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1. Comparison of metabolic alterations, hepatic and cardiovascular damage between primary NAFLD and HIV-associated NAFLD: Role of low visceral adiposity

Author

Lombardi, R., primary, Cinque, F., additional, Cespiati, A., additional, Marchesi, L., additional, Francione, P., additional, Fatta, E., additional, Bertelli, C., additional, Pisano, G., additional, Oberti, G., additional, Colavolpe, L., additional, Alletto, F., additional, Dongiovanni, P., additional, Meroni, M., additional, Bozzi, G., additional, Bandera, A., additional, and Fracanzani, A.L., additional

Published
2023
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3. The Swiss Pathogen Surveillance Platform - towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata

Author

Neves, A., Walther, D., Martin-Campos, T., Barbie, V., Bertelli, C., Blanc, D., Bouchet, G., Erard, F., Greub, G., Hirsch, H.H., Huber, M., Kaiser, L., Leib, S.L., Leuzinger, K., Lazarevic, V., Mäusezahl, M., Molina, J., Neher, R.A., Perreten, V., Ramette, A., Roloff, T., Schrenzel, J., Seth-Smith, HMB, Stephan, R., Terumalai, D., Wegner, F., and Egli, A.

Subjects
Humans, Switzerland/epidemiology, Genome, Bacterial, Metadata, One Health, Genomics/methods, antibiotic resistance, bacteria, bioinformatics, database, epidemiology, fungi, molecular surveillance, outbreaks, research, sequencing, typing, virulence, virus
Abstract

The Swiss Pathogen Surveillance Platform (SPSP) is a shared secure surveillance platform between human and veterinary medicine, to also include environmental and foodborne isolates. It enables rapid and detailed transmission monitoring and outbreak surveillance of pathogens using whole genome sequencing data and associated metadata. It features controlled data access, complex dynamic queries, dedicated dashboards and automated data sharing with international repositories, providing actionable results for public health and the vision to improve societal well-being and health.

Published
2023

6. Building up a clinical microbiota profiling: a quality framework proposal

Author

Scherz, V., Greub, G., and Bertelli, C.

Subjects
Humans, Metagenomics/methods, Microbiota, Reproducibility of Results, Metagenomics, biomarkers, microbiome, microbiota profiling, quality management
Abstract

Extensive characterization of the human microbiota has revealed promising relationships between microbial composition and health or disease, generating interest in biomarkers derived from microbiota profiling. However, microbiota complexity and technical challenges strongly influencing the results limit the generalization of microbiota profiling and question its clinical utility. In addition, no quality management scheme has been adapted to the specificities of microbiota profiling, notably due to the heterogeneity in methods and results. In this review, we discuss possible adaptation of classical quality management tools routinely used in diagnostic laboratories to microbiota profiling and propose a specific framework. Multiple quality controls are needed to cover all steps, from sampling to data processing. Standard operating procedures, primarily developed for wet lab analyses, must be adapted to the use of bioinformatic tools. Finally, requirements for test validation and proficiency testing must take into account expected discrepancies in results due to the heterogeneity of the processes. The proposed quality management framework should support the implementation of routine microbiota profiling by clinical laboratories to support patient care. Furthermore, its use in research laboratories would improve publication reproducibility as well as transferability of methods and results to routine practice.

Published
2022

7. Comparison of severity of liver damage and metabolic alterations in patients with NAFLD attending the hepatology clinic over the last three decades

Author

Colavolpe, L., primary, Lombardi, R., additional, Alletto, F., additional, Pulixi, E., additional, Francione, P., additional, Cinque, F., additional, Maffi, G., additional, Bertelli, C., additional, Fatta, E., additional, Spreafico, S., additional, Fagiani, V., additional, Morello, G., additional, Dongiovanni, P., additional, Fargion, S., additional, and Fracanzani, A.L., additional

Published
2022
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8. Prevalence of sarcopenia and cardiovascular alterations in a cohort of non-cirrhotic MAFLD patients

Author

Cespiati, A., primary, Lombardi, R., additional, Cinque, F., additional, Pisano, G., additional, Fatta, E., additional, Sigon, G., additional, Oberti, G., additional, Bertelli, C., additional, Colavolpe, L., additional, Alletto, F., additional, Maffi, G., additional, Francione, P., additional, Fargion, S., additional, and Fracanzani, A.L., additional

Published
2022
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9. Un nuovo biostimolante dai sottoprodotti della filiera ittica

Author

Caser, M, Masino, F, Gervasio, S, Fassio, F, Ben Hassine, M, Benedetti, P, Caradonia, F, Cocchiara, S, Milc, J. A., Caccialupi, G, Pulvirenti, A, Antonelli, A, Torri, L, Cevasco, R, Rovera, F, Scariot, V, Francia, E, Bertora, C, Ertani, A, and Bertelli, C.

Published
2022

11. Nutrient additions to seagrass seed planting improve seedling emergence and growth.

Author

Unsworth, R. K. F., Rees, S. C., Bertelli, C. M., Esteban, N. E., Furness, E. J., and Walter, B.

Subjects
SEAGRASS restoration, SEAGRASSES, ZOSTERA marina, SEEDS, SEEDLINGS, FACTORIAL experiment designs
Abstract

To maximize the opportunities of seagrass as a nature-based solution requires restoration to occur on a large scale. New methods and knowledge are required that can solve ecological bottlenecks, improving its reliability and effectiveness. Although there is increasing interest in the use of seeds for seagrass restoration there exists a limited understanding of how best to plant them with the most knowledge on germination and seedling emergence coming from laboratory studies. Here we present the results of a novel field study on the emergence success of seeds of the seagrass Zostera marina when subjected to varied planting treatments. Seeds were planted into hessian bags according to a factorial design of three treatments (sediment type, detritus addition, and nutrient addition). By adding nutrients to natural sediment, the present study provides some evidence of seagrass shoot emergence and maximum shoot length doubling. The present study provides evidence that even in heavily nutrient-rich environments, seagrass sediments may require additional nutrients to improve seedling emergence and growth. It also highlights the highly variable nature of planting seagrass seeds in shallow coastal environments. Critically this study provides increasing levels of evidence that small subtleties in the method can have large consequences for seagrass restoration and that for restoration to scale to levels that are relevant for nature-based solutions there remain many unknowns that require consideration. [ABSTRACT FROM AUTHOR]

Published
2022
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13. Chlamydia pneumoniae and Mycoplasma pneumoniae in children with cystic fibrosis: impact on bacterial respiratory microbiota diversity

Author

Pittet, LF, Bertelli, C, Scherz, V, Rochat, I, Mardegan, C, Brouillet, R, Jaton, K, Mornand, A, Kaiser, L, Posfay-Barbe, K, Asner, SA, Greub, G, Pittet, LF, Bertelli, C, Scherz, V, Rochat, I, Mardegan, C, Brouillet, R, Jaton, K, Mornand, A, Kaiser, L, Posfay-Barbe, K, Asner, SA, and Greub, G

Abstract

OBJECTIVES: The contribution of intracellular and fastidious bacteria in Cystic fibrosis (CF) pulmonary exacerbations, and progressive lung function decline remains unknown. This project aimed to explore their impact on bacterial microbiota diversity over time in CF children. METHODS: Sixty-one children enrolled in the MUCOVIB multicentre prospective cohort provided 746 samples, mostly nasopharyngeal swabs, throat swabs and sputa which were analysed using culture, specific real-time qPCRs and 16S rRNA amplicon metagenomics. RESULTS: Chlamydia pneumoniae (n = 3) and Mycoplasma pneumoniae (n = 1) were prospectively documented in 6.6% of CF children. Microbiota alpha-diversity in children with a documented C. pneumoniae was highly variable, similarly to children infected with Staphylococcus aureus or Pseudomonas aeruginosa. The transition from routine follow-up visits to pulmonary exacerbation (n = 17) yielded variable changes in diversity indexes with some extreme loss of diversity. CONCLUSIONS: The high rate of C. pneumoniae detection supports the need for regular screenings in CF patients. A minor impact of C. pneumoniae on the microbial community structure was documented. Although detected in a single patient, M. pneumoniae should also be considered as a possible aetiology of lung infection in CF subjects.

Published
2021

14. New onset steatosis but not persistent steatosis prevents hepatic fibrosis improvement after viral eradication by direct-acting antiviral therapy (DAAs) in patients with chronic hepatitis C: Evaluation by controlled attenuation parameter (CAP) and liver stiffness measurement LSM

Author

Cespiati, A., primary, Petta, S., additional, Lombardi, R., additional, Di Marco, V., additional, Calvaruso, V., additional, Bertelli, C., additional, Pisano, G., additional, Fatta, E., additional, Sigon, G., additional, Iuculano, F., additional, Crapanzano, L., additional, Gibilaro, G., additional, Francione, P., additional, Craxì, A., additional, Fargion, S., additional, and Fracanzani, A.L., additional

Published
2021
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15. Genome sequencing of Mycobacterium tuberculosis clinical isolates revealed isoniazid resistance mechanisms undetected by conventional molecular methods

Author

Laurent, S., Zakham, F., Bertelli, C., Merz, L., Nicod, L., Mazza-Stalder, J., Greub, G., Jaton, K., and Opota, O.

Subjects
Isoniazid, Mycobacterium tuberculosis, Resistance, Whole genome sequencing, ahpC, katG, IS6110, MDR-TB, PCR, isoniazid, isoniazid mono-resistance, isoniazid-resistance, molecular diagnostic, resistance, whole-genome sequencing
Abstract

A combination of targeted molecular methods and phenotypic drug-susceptibility testing is the most widely used approach to detect drug resistance in Mycobacterium tuberculosis isolates. We report the delay in the introduction of an efficient anti-tuberculous drug regimen because of a M. tuberculosis strain displaying a high level of resistance to isoniazid, in the absence of the common mutations associated with isoniazid-resistance, including katG mutations and inhA promoter mutations. Whole-genome sequencing (WGS) identified a large loss-of-function insertion (>1000 pb) at the end of katG in the isolate together with a -57C>T ahpC mutation, a resistance mechanism that would have remained undetected by a conventional molecular targeted approach. A retrospective search using publicly available WGS data of more than 1200 isoniazid-resistant isolates and a similar sized control dataset of isoniazid-susceptible isolates revealed that most (22/31) isoniazid-resistant, KatG loss-of-function mutants had an associated rare ahpC promoter mutation. In contrast, only 7 of 1411 isoniazid-susceptible strains carried a rare ahpC promoter mutation, including shared mutations with the 31 isoniazid-resistant KatG loss-of-function mutants. These results indicate that rare ahpC promoter mutations could be used as a proxy for investigating simultaneous KatG loss-of-function or missense mutations. In addition, WGS in routine diagnosis would improve drug susceptibility testing in M. tuberculosis clinical isolates and is an efficient tool for detecting resistance mechanisms undetected by conventional molecular methods.

Published
2020

16. The Chiaravalle Cross: Results of a Multidisciplinary Study

Author

Di Martino, D, Benati, G, Alberti, R, Baroni, S, Bertelli, C, Blumer, F, Caselli, L, Cattaneo, R, Cucini, C, D’Amico, F, Frizzi, T, Gagetti, E, Gironda, M, Greggio, L, Lazzarini, L, Musa, M, Perelli Cippo, E, Riccardi, M, Gorini, G, Riccardi, MP, Di Martino, D, Benati, G, Alberti, R, Baroni, S, Bertelli, C, Blumer, F, Caselli, L, Cattaneo, R, Cucini, C, D’Amico, F, Frizzi, T, Gagetti, E, Gironda, M, Greggio, L, Lazzarini, L, Musa, M, Perelli Cippo, E, Riccardi, M, Gorini, G, and Riccardi, MP

Abstract

he Chiaravalle Cross, a masterpiece of Mediaeval goldsmithery, went under restoration in 2016. This was a unique opportunity to undertake an in-depth multidisciplinary study. Several issues were addressed, as for example the chronology of the Cross, lacking any official document about it. The scientific investigations included in situ and laboratory measurements, and the analyses, part of a multidisciplinary protocol, completely characterized the gemstones adorning the Cross, the cameos, the gold, silver, jasper and glass parts, to derive indications on their provenance, authenticity and dating issues. All the results were shared with the whole collaboration of experts, which included art historians, a restorer, a conservator, a scholar in ancient glyptic, gemologists, archaeometallurgists, physicists and scientists in a very fruitful exchange of knowledge. This work is an example of a real multidisciplinary research, gathering good practices in the study of a complex piece of art.

Published
2019

24. The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

Author

Bultet, LA, Aguilar-Rodriguez, J, Ahrens, CH, Ahrne, EL, Ai, N, Aimo, L, Akalin, A, Aleksiev, T, Alocci, D, Altenhoff, A, Alves, I, Ambrosini, G, Pedone, PA, Angelina, P, Anisimova, M, Appel, R, Argoud-Puy, G, Arnold, K, Arpat, B, Artimo, P, Ascencao, K, Auchincloss, A, Axelsen, K, Gerritsen, VB, Bairoch, A, Barisal, P, Baratin, D, Barbato, A, Barbie, V, Barras, D, Barreiro, M, Barret, S, Bastian, F, Batista Neto, TM, Baudis, M, Beaudoing, E, Beckmann, JS, Bekkar, AK, Cammoun, LBH, Benmohammed, S, Bernard, M, Bertelli, C, Bertoni, M, Bienert, S, Bignucolo, O, Bilbao, A, Bilican, A, Blank, D, Blatter, M-C, Blum, L, Bocquet, J, Boeckmann, B, Bolleman, JT, Bordoli, L, Bosshard, L, Boucher, G, Bougueleret, L, Boutet, E, Bovigny, C, Bratulic, S, Breuza, L, Bridge, AJ, Britan, A, Brito, F, Frazao, JB, Bruggmann, R, Bucher, P, Burdet, F, Burger, L, Cabello, EM, Gomez, RMC, Calderon, S, Cannarozzi, G, Carl, S, Casas, CC, Catherinet, S, Perier, RC, Charpilloz, C, Chaskar, PD, Chen, W, Pepe, AC, Chopard, B, Chu, HY, Civic, N, Claassen, M, Clottu, S, Colombo, M, Cosandier, I, Coudert, E, Crespo, I, Creus, M, Cuche, B, Cuendet, MA, Cusin, I, Daga, N, Daina, A, Dauvillier, J, David, F, Davydov, I, Ferreira, MDSRM, de Beer, T, de Castro, E, de Santana, C, Delafontaine, J, Delorenzi, M, Delucinge-Vivier, C, Demirel, O, Derham, R, Dermitzakis, EM, Dib, L, Diene, S, Dilek, N, Dilmi, J, Domagalski, MJ, Dorier, J, Dornevil, D, Dousse, A, Dreos, R, Duchen, P, Roggli, PD, Duperret, ID, Durinx, C, Duvaud, S, Engler, R, Frkek, S, Lopez, PE, Fstreicher, A, Excoffier, L, Fabbretti, R, Falcone, J-L, Falquet, L, Famiglietti, ML, Ferreira, A-M, Feuermann, M, Filliettaz, M, Hegel, V, Foucal, A, Franceschini, A, Fucile, G, Gaidatzis, D, Garcia, V, Gasteiger, E, Gateau, A, Gatti, L, Gaudet, P, Gaudinat, A, Gehant, S, Gfeller, D, Gharib, WH, Ghraichy, M, Gidoin, C, Gil, M, Gleizes, A, Gobeill, J, Gonnet, G, Gos, A, Gotz, L, Gouy, A, Grbic, D, Groux, R, Gruaz-Gumowski, N, Grun, D, Gschwind, A, Guex, N, Gupta, S, Getaz, M, Haake, D, Haas, J, Hatzimanikatis, V, Heckel, G, Gardiol, DFH, Hinard, V, Hinz, U, Homicsko, K, Horlacher, O, Hosseini, S-R, Hotz, H-R, Hulo, C, Hundsrucker, C, Ibberson, M, Ilmjarv, S, Ioannidis, V, Ioannidis, P, Iseli, C, Ivanek, R, Iwaszkiewicz, J, Jacquet, P, Jacquot, M, Jagannathan, V, Jan, M, Jensen, J, Johansson, MU, Johner, N, Jungo, F, Junier, T, Kahraman, A, Katsantoni, M, Keller, G, Kerhornou, A, Khalid, F, Klingbiel, D, Kimljenovic, A, Kriventseva, E, Kryuchkova, N, Kumar, S, Kutalik, Z, Kuznetsov, D, Kuzyakiv, R, Lane, L, Lara, V, Ledesma, L, Leleu, M, Lemercier, P, Lew, D, Lieberherr, D, Liechti, R, Lisacek, F, Fischer, H, Litsios, G, Liu, J, Lombardot, T, Mace, A, Maffioletti, S, Mahi, M-A, Maiolo, M, Majjigapu, SR, Malmstrom, L, Mangold, V, Marek, D, Mariethoz, J, Marin, R, Martin, O, Martin, X, Martin-Campos, T, Mary, C, Masclaux, F, Masson, P, Meier, C, Messina, A, Lenoir, MM, Meyer, X, Michel, P-A, Michielin, O, Milanese, A, Missiaglia, E, Perez, JM, Caria, VM, Moret, P, Moretti, S, Morgat, A, Mottaz, A, Mottin, L, Mouscaz, Y, Mueller, M, Murri, R, Mylonas, R, Neuenschwander, S, Nikitin, F, Niknejad, A, Nouspikel, N, Nso, LN, Okoniewski, M, Omasits, U, Paccaud, B, Pachkov, M, Paesano, SG, Pagni, M, Palagi, PM, Pasche, E, Payne, JL, Pedruzzi, I, Peischl, S, Peitsch, M, Perlini, S, Pilbout, S, Podvinec, M, Pohlmann, R, Polizzi, D, Potter, D, Poux, S, Pozzato, M, Pradervand, S, Praz, V, Pruess, M, Pujadas, E, Racle, J, Raschi, M, Ratib, O, Rausell, A, de Laval, VR, Redaschi, N, Rempfer, C, Ren, G, Vandati, RAR, Rib, L, Grognuz, OR, Altimiras, ER, Rivoire, C, Robin, T, Robinson-Rechavi, M, Rodrigues, J, Roechert, B, Roelli, P, Romano, V, Rossier, G, Roth, A, Rougemont, J, Roux, J, Royo, H, Ruch, P, Ruinelli, M, Rustom, M, Sates, A, Roehrig, UF, Rueeger, S, Salamin, N, Sankar, M, Sarkar, N, Saxenhofer, M, Schaeffer, M, Schaerli, Y, Schaper, E, Schmid, A, Schmid, E, Schmid, C, Schmid, M, Schmidt, S, Schmocker, D, Schneider, M, Schuepbach, T, Schwede, T, Schuetz, F, Sengstag, T, Serrano, M, Sethi, A, Shahmirzadi, O, Sigrist, C, Silvestro, D, Simao Neto, FA, Simillion, C, Simonovic, M, Skunca, N, Sluzek, K, Soneson, C, Sprouffske, K, Stadler, M, Staehli, S, Stevenson, B, Stockinger, H, Straszewski, J, Stricker, T, Studer, G, Stutz, A, Suffiotti, M, Sundaram, S, Szklarczyk, D, Szovenyi, P, Tegenfeldt, F, Teixeira, D, Tellenbach, S, Smith, AAT, Tognolli, M, Topolsky, I, Thuong, VDT, Tsantoulis, P, Tzika, AC, Agote, AU, van Nimwegen, E, von Mering, C, Varadarajan, A, Veranneman, M, Verbregue, L, Veuthey, A-L, Vishnyakova, D, Vyas, R, Wagner, A, Walther, D, Wan, HW, Wang, M, Waterhouse, R, Waterhouse, A, Wicki, A, Wigger, L, Wirapati, P, Witschi, U, Wyder, S, Wyler, K, Wuethrich, D, Xenarios, I, Yamada, K, Yan, Z, Yasrebi, H, Zahn, M, Zangger, N, Zdobnov, E, Zerzion, D, Zoete, V, Zoller, S, Bultet, LA, Aguilar-Rodriguez, J, Ahrens, CH, Ahrne, EL, Ai, N, Aimo, L, Akalin, A, Aleksiev, T, Alocci, D, Altenhoff, A, Alves, I, Ambrosini, G, Pedone, PA, Angelina, P, Anisimova, M, Appel, R, Argoud-Puy, G, Arnold, K, Arpat, B, Artimo, P, Ascencao, K, Auchincloss, A, Axelsen, K, Gerritsen, VB, Bairoch, A, Barisal, P, Baratin, D, Barbato, A, Barbie, V, Barras, D, Barreiro, M, Barret, S, Bastian, F, Batista Neto, TM, Baudis, M, Beaudoing, E, Beckmann, JS, Bekkar, AK, Cammoun, LBH, Benmohammed, S, Bernard, M, Bertelli, C, Bertoni, M, Bienert, S, Bignucolo, O, Bilbao, A, Bilican, A, Blank, D, Blatter, M-C, Blum, L, Bocquet, J, Boeckmann, B, Bolleman, JT, Bordoli, L, Bosshard, L, Boucher, G, Bougueleret, L, Boutet, E, Bovigny, C, Bratulic, S, Breuza, L, Bridge, AJ, Britan, A, Brito, F, Frazao, JB, Bruggmann, R, Bucher, P, Burdet, F, Burger, L, Cabello, EM, Gomez, RMC, Calderon, S, Cannarozzi, G, Carl, S, Casas, CC, Catherinet, S, Perier, RC, Charpilloz, C, Chaskar, PD, Chen, W, Pepe, AC, Chopard, B, Chu, HY, Civic, N, Claassen, M, Clottu, S, Colombo, M, Cosandier, I, Coudert, E, Crespo, I, Creus, M, Cuche, B, Cuendet, MA, Cusin, I, Daga, N, Daina, A, Dauvillier, J, David, F, Davydov, I, Ferreira, MDSRM, de Beer, T, de Castro, E, de Santana, C, Delafontaine, J, Delorenzi, M, Delucinge-Vivier, C, Demirel, O, Derham, R, Dermitzakis, EM, Dib, L, Diene, S, Dilek, N, Dilmi, J, Domagalski, MJ, Dorier, J, Dornevil, D, Dousse, A, Dreos, R, Duchen, P, Roggli, PD, Duperret, ID, Durinx, C, Duvaud, S, Engler, R, Frkek, S, Lopez, PE, Fstreicher, A, Excoffier, L, Fabbretti, R, Falcone, J-L, Falquet, L, Famiglietti, ML, Ferreira, A-M, Feuermann, M, Filliettaz, M, Hegel, V, Foucal, A, Franceschini, A, Fucile, G, Gaidatzis, D, Garcia, V, Gasteiger, E, Gateau, A, Gatti, L, Gaudet, P, Gaudinat, A, Gehant, S, Gfeller, D, Gharib, WH, Ghraichy, M, Gidoin, C, Gil, M, Gleizes, A, Gobeill, J, Gonnet, G, Gos, A, Gotz, L, Gouy, A, Grbic, D, Groux, R, Gruaz-Gumowski, N, Grun, D, Gschwind, A, Guex, N, Gupta, S, Getaz, M, Haake, D, Haas, J, Hatzimanikatis, V, Heckel, G, Gardiol, DFH, Hinard, V, Hinz, U, Homicsko, K, Horlacher, O, Hosseini, S-R, Hotz, H-R, Hulo, C, Hundsrucker, C, Ibberson, M, Ilmjarv, S, Ioannidis, V, Ioannidis, P, Iseli, C, Ivanek, R, Iwaszkiewicz, J, Jacquet, P, Jacquot, M, Jagannathan, V, Jan, M, Jensen, J, Johansson, MU, Johner, N, Jungo, F, Junier, T, Kahraman, A, Katsantoni, M, Keller, G, Kerhornou, A, Khalid, F, Klingbiel, D, Kimljenovic, A, Kriventseva, E, Kryuchkova, N, Kumar, S, Kutalik, Z, Kuznetsov, D, Kuzyakiv, R, Lane, L, Lara, V, Ledesma, L, Leleu, M, Lemercier, P, Lew, D, Lieberherr, D, Liechti, R, Lisacek, F, Fischer, H, Litsios, G, Liu, J, Lombardot, T, Mace, A, Maffioletti, S, Mahi, M-A, Maiolo, M, Majjigapu, SR, Malmstrom, L, Mangold, V, Marek, D, Mariethoz, J, Marin, R, Martin, O, Martin, X, Martin-Campos, T, Mary, C, Masclaux, F, Masson, P, Meier, C, Messina, A, Lenoir, MM, Meyer, X, Michel, P-A, Michielin, O, Milanese, A, Missiaglia, E, Perez, JM, Caria, VM, Moret, P, Moretti, S, Morgat, A, Mottaz, A, Mottin, L, Mouscaz, Y, Mueller, M, Murri, R, Mylonas, R, Neuenschwander, S, Nikitin, F, Niknejad, A, Nouspikel, N, Nso, LN, Okoniewski, M, Omasits, U, Paccaud, B, Pachkov, M, Paesano, SG, Pagni, M, Palagi, PM, Pasche, E, Payne, JL, Pedruzzi, I, Peischl, S, Peitsch, M, Perlini, S, Pilbout, S, Podvinec, M, Pohlmann, R, Polizzi, D, Potter, D, Poux, S, Pozzato, M, Pradervand, S, Praz, V, Pruess, M, Pujadas, E, Racle, J, Raschi, M, Ratib, O, Rausell, A, de Laval, VR, Redaschi, N, Rempfer, C, Ren, G, Vandati, RAR, Rib, L, Grognuz, OR, Altimiras, ER, Rivoire, C, Robin, T, Robinson-Rechavi, M, Rodrigues, J, Roechert, B, Roelli, P, Romano, V, Rossier, G, Roth, A, Rougemont, J, Roux, J, Royo, H, Ruch, P, Ruinelli, M, Rustom, M, Sates, A, Roehrig, UF, Rueeger, S, Salamin, N, Sankar, M, Sarkar, N, Saxenhofer, M, Schaeffer, M, Schaerli, Y, Schaper, E, Schmid, A, Schmid, E, Schmid, C, Schmid, M, Schmidt, S, Schmocker, D, Schneider, M, Schuepbach, T, Schwede, T, Schuetz, F, Sengstag, T, Serrano, M, Sethi, A, Shahmirzadi, O, Sigrist, C, Silvestro, D, Simao Neto, FA, Simillion, C, Simonovic, M, Skunca, N, Sluzek, K, Soneson, C, Sprouffske, K, Stadler, M, Staehli, S, Stevenson, B, Stockinger, H, Straszewski, J, Stricker, T, Studer, G, Stutz, A, Suffiotti, M, Sundaram, S, Szklarczyk, D, Szovenyi, P, Tegenfeldt, F, Teixeira, D, Tellenbach, S, Smith, AAT, Tognolli, M, Topolsky, I, Thuong, VDT, Tsantoulis, P, Tzika, AC, Agote, AU, van Nimwegen, E, von Mering, C, Varadarajan, A, Veranneman, M, Verbregue, L, Veuthey, A-L, Vishnyakova, D, Vyas, R, Wagner, A, Walther, D, Wan, HW, Wang, M, Waterhouse, R, Waterhouse, A, Wicki, A, Wigger, L, Wirapati, P, Witschi, U, Wyder, S, Wyler, K, Wuethrich, D, Xenarios, I, Yamada, K, Yan, Z, Yasrebi, H, Zahn, M, Zangger, N, Zdobnov, E, Zerzion, D, Zoete, V, and Zoller, S

Abstract

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.

Published
2016

25. Epicardial Adipose Tissue (EAT) thickness is associated with cardiovascular and liver damage in nonalcoholic fatty liver disease

Author

Fracanzani, A., Pisano, G., Consonni, D., Tiraboschi, S., Baragetti, A., Bertelli, C., Norata, Giuseppe, Dongiovanni, P., Valenti, L., Grigore, L., Tonella, T., Catapano, A., Fargion, S., Fracanzani, A., Pisano, G., Consonni, D., Tiraboschi, S., Baragetti, A., Bertelli, C., Norata, Giuseppe, Dongiovanni, P., Valenti, L., Grigore, L., Tonella, T., Catapano, A., and Fargion, S.

Abstract

Background and Aims Epicardial adipose tissue (EAT) has been proposed as a cardiometabolic and hepatic fibrosis risk factor in patients with non alcoholic fatty liver disease (NAFLD). Aim of this study was to evaluate the role of EAT in NAFLD by analyzing 1) the association between EAT, the other metabolic parameters and the severity of steatosis 2) the relationship between cardiovascular (cIMT, cplaques, E/A), liver (presence of NASH and significant fibrosis) damage and metabolic risk factors including EAT 3) the relationship between EAT and genetic factors strongly influencing liver steatosis. Methods In a cross-sectional study, we considered 512 consecutive patients with NAFLD (confirmed by biopsy in 100). EAT, severity of steatosis, carotid intima-media thickness (cIMT) and plaques were evaluated by ultrasonography and results analysed by multiple linear and logistic regression models. Variables independently associated with EAT (mm)were female gender (p = 0.003), age (p = 0.001), BMI (p = 0.01), diastolic blood pressure (p = 0.009), steatosis grade 2 (p = 0.01) and 3 (p = 0.04), fatty liver index (p = 0.001) and statin use (p = 0.03). Variables independently associated with carotid IMT were age (p = 0.0001), hypertension (p = 0.009), diabetes (p = 0.04), smoking habits (p = 0.04) and fatty liver index (p = 0.02), with carotid plaques age (p = 0.0001), BMI (p = 0.03), EAT (p = 0.02),) and hypertension (p = 0.02), and with E/A age (p = 0.0001), diabetes (p = 0.005), hypertension (p = 0.04) and fatty liver index (p = 0.004). In the 100 patients with available liver histology non alcoholic steatohepatitis (NASH) was independently associated with EAT (p = 0.04) and diabetes (p = 0.054) while significant fibrosis with EAT (p = 0.02), diabetes (p = 0.01) and waist circumference (p = 0.05). No association between EAT and PNPLA3 and TM6SF2 polymorphisms was found. Conclusion In patients with NAFLD, EAT is associated with the severity of liver and vascular damage besides

Published
2016

26. Progression of carotid vascular damage and cardiovascular events in non-alcoholic fatty liver disease patients compared to the general population during 10 years of follow-up

Author

Fracanzani, A., Tiraboschi, S., Pisano, G., Consonni, D., Baragetti, A., Bertelli, C., Norata, Giuseppe, Valenti, L., Grigore, L., Porzio, M., Catapano, A., Fargion, S., Fracanzani, A., Tiraboschi, S., Pisano, G., Consonni, D., Baragetti, A., Bertelli, C., Norata, Giuseppe, Valenti, L., Grigore, L., Porzio, M., Catapano, A., and Fargion, S.

Abstract

© 2016 Elsevier Ireland Ltd. Background and aim: Non-alcoholic fatty liver disease (NAFLD) is associated not only with liver related morbidity and mortality but also with an increased risk of cardiovascular disease. Aim: to evaluate in patients with NAFLD and in matched Controls after 10 years of follow-up 1 the incidence of major cardiovascular and cerebral events 2 the progression of vascular damage. Methods: Clinical and cardio-metabolic data were collected in 125 NAFLD patients and 250 age and gender matched Controls at baseline and 10 years later. Incidence of cardiovascular and cerebral events was recorded. By ultrasonography, carotid intima-media thickness (cIMT), presence of plaques and presence of fatty liver were evaluated. Results: 25% of the overall series was lost to follow-up. Sixty-eight (37%) Controls developed steatosis. Major cardiovascular events were observed in thirty-five subjects (17/91 (19%) NAFLD and 18/182 (10%) Controls), with an estimated cumulative risk significantly higher in NAFLD than in Controls, log-rank test for equality of failure functions p = 0.007. At multivariate analysis, presence of plaques (hazard ratio 5.08 (95% C.I. 2.56-10.96) and of steatosis (hazard ratio 1.99 (1.01-3.94)) were the strongest predictors for cardiovascular events. Grade of steatosis, ALT and GGT levels were higher in NAFLD patients who developed cardiovascular events. cIMT value after 10 years was significantly higher in NAFLD than in Controls, but the mean progression rate was higher in Controls (0.015 and 0.006 mm/year, p = 0.001). In conclusion our results suggest that NAFLD has to be included among risk factors for cardiovascular damage and underline the utility to evaluate, once NAFLD is diagnosed, the presence of atherosclerotic lesions.

Published
2016

27. Subclinical atherosclerosis is associated with Epicardial Fat Thickness and hepatic steatosis in the general population

Author

Baragetti, A., Pisano, G., Bertelli, C., Garlaschelli, K., Grigore, L., Fracanzani, A., Fargion, S., Norata, Giuseppe, Catapano, A., Baragetti, A., Pisano, G., Bertelli, C., Garlaschelli, K., Grigore, L., Fracanzani, A., Fargion, S., Norata, Giuseppe, and Catapano, A.

Abstract

© 2015 The Italian Society of Diabetology, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition, and the Department of Clinical Medicine and Surgery, Federico II University. Background and aims: Abdominal obesity and hepatic steatosis are ectopic fat depots associated with Metabolic Syndrome (MetS). Epicardial Fat Thickness (EFT) is a newly discovered one, increasing with obesity, insulin resistance and MetS. Therefore we studied whether different ectopic fat markers, and EFT in particular, are associated with MetS and markers of subclinical cardiovascular disease. Methods and results: 868 subjects from the PLIC Study were included, EFT, aortic calcifications, carotid Intima-Media Thickness (c-IMT) and echocardiographic parameters were determined by ultrasound; extra-cardiac atherosclerotic lesions were defined in presence of plaques at both carotid and aortic levels. Hepatic steatosis degrees were defined according to a scoring system. Abdominal adiposity was determined using Dual X-ray Absorbimetry (DEXA). Independently from age, women showed higher EFT versus men (4.5 (0.20-9.00) mm vs 4.00 (0.10-8.00) mm, p = 0.013); EFT was thicker in post-menopausal women (independently from hormone-replacement therapy). EFT, liver steatosis and abdominal adiposity increased with MetS (p < 0.001). EFT was the only ectopic fat marker associated with cardiac dysfunction (OR = 1.340 [1.088-1.651 95% C.I., p = 0.006); liver steatosis and EFT were associated with extra-cardiac plaques (OR = 2.529 [1.328-4.819] 95% C.I., p < 0.001 and OR = 1.195 [1.008-1.299] 95% C.I., p = 0.042; respectively). On top of cardiovascular risk factors, only EFT improved the discrimination of subjects with cardiac dysfunction and atherosclerotic plaques. Conclusions: EFT is associated with left ventricular dysfunction and subclinical atherosclerosis. Our data suggest that EFT may represent an additional tool for the stratification of cardiovascular risk.

Published
2016

28. Génomique et métagénomique bactériennes: applications cliniques et importance médicale [Bacterial genomics and metagenomics: clinical applications and medical relevance]

Author

Diene, S.M., Bertelli, C., Pillonel, T., Schrenzel, J., and Greub, G.

Subjects
Anti-Bacterial Agents/pharmacology, Bacteria/genetics, Bacteria/isolation & purification, Bacterial Infections/diagnosis, Bacterial Infections/microbiology, Drug Resistance, Bacterial, Genome, Bacterial, Genomics/methods, Humans, Metagenomics/methods
Abstract

New sequencing technologies provide in a short time and at low cost high amount of genomic sequences useful for applications such as: a) development of diagnostic PCRs and/or serological tests; b) detection of virulence factors (virulome) or genes/SNPs associated with resistance to antibiotics (resistome) and c) investigation of transmission and dissemination of bacterial pathogens. Thus, bacterial genomics of medical importance is useful to clinical microbiologists, to infectious diseases specialists as well as to epidemiologists. Determining the microbial composition of a sample by metagenomics is another application of new sequencing technologies, useful to understand the impact of bacteria on various non-infectious diseases such as obesity, asthma, or diabetes. Genomics and metagenomics will likely become a specialized diagnostic analysis.

Published
2014

29. Génomique et métagénomique bactériennes : applications cliniques et importance médicale

Author

Diene, S M, Bertelli, C, Pillonel, Trestan, Schrenzel, Jacques, and Greub, Gilbert Daniel

Subjects
ddc:616, Metagenomics/methods, Drug Resistance, Bacterial, Bacteria/genetics/isolation & purification, Humans, Genome, Bacterial, Anti-Bacterial Agents/pharmacology, Bacterial Infections/diagnosis/microbiology, Genomics/methods
Abstract

New sequencing technologies provide in a short time and at low cost high amount of genomic sequences useful for applications such as: a) development of diagnostic PCRs and/or serological tests; b) detection of virulence factors (virulome) or genes/SNPs associated with resistance to antibiotics (resistome) and c) investigation of transmission and dissemination of bacterial pathogens. Thus, bacterial genomics of medical importance is useful to clinical microbiologists, to infectious diseases specialists as well as to epidemiologists. Determining the microbial composition of a sample by metagenomics is another application of new sequencing technologies, useful to understand the impact of bacteria on various non-infectious diseases such as obesity, asthma, or diabetes. Genomics and metagenomics will likely become a specialized diagnostic analysis.

Published
2014

35. Schede di catalogo

Author

Anselmi, C.M., Bertelli, C., Bianchi Janetti, F., Cuscito, G., Dell'Acqua A., Fiorio, M.T., Fortunato, V., Franco, L., Galimberti, P.M., Gritti, J., Mainini, C., Mattei, C., Monferrini, C., Petoletti, M., Riccobono, M., Sartori, A., Slavazzi, F., Vaccaro, M., Vergani, G.A., Zanuso, S., Dell'Acqua, Antonio, Dell'Acqua, Antonio (ORCID:0000-0002-8697-3115), Anselmi, C.M., Bertelli, C., Bianchi Janetti, F., Cuscito, G., Dell'Acqua A., Fiorio, M.T., Fortunato, V., Franco, L., Galimberti, P.M., Gritti, J., Mainini, C., Mattei, C., Monferrini, C., Petoletti, M., Riccobono, M., Sartori, A., Slavazzi, F., Vaccaro, M., Vergani, G.A., Zanuso, S., Dell'Acqua, Antonio, and Dell'Acqua, Antonio (ORCID:0000-0002-8697-3115)

Abstract

Vengono presentati alcuni materiali scultorei e architettonici conservati presso il Museo d'Arte antica del castello sforzesco di Milano

Published
2015

37. Randomised study comparing 48 and 96 weeks peginterferon α-2a therapy in genotype D HBeAg-negative chronic hepatitis B

Author

Pegbeliver, Study Group, Colombo, M, Facchetti, F, Massetto, B, Regep, L, Iannacone, C, Giuberti, T, Fargion, S, Farci, P, Boninsegna, S, Di Marco, V, Fasano, M, Sagnelli, E, Di Costanzo, Gg, Viganò, M, Lampertico, P, Andreone, P, Riili, A, Scuteri, A, Cursaro, C, Andriulli, A, Niro, Ga, Angarano, G, Santantonio, Ta, Palattella, Ms, Brunetto, MAURIZIA ROSSANA, Colombatto, P, Coco, B, Ciccorossi, P, Oliveri, F, Sacco, R, Bruno, S, Bollani, S, Chiesa, A, Carosi, G, Baiguera, C, Rossi, S, Zaltron, S, Puoti, M, Cozzolongo, R, Giannuzzi, V, Craxì, A, Calvaruso, V, Venezia, G, Lanza, Ag, Di Perri, G, Cariti, G, Mollaretti, O, De Blasi, T, Kulmiye, C, Rostagno, R, Lai, Me, Serra, G, Chessa, L, Balestrieri, C, Cauli, C, Fargion, Sr, Bertelli, C, Fatta, E, Fattovich, G, Pasino, M, Zanni, S, Olivari, N, Zagni, I, Ferrari, C, Schivazappa, S, Laccabue, D, Penna, A, Gaeta, G, Stanzione, M, Stornaiuolo, G, Martines, D, Raimondo, G, Caccamo, G, Squadrito, G, Isgrò, G, Rizzetto, M, Lagget, M, Carenzi, S, Ruggiero, G, Marrone, A, Messina, V, Di Caprio, Du, Selva, V, Toniutto, P., Lampertico, P, Viganò, M, Di Costanzo, GG, Sagnelli, E, Fasano, M, Di Marco, V, Boninsegna, S, Farci, P, Fargion, S, Giuberti, T, Iannacone, C, Regep, L, Massetto, B, Facchetti, F, Colombo, M, and Calvaruso, V

Subjects
Adult, Male, HBsAg, medicine.medical_specialty, Hepatitis B virus, Time Factors, Anti-HIV Agents, medicine.disease_cause, Gastroenterology, Antiviral Agents, Group B, law.invention, Polyethylene Glycols, Pharmacotherapy, Hepatitis B, Chronic, Randomized controlled trial, law, Pegylated interferon, Internal medicine, medicine, Humans, Hepatitis B e Antigens, business.industry, Lamivudine, Interferon-alpha, Alanine Transaminase, Hepatitis B, Middle Aged, medicine.disease, Recombinant Proteins, Treatment Outcome, Immunology, DNA, Viral, Interferon, Drug Therapy, Combination, Female, business, medicine.drug
Abstract

Treatment with peginterferon α-2a (PegIFN) for 48 weeks is the standard of care for selected HBeAg-negative patients chronically infected with hepatitis B virus (HBV), but with limited treatment efficacy. A study was undertaken to investigate whether treatment extension to 96 weeks improves the outcome in this patient population.128 HBeAg-negative patients (120 genotype D) were randomised to weekly 180 μg PegIFN for 48 weeks (group A, n=51), 180 μg PegIFN for 48 weeks followed by 135 μg weekly for an additional 48 weeks (group B, n=52) or 180 μg PegIFN plus lamivudine (100 mg/day) for 48 weeks then 135 μg PegIFN for 48 weeks (group C, n=25). Endpoints were alanine aminotransferase normalisation plus HBV DNA3400 IU/ml (primary), HBV DNA2000 IU/ml and HBsAg clearance at 48 weeks after treatment.Forty-eight weeks after treatment, six patients in group A and 13 in group B achieved alanine aminotransferase normalisation plus HBV DNA3400 IU/ml (11.8% vs 25.0%, p=0.08), 6 vs 15 patients had HBV DNA2000 IU/ml (11.8% vs 28.8%, p=0.03), 0 vs 3 achieved HBsAg clearance (0% vs 5.8%, p=0.24) and 0 vs 5 had HBsAg10 IU/ml (0% vs 9.6%, p=0.06). While extended PegIFN treatment was the strongest independent predictor of response, the combination with lamivudine did not improve responses. Discontinuation rates were similar among the groups (19.6%, 23.1%, 32.0%, p=0.81) and were mostly due to PegIFN-related adverse events.In HBeAg-negative genotype D patients with chronic hepatitis B, PegIFN treatment for 96 weeks was well tolerated and the post-treatment virological response improved significantly compared with 48 weeks of treatment.http://ClinicalTrials.gov registration number: NCT01095835.

Published
2013

38. Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms

Author

Bertelli, C. and Greub, G.

Subjects
Amoeba/microbiology, Bacteria/genetics, Evolution, Molecular, Gene Transfer, Horizontal, Genetic Variation, Genome, Bacterial, Selection, Genetic
Abstract

Based on Darwin's concept of the tree of life, vertical inheritance was thought to be dominant, and mutations, deletions, and duplication were streaming the genomes of living organisms. In the current genomic era, increasing data indicated that both vertical and lateral gene inheritance interact in space and time to trigger genome evolution, particularly among microorganisms sharing a given ecological niche. As a paradigm to their diversity and their survival in a variety of cell types, intracellular microorganisms, and notably intracellular bacteria, were considered as less prone to lateral genetic exchanges. Such specialized microorganisms generally have a smaller gene repertoire because they do rely on their host's factors for some basic regulatory and metabolic functions. Here we review events of lateral gene transfer (LGT) that illustrate the genetic exchanges among intra-amoebal microorganisms or between the microorganism and its amoebal host. We tentatively investigate the functions of laterally transferred genes in the light of the interaction with their host as they should confer a selective advantage and success to the amoeba-resisting microorganisms (ARMs).

Published
2012

42. P1009 : Incidence of major cardiovascular and cerebral events in patients with NAFLD and in controls of general population during 10 years of follow up: correlation between vascular and liver damage

Author

Pisano, G., primary, Tiraboschi, S., additional, Lombardi, R., additional, Bertelli, C., additional, Valenti, L., additional, Baragetti, A., additional, Grigore, L., additional, Porzio, M., additional, Catapano, A., additional, Fargion, S., additional, and Fracanzani, A.L., additional

Published
2015
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45. Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum

Author

Bachmann, NL, Fraser, TA, Bertelli, C, Jelocnik, M, Gillett, A, Funnell, O, Flanagan, C, Myers, GSA, Timms, P, Polkinghorne, A, Bachmann, NL, Fraser, TA, Bertelli, C, Jelocnik, M, Gillett, A, Funnell, O, Flanagan, C, Myers, GSA, Timms, P, and Polkinghorne, A

Abstract

© 2014 Bachmann et al.; licensee BioMed Central Ltd. Background: Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koalas. The genome of the C. pecorum VR629 (IPA) strain, isolated from a sheep with polyarthritis, was also sequenced.Results: Comparisons of the draft C. pecorum genomes against the complete genomes of livestock C. pecorum isolates revealed that these strains have a conserved gene content and order, sharing a nucleotide sequence similarity > 98%. Single nucleotide polymorphisms (SNPs) appear to be key factors in understanding the adaptive process. Two regions of the chromosome were found to be accumulating a large number of SNPs within the koala strains. These regions include the Chlamydia plasticity zone, which contains two cytotoxin genes (toxA and toxB), and a 77 kbp region that codes for putative type III effector proteins. In one koala strain (MC/MarsBar), the toxB gene was truncated by a premature stop codon but is full-length in IPTaLE and DBDeUG. Another five pseudogenes were also identified, two unique to the urogenital strains C. pecorum MC/MarsBar and C. pecorum DBDeUG, respectively, while three were unique to the koala C. pecorum conjunctival isolate IPTaLE. An examination of the distribution of these pseudogenes in C. pecorum strains from a variety of koala populations, alongside a number of sheep and cattle C. pecorum positive samples from Australian livestock, confirmed the presence of four predicted pseudogenes in koala C. pecorum clinical samples. Consistent with our genomics analyses, none of these pseudogenes were observed in the livestock C. pecorum samples examined. Interestingly, three SNPs resulting in pseudogenes identified in the IPTaLE isolate were not found in any other C. pec

Published
2014

46. materiali archeologici

Author

Anselmi, C.M., Bertelli, C., Bianchi Janetti, F., Cuscito, G., Dell'Acqua A., Fiorio, M.T., Fortunato, V., Franco, L., Galimberti, P.M., Gritti, J., Mainini, C., Mattei, C., Monferrini, C., Petoletti, M., Riccobono, M., Sartori, A., Slavazzi, F., Vaccaro, M., Vergani, G.A., Zanuso, S., Dell'Acqua, Antonio, Dell'Acqua, Antonio (ORCID:0000-0002-8697-3115), Anselmi, C.M., Bertelli, C., Bianchi Janetti, F., Cuscito, G., Dell'Acqua A., Fiorio, M.T., Fortunato, V., Franco, L., Galimberti, P.M., Gritti, J., Mainini, C., Mattei, C., Monferrini, C., Petoletti, M., Riccobono, M., Sartori, A., Slavazzi, F., Vaccaro, M., Vergani, G.A., Zanuso, S., Dell'Acqua, Antonio, and Dell'Acqua, Antonio (ORCID:0000-0002-8697-3115)

Abstract

Si presentano alcuni materiali architettonici conservati nel cortile dell'Armi del Castello Sforzesco di Milano

Published
2014

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