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16. Towards the standardization of mitochondrial proteomics: the Italian mt-HPP initiative

Author

Alberio, T., Pieroni, L., Ronci, M., Banfi, C., Bongarzone, I., Bottoni, P., Brioschi, M., Caterino, M., Chinello, C., Cormio, A., Cozzolino, F., Cunsolo, V., FONTANA, Simona, Garavaglia, B., Giusti, L., Greco, V., Lucacchini, A., Maffioli, E., Magni, F., Monteleone, Francesca, Monti, M., Monti, V., Musicco, C., Petrosillo, G., Porcelli, V., Saletti, R., Scatena, R., Soggiu, A., Tedeschi, G., Zilocchi, M., Roncada, P., Urbani, A., Fasano, M., Alberio, T, Pieroni, L, Ronci, M, Banfi, C, Bongarzone, I, Bottoni, P, Brioschi, M, Caterino, M, Chinello, C, Cormio, A, Cozzolino, F, Cunsolo, V, Fontana, S, Garavaglia, B, Giusti, L, Greco, V, Lucacchini, A, Maffioli, E, Magni, F, Monteleone, F, Monti, M, Monti, V, Musicco, C, Petrosillo, G, Porcelli, V, Saletti, R, Scatena, R, Soggiu, A, Tedeschi, G, Zilocchi, M, Roncada, P, Urbani, A, Fasano, M, Alberio, T., Pieroni, L., Ronci, M., Banfi, C., Bongarzone, I., Bottoni, P., Brioschi, M., Caterino, M., Chinello, C., Cormio, A., Cozzolino, F., Cunsolo, V., Fontana, S., Garavaglia, B., Giusti, L., Greco, V., Lucacchini, A., Maffioli, E., Magni, F., Monteleone, F., Monti, M., Monti, V., Musicco, C., Petrosillo, G., Porcelli, V., Saletti, R., Scatena, R., Soggiu, A., Tedeschi, G., Zilocchi, M., Roncada, P., Urbani, A., and Fasano, M.

Subjects
itlian mt-HPP iniziative, Mitochondria, standardization, enrichment protocol, Mitochondrial Human Proteome Project, mitochondrial proteomic, BIO/10 - BIOCHIMICA, proteomic
Abstract

The mitochondrial Human Proteome Project aims at understanding the function of the mitochondrial proteome and its crosstalk with the proteome of other organelles. Being able to choose a suitable and validated enrichment protocol of functional mitochondria, based on the specific needs of the downstream proteomics analysis, would greatly help the researchers in the field. Mitochondrial fractions from ten model cell lines were prepared using three enrichment protocols and analyzed on seven different LC-MS/MS platforms. All data were processed using neXtProt as reference database. The data are available for the Human Proteome Project purposes through the ProteomeXchange Consortium with the identifier PXD007053. The processed datasets were analysed using a suite of R routines to perform a statistical analysis and to retrieve subcellular and sub-mitochondrial localizations. Although the overall number of identified total and mitochondrial proteins was not significantly dependent on the enrichment protocol, specific line to line differences were observed. Moreover, the protein lists were mapped to a network representing the functional mitochondrial proteome, encompassing mitochondrial proteins and their first interactors. More than 80% of the identified proteins resulted nodes of this network but with a different ability in co-isolating mitochondria-associated structures for each enrichment protocol/cell line pair.

Published
2017

18. Correction to: Echinodermata: The complex immune system in echinoderms (Advances in Comparative Immunology, 10.1007/978-3-319-76768-0_13)

Author

Smith L. C., Arizza V., Hudgell M. A. B., Barone G., Bodnar A. G., Buckley K. M., Cunsolo V., Dheilly N. M., Franchi N., Fugmann S. D., Furukawa R., Garcia-Arraras J., Henson J. H., Hibino T., Irons Z. H., Li C., Lun C. M., Majeske A. J., Oren M., Pagliara P., Pinsino A., Raftos D. A., Rast J. P., Samasa B., Schillaci D., Schrankel C. S., Stabili L., Stensv K., Sutton E., Smith L.C., Arizza V., Hudgell M.A.B., Barone G., Bodnar A.G., Buckley K.M., Cunsolo V., Dheilly N.M., Franchi N., Fugmann S.D., Furukawa R., Garcia-Arraras J., Henson J.H., Hibino T., Irons Z.H., Li C., Lun C.M., Majeske A.J., Oren M., Pagliara P., Pinsino A., Raftos D.A., Rast J.P., Samasa B., Schillaci D., Schrankel C.S., Stabili L., Stensv K., and Sutton E.

Subjects
Asteroidea, Brittle stars, Coelomocytes, Crinoidea, Diseases, Echinoidea, Genomics, Holothuroidea, Immune development, Immune responses, Immuno-toxicology, Larval immune cells, Ophiuroidea, Proteomics, Sea cucumbers, Sea lilies, Sea stars, Sea urchins, Senescence, Settore CHIM/03 - Chimica Generale E Inorganica, Settore BIO/05 - Zoologia, Settore BIO/19 - Microbiologia Generale
Abstract

This chapter was inadvertently published with an incorrect spelling of the author's name as V. Arriza whereas it should be V. Arizza. In addition to this the affiliation of one of the chapter authors Elisse Sutton was published incorrectly and it has now been corrected to read as Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia.

Published
2018

29. New antimicrobial peptides from Tirmania pinoyi and Terfezia boudieri in the struggle against antibiotic resistance

Author

Schillaci, D, Cusimano, MG, CAscioferro, S, Arizza, V, Chiaramonte, Marco, Inguglia, L, Davino, S, Saletti, R, Cunsolo, V, Venturella, G, Gargano, ML, Schillaci, D, Cusimano, MG, CAscioferro, S, Arizza, V, Chiaramonte, M, Inguglia, L, Davino, S, Saletti, R, Cunsolo, V, Venturella, G, and Gargano, ML

Subjects
Settore BIO/03 - Botanica Ambientale E Applicata, Peptides, Desert truffles, antibiotic resistance, Settore BIO/19 - Microbiologia Generale
Abstract

Antibiotic resistance of common pathogenic microorganisms is a topic of great concern that has finally received media attention and entered into the political agenda of world leaders. Drug-resistant bacteria are cause of thousands of deaths worldwide, then there is an urgent need for new antimicrobials, otherwise we risk losing the ability to control effectively the infectious diseases. Such emergence can be faced looking also at not usual source of antimicrobial agents, for example medicinal mushrooms. With the objective to tackle Gram-positive and Gram-negative pathogens, we focused on two edible desert truffles mushrooms Tirmania pinoyi and Terfezia boudieri as origin of new antimicrobial peptides (AMPs), active not only against free-living microorganisms (planktonic), but also against complex communities of pathogens (biofilms) that are intrinsically resistant to conventional antibiotics. In particular, in vitro antibacterial activity of acid-soluble protein extracts (aqueous extracts) of the two above-mentioned species were investigated against two important human pathogenic reference strains Staphylococcus aureus ATCC 29213 and Pseudomonas aeruginosa ATCC 15442. The acid-soluble protein extracts peptide fractions (

Published
2017

40. Towards the standardization of mitochondrial proteomics: the Italian mt-HPP initiative

Author

Alberio, T, Pieroni, L, Ronci, M, Banfi, C, Bongarzone, I, Bottoni, P, Brioschi, M, Caterino, M, Chinello, C, Cormio, A, Cozzolino, F, Cunsolo, V, Fontana, S, Garavaglia, B, Giusti, L, Greco, V, Lucacchini, A, Maffioli, E, Magni, F, Monteleone, F, Monti, M, Monti, V, Musicco, C, Petrosillo, G, Porcelli, V, Saletti, R, Scatena, R, Soggiu, A, Tedeschi, G, Zilocchi, M, Roncada, P, Urbani, A, Fasano, M, CHINELLO, CLIZIA, MAGNI, FULVIO, MONTI, MARIA GIOVANNA, Fasano, M., Alberio, T, Pieroni, L, Ronci, M, Banfi, C, Bongarzone, I, Bottoni, P, Brioschi, M, Caterino, M, Chinello, C, Cormio, A, Cozzolino, F, Cunsolo, V, Fontana, S, Garavaglia, B, Giusti, L, Greco, V, Lucacchini, A, Maffioli, E, Magni, F, Monteleone, F, Monti, M, Monti, V, Musicco, C, Petrosillo, G, Porcelli, V, Saletti, R, Scatena, R, Soggiu, A, Tedeschi, G, Zilocchi, M, Roncada, P, Urbani, A, Fasano, M, CHINELLO, CLIZIA, MAGNI, FULVIO, MONTI, MARIA GIOVANNA, and Fasano, M.

Abstract

The mitochondrial Human Proteome Project aims at understanding the function of the mitochondrial proteome and its crosstalk with the proteome of other organelles. Being able to choose a suitable and validated enrichment protocol of functional mitochondria, based on the specific needs of the downstream proteomics analysis, would greatly help the researchers in the field. Mitochondrial fractions from ten model cell lines were prepared using three enrichment protocols and analyzed on seven different LC-MS/MS platforms. All data were processed using neXtProt as reference database. The data are available for the Human Proteome Project purposes through the ProteomeXchange Consortium with the identifier PXD007053. The processed datasets were analysed using a suite of R routines to perform a statistical analysis and to retrieve subcellular and sub-mitochondrial localizations. Although the overall number of identified total and mitochondrial proteins was not significantly dependent on the enrichment protocol, specific line to line differences were observed. Moreover, the protein lists were mapped to a network representing the functional mitochondrial proteome, encompassing mitochondrial proteins and their first interactors. More than 80% of the identified proteins resulted nodes of this network but with a different ability in co-isolating mitochondria-associated structures for each enrichment protocol/cell line pair.

Published
2017

41. Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative

Author

Alberio, T., Pieroni, L., Ronci, M., Banfi, C., Bongarzone, I., Bottoni, P., Brioschi, M., Caterino, M., Chinello, C., Cormio, A., Cozzolino, F., Cunsolo, V., Fontana, S., Garavaglia, B., Giusti, L., Greco, Viviana, Lucacchini, A., Maffioli, E., Magni, F., Monteleone, F., Monti, M., Monti, V., Musicco, C., Petrosillo, G., Porcelli, V., Saletti, R., Scatena, Roberto, Soggiu, A., Tedeschi, G., Zilocchi, M., Roncada, P., Urbani, Andrea, Fasano, M., Greco V. (ORCID:0000-0003-4521-0020), Scatena R. (ORCID:0000-0002-9425-8293), Urbani A. (ORCID:0000-0001-9168-3174), Alberio, T., Pieroni, L., Ronci, M., Banfi, C., Bongarzone, I., Bottoni, P., Brioschi, M., Caterino, M., Chinello, C., Cormio, A., Cozzolino, F., Cunsolo, V., Fontana, S., Garavaglia, B., Giusti, L., Greco, Viviana, Lucacchini, A., Maffioli, E., Magni, F., Monteleone, F., Monti, M., Monti, V., Musicco, C., Petrosillo, G., Porcelli, V., Saletti, R., Scatena, Roberto, Soggiu, A., Tedeschi, G., Zilocchi, M., Roncada, P., Urbani, Andrea, Fasano, M., Greco V. (ORCID:0000-0003-4521-0020), Scatena R. (ORCID:0000-0002-9425-8293), and Urbani A. (ORCID:0000-0001-9168-3174)

Abstract

The Mitochondrial Human Proteome Project aims at understanding the function of the mitochondrial proteome and its crosstalk with the proteome of other organelles. Being able to choose a suitable and validated enrichment protocol of functional mitochondria, based on the specific needs of the downstream proteomics analysis, would greatly help the researchers in the field. Mitochondrial fractions from ten model cell lines were prepared using three enrichment protocols and analyzed on seven different LC-MS/MS platforms. All data were processed using neXtProt as reference database. The data are available for the Human Proteome Project purposes through the ProteomeXchange Consortium with the identifier PXD007053. The processed data sets were analyzed using a suite of R routines to perform a statistical analysis and to retrieve subcellular and submitochondrial localizations. Although the overall number of identified total and mitochondrial proteins was not significantly dependent on the enrichment protocol, specific line to line differences were observed. Moreover, the protein lists were mapped to a network representing the functional mitochondrial proteome, encompassing mitochondrial proteins and their first interactors. More than 80% of the identified proteins resulted in nodes of this network but with a different ability in coisolating mitochondria-associated structures for each enrichment protocol/cell line pair.

Published
2017

43. Review: Applications of HPLC–MS for food analysis

Author

DI STEFANO, Vita, AVELLONE, Giuseppe, BONGIORNO, David, Cunsolo, V, Muccilli, V, Sforza, S, Dossena, A, Drahos, L, Vékey, K., Di Stefano, V, Avellone, G, Bongiorno, D, Cunsolo, V, Muccilli, V, Sforza, S, Dossena, A, Drahos, L, and Vékey, K

Subjects
Mass spectrometry, HPLC–MS, Food analysis, Pesticides, Wine, Flavonoids, Glycoproteins
Abstract

HPLC–MS applications in the agrifood sector are among the fastest developing fields in science and industry. The present tutorial mini-review briefly describes this analytical methodology: HPLC, UHPLC, nano-HPLC on one hand, mass spectrometry (MS) and tandem mass spectrometry (MS/MS) on the other hand. Analytical results are grouped together based on the type of chemicals analyzed (lipids, carbohydrates, glycoproteins, vitamins, flavonoids, mycotoxins, pesticides, allergens and food additives). Results are also shown for various types of food (ham, cheese, milk, cereals, olive oil and wines). Although it is not an exhaustive list, it illustrates the main current directions of applications. Finally, one of the most important features, the characterization of food quality (including problems of authentication and adulteration) is discussed, together with a future outlook on future directions.

Published
2012

45. MS-Based Characterization of αs2-casein isoforms in donkey’s milk

Author

Saletti, R., Muccilli, V., Cunsolo, V., Fontanini, Debora, Capocchi, Antonella, and Foti, S.

Subjects
Spectrometry, Mass, Electrospray Ionization, Milk, Sequence Analysis, Protein, Tandem Mass Spectrometry, Molecular Sequence Data, Animals, Caseins, Protein Isoforms, Electrophoresis, Gel, Two-Dimensional, Amino Acid Sequence, Equidae, Sequence Alignment, Chromatography, High Pressure Liquid
Abstract

The primary structure of four α(s2)-casein (CN) isoforms, present as minor components in the dephosphorylated CN fraction of a milk sample collected in Eastern Sicily from an individual donkey belonging to the Ragusano breed at middle lactation stage, was determined, using the known donkey's α(s2)-CN (GenBank Acc. No. CAV00691; M(r) 26,028 Da) as reference. Proteins, with experimentally measured M(r) of 25,429, 21,939, 25,203 and 21,713 Da, were isolated by the combined use of reversed-phase high-performance liquid chromatography (RP-HPLC) and two-dimensional polyacrylamide gel electrophoresis. The major spot of each gel, corresponding to a single protein, was digested by trypsin, α-chymotrypsin and endoproteinase Glu-C. The resulting peptide mixtures were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and capillary RP-HPLC/nano-electrospray ionization tandem mass spectrometry, and the data obtained were used for the sequence determination. The isoforms are produced from differential splicing events involving exons 4, 5 and 6 and parts of the exon 17.

Published
2012

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