID:0000-0002-9165-2367), Putignani L., Sanguinetti M. (ORCID:0000-0002-9780-7059), Pompili M. (ORCID:0000-0001-6699-7980), Gasbarrini A. (ORCID:0000-0002-7278-4823), Ponziani, Francesca Romana, Picca, A., Marzetti, Emanuele, Calvani, Riccardo, Conta, G., Del Chierico, F., Capuani, G., Faccia, M., Fianchi, Francesca, Funaro, B., Jose Coelho-Junior, H., Petito, Valentina, Rinninella, Emanuele, Paroni Sterbini, F., Reddel, S., Vernocchi, P., Cristina Mele, M., Miccheli, A., Putignani, Lorenza, Sanguinetti, Maurizio, Pompili, Maurizio, Gasbarrini, Antonio, Ponziani F. R. (ORCID:0000-0002-5924-6238), Marzetti E. (ORCID:0000-0001-9567-6983), Calvani R. (ORCID:0000-0001-5472-2365), Fianchi F., Petito V., Rinninella E. (ORCID:0000-0002-9165-2367), Putignani L., Sanguinetti M. (ORCID:0000-0002-9780-7059), Pompili M. (ORCID:0000-0001-6699-7980), and Gasbarrini A. (ORCID:0000-0002-7278-4823)

Abstract

Background & Aim: Sarcopenia is frequent in cirrhosis and is associated with unfavourable outcomes. The role of the gut-liver-muscle axis in this setting has been poorly investigated. The aim of this study was to identify gut microbiota, metabolic and inflammatory signatures associated with sarcopenia in cirrhotic patients. Methods: Fifty cirrhotic patients assessed for the presence of sarcopenia by the quantification of muscle mass and strength were compared with age- and sex-matched controls. A multiomic analysis, including gut microbiota composition and metabolomics, serum myokines and systemic and intestinal inflammatory mediators, was performed. Results: The gut microbiota of sarcopenic cirrhotic patients was poor in bacteria associated with physical function (Methanobrevibacter, Prevotella and Akkermansia), and was enriched in Eggerthella, a gut microbial marker of frailty. The abundance of potentially pathogenic bacteria, such as Klebsiella, was also increased, to the detriment of autochthonous ones. Sarcopenia was associated with elevated serum levels of pro-inflammatory mediators and of fibroblast growth factor 21 (FGF21) in cirrhotic patients. Gut microbiota metabolic pathways involved in amino acid, protein and branched-chain amino acid metabolism were up-regulated, in addition to ethanol, trimethylamine and dimethylamine production. Correlation networks and clusters of variables associated with sarcopenia were identified, including one centred on Klebsiella/ethanol/FGF21/Eggerthella/Prevotella. Conclusions: Alterations in the gut-liver-muscle axis are associated with sarcopenia in patients with cirrhosis. Detrimental but also compensatory functions are involved in this complex network.

Published
2021

22. Proteomics and metabolomics approaches towards a functional insight onto autism spectrum disorders: Phenotype stratification and biomarker discovery

Author

Ristori, M. V., Mortera, S. L., Marzano, Valeria, Guerrera, S., Vernocchi, P., Ianiro, Gianluca, Gardini, S., Torre, Giuliano, Valeri, Giovanni, Vicari, Stefano, Gasbarrini, Antonio, Putignani, Lorenza, Marzano V., Ianiro G. (ORCID:0000-0002-8318-0515), Torre G., Valeri G., Vicari S. (ORCID:0000-0002-5395-2262), Gasbarrini A. (ORCID:0000-0002-7278-4823), Putignani L., Ristori, M. V., Mortera, S. L., Marzano, Valeria, Guerrera, S., Vernocchi, P., Ianiro, Gianluca, Gardini, S., Torre, Giuliano, Valeri, Giovanni, Vicari, Stefano, Gasbarrini, Antonio, Putignani, Lorenza, Marzano V., Ianiro G. (ORCID:0000-0002-8318-0515), Torre G., Valeri G., Vicari S. (ORCID:0000-0002-5395-2262), Gasbarrini A. (ORCID:0000-0002-7278-4823), and Putignani L.

Abstract

Autism spectrum disorders (ASDs) are neurodevelopmental disorders characterized by behavioral alterations and currently affect about 1% of children. Significant genetic factors and mechanisms underline the causation of ASD. Indeed, many affected individuals are diagnosed with chromosomal abnormalities, submicroscopic deletions or duplications, single-gene disorders or variants. However, a range of metabolic abnormalities has been highlighted in many patients, by identifying biofluid metabolome and proteome profiles potentially usable as ASD biomarkers. Indeed, next-generation sequencing and other omics platforms, including proteomics and metabolomics, have uncovered early age disease biomarkers which may lead to novel diagnostic tools and treatment targets that may vary from patient to patient depending on the specific genomic and other omics findings. The progressive identification of new proteins and metabolites acting as biomarker candidates, combined with patient genetic and clinical data and environmental factors, including microbiota, would bring us towards advanced clinical decision support systems (CDSSs) assisted by machine learning models for advanced ASD-personalized medicine. Herein, we will discuss novel computational solutions to evaluate new proteome and metabolome ASD biomarker candidates, in terms of their recurrence in the reviewed literature and laboratory medicine feasibility. Moreover, the way to exploit CDSS, performed by artificial intelligence, is presented as an effective tool to integrate omics data to electronic health/medical records (EHR/EMR), hopefully acting as added value in the near future for the clinical management of ASD.

Published
2020

23. Cystic fibrosis linked functional impairment and gut microbiota signatures: from omics data to clinical cue

Author

Vernocchi, P., Del Chierico, F., Russo, A., Majo, F., Valerio, M. C., Casadei, L., La Storia, A., Rizzo, C., Manetti, C., Paci, P., Montemitro, E., Ercolini, D., Marini, F., Fiscarelli, E., Dallapiccola, B., Miccheli, A., Lucidi, V., Putignani, L., DE FILIPPIS, FRANCESCA, European Society for Paediatric Gastroenterology, Hepatology and Nutrition, Vernocchi, P., Del Chierico, F., Russo, A., Majo, F., Valerio, M. C., Casadei, L., La Storia, A., DE FILIPPIS, Francesca, Rizzo, C., Manetti, C., Paci, P., Montemitro, E., Ercolini, D., Marini, F., Fiscarelli, E., Dallapiccola, B., Miccheli, A., Lucidi, V., and Putignani, L.

Published
2017

24. Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach

Author

Mortera, Sl, Soggiu, A, Vernocchi, P, Del Chierico, F, Piras, C, Carsetti, R, Marzano, V, Britti, D, Urbani, Andrea, Roncada, P, Putignani, Lorenza, Urbani, A (ORCID:0000-0001-9168-3174), Putignani, L, Mortera, Sl, Soggiu, A, Vernocchi, P, Del Chierico, F, Piras, C, Carsetti, R, Marzano, V, Britti, D, Urbani, Andrea, Roncada, P, Putignani, Lorenza, Urbani, A (ORCID:0000-0001-9168-3174), and Putignani, L

Abstract

Breastfeeding is nowadays known to be one of the most critical factors contributing to the development of an efficient immune system. In the last decade, a consistent number of pieces of evidence demonstrated the relationship between a healthy organism and its gut microbiota. However, this link is still not fully understood and requires further investigation. We recently adopted a murine model to describe the impact of either maternal milk or parental genetic background, on the composition of the gut microbial population in the first weeks of life. A metaproteomic approach to such complex environments is a big challenge that requires a strong effort in both data production and analysis, including the set-up of dedicated multitasking bioinformatics pipelines. Herein we present an LC-MS/MS based investigation to monitor mouse gut microbiota in the early life, aiming at characterizing its functions and metabolic activities together with a taxonomic description in terms of operational taxonomic units. We provided a quantitative evaluation of bacterial metaproteins, taking into account differential expression results in relation to the functional and taxonomic classification, particularly with proteins from orthologues groups. This allowed the reduction of the bias arising from the presence of a high number of shared peptides, and proteins, among different bacterial species. We also focused on host mucosal proteome and its modulation, according to different microbiota composition.

Published
2019

26. Proceedings of the 2017 WAO Symposium on Hot Topics in Allergy: Pediatric & Regulatory Aspects: Rome, Italy/Vatican City. 27-29 April 2017

Author

Traina G, Valluzzi RL, Fierro V, Riccardi C, Artesani MC, De Vuono A, Fiocchi A, Martelli AG, Ríos LA, Alcocer CR, Navarrete E, Del Rio Navarro BE, Gonzalez V, Velasco B, Perez Aviles HJ, Fernandez RJ, Pozo FC, Farhan AJ, Arshad H, Hussain A, Sharikadze O, Okhotnikova O, Alcover J, Rodríguez Rius D, Pineda F, Dalal I, Weinbrand-Goichberg J, Benor S, Rottem M, Kivity S, Sato S, Yanagida N, Ebisawa M, Umanets T, Antipkin Y, Barzylovich V, Lapshyn V, Umanets M, Yuriev S, Rodriguez D, Bekir S, Pincock T, Vieira Hernandez A, Capriles Hulett A, Sánchez Borges M, Fabiano F, Albarran C, Goyal R, Gupta S, Gaurav G, Luskin AT, Griffin NM, Wagelie-Steffen A, Trzaskoma BL, Limb SL, Busse WW, Zeiger RS, Gonzalez-Reyes E, Casale TB, Chipps BE, Sugizaki C, Goto F, Yamaide A, Mitsunaga K, Tomiita M, Hoshioka A, Shimojo N, Pop LL, Ciuca IM, Tamas L, Lazarescu M, Pienar C, Yamaide F, Fikri B, Sato H, Okishima N, Kobayashi M, Takai M, Nishigata K, Yoda R, Oana YT, Kajiwara C, Shimodaira M, Suzuki T, Iizawa H, Kamijo K, Karmakar B, Bhattacharya SG, Blohlávková S, Kopelentová E, Víšek P, Štádler J, Šetinová I, Novobílská J, Lundelin K, Salminen S, Isolauri E, Pitt T, Flanders T, Peñalver M, Martínez P, Lluch-Canut T, Malet A, Nam YH, Jin HJ, Lee SK, Kulalert P, Sritipsukho P, Pathumanond J, Baynova K, Labella M, De Aramburu T, Prados M, Haanpää L, Aarnio J, Nermes M, Af Ursin P, Kaljonen A, Bala N, Bhagwat K, Hindley J, Chapman M, Baalasubramanian S, Besednjak-Kocijancic L, SenGupta K, Antonova E, Kong AM, Iqbal A, Teague WG, Ortiz B, Paknis B, Rosen K, Szefler S, Alblooshi A, Al-Hammadi S, Vega A, Gutiérrez-Rivas R, Alonso AM, Beitia JM, Belén Mateo M, Cárdenas R, García-Domínguez JJ, Pitchon Dos Reis R, Gonçalves Alvim C, Andrade C, Reis A, Ribeiro H, Panaitescu Bunu C, Marusciac L, Paralescu S, Tamas P, Martí Guadaño E, Escobar Bolaños C, Martí José N, Pau Casanovas P, Biarnés Rib G, Castells M, de Vicente Jiménez T, Mennini M, De Angelis P, Rea F, Malamisura M, Tambucci R, Dall'Oglio L, Del Chierico F, Napolitano T, Reddel S, Vernocchi P, D'Ambrosio A, Putignani L, Dahdah L, Banzato C, Plaza-Martín AM, Bosque García M, Íbero M, Mazzina O, Marzano V, Pecora V, Koch P, Valentini D, Santamaria F, Mukherjee A, Kandhare A, and Bodhankar S

Published
2017

28. Gut Microbiota Dysbiosis as Risk and Premorbid Factors of IBD and IBS Along the Childhood-Adulthood Transition

Author

Putignani, L, Del Chierico, F, Vernocchi, P, Cicala, M, Cucchiara, S, Dallapiccola, B, Dysbiotrack Study Group Collaborators: Alisi, A, Altomare, A, Aloi, M, Belzer, C, Cavalieri, D, Carapito, C, Comera, C, De Angelis, P, Delaere, F, De Filippo, C, de Vos, W, Dorè, J, Donati, C, Furlanello, C, Gasbarrini, A, Gil, C, Guarino, M, Hugot, Jp, Juste, C, Knol, J, Koletzko, B, Monnet, V, Nobili, V, Oozeer, R, Scaldaferri, F, Stensvold, Cr, Stronati, L, Tack, J, Theodoridis, G, Torre, G, and Urbani, A.

Subjects
digestive system, Gut Microbiota, Dysbiosis, Inflammatory Bowel Disease, Irritable Bowel Syndrome, Childhood
Published
2016

30. 168 Loss of CFTR function drives the host-gut microbiota interaction: from omics data to clinical cue

Author

Vernocchi, P., primary, Del Chierico, F., additional, Russo, A., additional, Majo, F., additional, Valerio, M., additional, Casadei, L., additional, La Storia, A., additional, De Filippis, F., additional, Rizzo, C., additional, Manetti, C., additional, Paci, P., additional, Ercolini, D., additional, Marini, F., additional, Fiscarelli, E., additional, Dallapiccola, B., additional, Lucidi, V., additional, Miccheli, A., additional, and Putignani, L., additional

Published
2017
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31. Characterization of the yeast population involved in the production of typical Italian bread

Author

Vernocchi, P., Dalai, I., Gianotti, A., Guerzoni, M.E., Gardini, F., Valmorri, S., Torriani, S., Suzzi, G., and Mastrocola, D.

Subjects
Yeast -- Research, Bread -- Research, Business, Food/cooking/nutrition
Abstract

The yeast population during the production of Ferrara bread obtained according to the protocol approved by European community is characterized. It is found that the yeast population of the sourdough used for the production of Ferrara bread is mainly constituted by yeasts belonging to the species Candida milleri and the factors determining the yeast species selection are their carbon requirement, their Ph, temperature profiles and their resistance to the organic acids produced by lactic acid bacteria.

Published
2004

32. The gut microbiota in cystic fibrosis: a complex community unveiled by meta-omics approaches'

Author

Federica Del Chierico, Vernocchi, P., Majo, F., Petrucca, A., Vannini, L., Guerzoni, M. E., Fiscarelli, E., Puylaert, P. G., Urbani, A., Muraca, M., Dallapiccola, B., Lucidi, V., Vos, W. M., Putignani, L., F Del Chierico, P Vernocchi, F Majo, A Petrucca, L Vannini, M E Guerzoni, E Fiscarelli, A Urbani, M Muraca, B Dallapiccola, V Lucidi, P Guilla Puylaert, W de Vos and L Putignani, Del Chierico F, Vernocchi P, Majo F, Petrucca A, Vannini L, Guerzoni ME, Fiscarelli E, Puylaert PG, Urbani A, Muraca M, Dallapiccola B, Lucidi V, De Vos WM, and Putignani L

Subjects
META-OMICS APPROACHE, FECAL METABOLITES, GUT MICROBIOTA, CYSTIC FIBROSIS
Abstract

In cystic fibrosis (CF) patients the normal community of commensal bacteria in the gut can be affected by intestinal exocrine alfunction, antibiotic usage and swallowing of infected respiratory mucus. However, CFrelated gut dysbiosis has only recently been subjected to detailed investigation. Herein we report on the integrated metaproteomic, metagenomic and metabolomic workflow for monitoring gut microbiota composition. Twenty-four faecal samples were collected from cystic fibrosis young patients (age range 0-6 years) and 6 faecal samples from healthy children. All samples were processed for peptide, DNA and metabolite analysis. Protein content was analyzed with a shotgun metaproteomic approach by a nano-scale LC-MS2 set-up (Bruker amaZon-ETD) and filtered for operational taxon units (OTUs) assignment. OTUs were corroborated by hybridization of the small subunit ribosomal RNA (SSU rRNA) gene variable regions against the human intestinal tract microarray platform HITChip. In order to evaluate the volatile metabolites a gas-chromatographic (GC)–mass spectrometer (MS)/solid-phase microextraction (SPME) analysis was performed. 1H-NMR spectra were acquired on a Varian 400 MHz Mercury-plus NMR. Pre-analytical steps of the metaproteomics workflow were devised to improve hit coverage, while the OTUs repository was guaranteed by metagenomics entries. 1H-NMR and GC-MS/SPME were used to identify and quantify fecal metabolites. The application of integrated meta-omics-based approaches to the characterization of the membership and dynamics of the polymicrobial communities colonizing the gut is expected to have important predictive potential in translational medicine, specially in CF-related gut dysbiosis.

Published
2012

36. Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development

Author

Del Chierico, F., Vernocchi, P., Petrucca, A., Paci, P., Fuentes Enriquez de Salamanca, S., Praticò, G., Capuani, G., Masotti, A., Reddel, S., Russo, A., Vallone, C., Salvatori, G., Buffone, E., Signore, F., Rigon, G., Dotta, A., Miccheli, A., de Vos, W.M., Dallapiccola, B., Putignani, L., Del Chierico, F., Vernocchi, P., Petrucca, A., Paci, P., Fuentes Enriquez de Salamanca, S., Praticò, G., Capuani, G., Masotti, A., Reddel, S., Russo, A., Vallone, C., Salvatori, G., Buffone, E., Signore, F., Rigon, G., Dotta, A., Miccheli, A., de Vos, W.M., Dallapiccola, B., and Putignani, L.

Abstract

The colonization and development of gut microbiota immediately after birth is highly variable and depends on several factors, such as delivery mode and modality of feeding during the first months of life. A cohort of 31 mother and neonate pairs, including 25 at-term caesarean (CS) and 6 vaginally (V) delivered neonates (DNs), were included in this study and 121 meconium/faecal samples were collected at days 1 through 30 following birth. Operational taxonomic units (OTUs) were assessed in 69 stool samples by phylogenetic microarray HITChip and inter- and intra-individual distributions were established by inter-OTUs correlation matrices and OTUs co-occurrence or co-exclusion networks. 1H-NMR metabolites were determined in 70 stool samples, PCA analysis was performed on 55 CS DNs samples, and metabolome/OTUs co-correlations were assessed in 45 CS samples, providing an integrated map of the early microbiota OTUs-metabolome. A microbiota "core" of OTUs was identified that was independent of delivery mode and lactation stage, suggesting highly specialized communities that act as seminal colonizers of microbial networks. Correlations among OTUs, metabolites, and OTUs-metabolites revealed metabolic profiles associated with early microbial ecological dynamics, maturation of milk components, and host physiology

Published
2015

48. Role of the 5′-untranslated regions in post-transcriptional regulation of the human glucocorticoid receptor.

Author

Turner, Jonathan D., Vernocchi, Sara, Schmitz, Stephanie, and Muller, Claude P.

Abstract

GR transcripts display a remarkable heterogeneity in their 5′ untranslated regions (5′UTRs). These variable 5′UTRs are encoded by a series of alternative 1st exons, and together with their associated promoters they maintain tissue-specific GR expression levels. In this study we over-expressed GR transcripts containing individual 1st exons, and assessed their effect on RNA stability, 3′-splicing, translation initiation and protein isoform production. We showed that these alternative 5′UTRs influence the predicted mRNA structure and free energy, and were associated with differential levels of functional spliced mRNA. However, the 5′UTR had little influence on the relative levels of the two principal 3′ splice transcripts, GR - α and - β . The overall mRNA length, the free energy of the transcript and the translational efficiency directly influenced total GR levels. However, individual N-terminal protein isoform levels appeared to depend upon elements within the 5′UTR. Membrane-GR specific labelling suggested that the mGR originates from transcripts containing exon 1D and possibly 1H, although the specific trafficking sequences or structures within these transcripts remain unidentified. The role of the alternative first exons and their associated 5′UTRs has now been expanded to translational control, influencing total GR levels, individual constituent isoform levels, as well as trafficking to the cell surface. [ABSTRACT FROM AUTHOR]

Published
2014
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50. Radiographic Periodontal Bone Loss in Chronic Kidney Disease.

Author

Messier, Marie-Danielle, Emde, Karin, Stern, Leonard, Radhakrishnan, Jai, Vernocchi, Linda, Cheng, Bin, Angelopoulos, Christos, and Papapanou, Panos N.

Abstract

Background: We examined the extent and severity of radiographic periodontal bone loss in patients with different stages of chronic kidney disease (CKD) and explored a potential dose-response relationship between bone loss and CKD-related biomarkers. Methods: Panoramic radiographs were obtained from 129 CKD patients (78 males and 51 females; mean age: 63.5 years, range: 24 to 91 years), including 63 patients undergoing dialysis for an average of 3.3 years (range: 0.5 to 14 years). Glomerular filtration rate (GFR), dialysis dose, and levels of serum biomarkers were obtained through a hospital database, Interproximal bone loss was assessed as a percentage of root length. Results: Twenty-nine participants were edentulous (23.8% of those on dialysis versus 21.2% of those with residual kidney function; X² test, P= 0.724). The extent of bone loss was higher among dialysis patients (analysis of variance [ANOVA], P = 0.007), but no clear dose-response association between CKD stage and extent was evident. GFR, dialysis dose, and levels of serum biomarkers did not differ between edentulous and dentate individuals, and only serum albumin was lower in patients with extensive bone loss (ANOVA, P-- 0.030). After adjusting for dialysis status, the severity of bone loss was positively associated with glucose levels (multiple regression, P= 0.019) and white blood cell count (P= 0.032), whereas the number of teeth present was positively associated with plasma phosphorus (P= 0.008) and negatively with glucose levels (P= 0.011 ). Conclusion: Despite a higher extent of bone loss in dialysis patients, the lack of a dose-response association between bone loss and CKD stage or the levels of CKD-related serum biomarkers underscores the complex relationship between the two conditions. [ABSTRACT FROM AUTHOR]

Published
2012
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