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Article ; Online: In-Depth Proteomic Analysis of Blood Circulating Small Extracellular Vesicles.

De Giorgis, Veronica / Barberis, Elettra / Falasca, Marco / Manfredi, Marcello

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2628, Page(s) 279–289

Abstract: Circulating small extracellular vesicles (sEVs), also called exosomes, are key players in the investigation of cell-cell communication mechanisms and in the identification of new potential biomarkers. These particles can carry proteins, DNA, mRNA, miRNA, ...

Abstract	Circulating small extracellular vesicles (sEVs), also called exosomes, are key players in the investigation of cell-cell communication mechanisms and in the identification of new potential biomarkers. These particles can carry proteins, DNA, mRNA, miRNA, lipids and metabolites that are transported all over the human body, potentially reaching all the cells. In particular, proteins, which are well-known biological actors in cell signalling, will be discussed in this context. In this article, we present a mass spectrometry approach for the in-depth characterization of the sEVs proteome. The protocols include strategies for the isolation and purification of sEVs, for the extraction of proteins and the purification of sEVs proteins by the immunodepletion of the most abundant plasmatic proteins. Finally, bioinformatic analysis for the extraction of the most important biological features associated with the proteomic content of sEVs is reported.
MeSH term(s)	Humans ; Proteomics/methods ; Extracellular Vesicles/metabolism ; Exosomes/genetics ; Biomarkers/metabolism ; Proteome/metabolism
Chemical Substances	Biomarkers ; Proteome
Language	English
Publishing date	2023-02-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2978-9_18
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Article ; Online: Modifications of Blood Molecular Components after Treatment with Low Ozone Concentrations.

Inguscio, Chiara Rita / Cisterna, Barbara / Carton, Flavia / Barberis, Elettra / Manfredi, Marcello / Malatesta, Manuela

International journal of molecular sciences

2023 Volume 24, Issue 24

Abstract: The ex vivo treatment of a limited volume of blood with gaseous oxygen-ozone ( ... ...

Abstract	The ex vivo treatment of a limited volume of blood with gaseous oxygen-ozone (O
MeSH term(s)	Humans ; Animals ; Sheep ; Antioxidants/metabolism ; Ozone/therapeutic use ; Oxidants ; Carbohydrates
Chemical Substances	Antioxidants ; Ozone (66H7ZZK23N) ; Oxidants ; Carbohydrates
Language	English
Publishing date	2023-12-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms242417175
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Article ; Online: Protein Subcellular Localization Prediction.

Barberis, Elettra / Marengo, Emilio / Manfredi, Marcello

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2361, Page(s) 197–212

Abstract: The elucidation of the subcellular localization of proteins is very important in order to deeply understand their functions. In fact, proteins activities are strictly correlated to the cellular compartment and microenvironment in which they are present ... ...

Abstract	The elucidation of the subcellular localization of proteins is very important in order to deeply understand their functions. In fact, proteins activities are strictly correlated to the cellular compartment and microenvironment in which they are present.In recent years, several effective and reliable proteomics techniques and computational methods have been developed and implemented in order to identify the proteins subcellular localization. This process is often time-consuming and expensive, but the recent technological and bioinformatics progress allowed the development of more accurate and simple workflows to determine the localization, interactions, and functions of proteins.In the following chapter, a brief introduction on the importance of knowing subcellular localization of proteins will be presented. Then, sample preparation protocols, proteomic methods, data analysis strategies, and software for the prediction of proteins localization will be presented and discussed. Finally, the more recent and advanced spatial proteomics techniques will be shown.
MeSH term(s)	Protein Transport ; Proteins/metabolism ; Proteomics ; Software ; Subcellular Fractions/metabolism
Chemical Substances	Proteins
Language	English
Publishing date	2021-07-08
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1641-3_12
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Article ; Online: Non-Invasive Paleo-Metabolomics and Paleo-Proteomics Analyses Reveal the Complex Funerary Treatment of the Early 18th Dynasty Dignitary NEBIRI (QV30).

Barberis, Elettra / Manfredi, Marcello / Ferraris, Enrico / Bianucci, Raffaella / Marengo, Emilio

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 21

Abstract: Biochemical investigations were carried out on the embalmed head of Nebiri (Museo Egizio, Turin; S-5109)-an 18th Dynasty Ancient Egyptian dignitary-and on the canopic jar containing his lungs (Museo Egizio, Turin; S. 5111/02) with the aim of ... ...

Abstract	Biochemical investigations were carried out on the embalmed head of Nebiri (Museo Egizio, Turin; S-5109)-an 18th Dynasty Ancient Egyptian dignitary-and on the canopic jar containing his lungs (Museo Egizio, Turin; S. 5111/02) with the aim of characterizing the organ's (lung) specific paleo-proteins and of identifying the compounds used in his embalming "recipe". The application of a functionalized film method allowed us to perform a non-invasive sampling. Paleo-proteomics confirmed the presence of lung tissue-specific proteins (organ specific) as well as the presence of proteins linked to severe inflammation. Paleoproteomics and paleometabolomics further allowed the identification of the main components of Nebiri's embalming recipe: animal fats and glue, balms, essential oils, aromatic plants, heated Pistacia, and coniferous resins. Both the use of Pistacia and coniferous resins in an early 18th Dynasty individual confirm Nebiri's high social status. The technique applied offers a targeted approach to the chemical characterization of human tissues, embalming compounds, and organic materials layering in pottery. The ability of the functionalized film method to harvest all types of compounds, from macromolecules (i.e., proteins) to small molecules (i.e., organic acids) opens a new path in the study of ancient material culture; furthermore, it allows to perform untargeted analysis, which is necessary when no a priori information is available.
MeSH term(s)	Animals ; Humans ; History, Ancient ; Mummies ; Proteomics ; Embalming/methods ; Metabolomics ; Resins, Plant ; Pistacia
Chemical Substances	Resins, Plant
Language	English
Publishing date	2022-10-25
Publishing country	Switzerland
Document type	Historical Article ; Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27217208
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Article ; Online: Modifications of Blood Molecular Components after Treatment with Low Ozone Concentrations

Chiara Rita Inguscio / Barbara Cisterna / Flavia Carton / Elettra Barberis / Marcello Manfredi / Manuela Malatesta

International Journal of Molecular Sciences, Vol 24, Iss 24, p

2023 Volume 17175

Abstract: The ex vivo treatment of a limited volume of blood with gaseous oxygen–ozone (O 2 –O 3 ) mixtures and its rapid reinfusion into the patient is a widespread medical procedure. O 3 instantly reacts with the blood’s antioxidant systems, disappearing before ... ...

Abstract	The ex vivo treatment of a limited volume of blood with gaseous oxygen–ozone (O 2 –O 3 ) mixtures and its rapid reinfusion into the patient is a widespread medical procedure. O 3 instantly reacts with the blood’s antioxidant systems, disappearing before reinfusion, although the molecules formed act as messengers in the organism, inducing multiple antioxidant and anti-inflammatory responses. An appropriate dose of O 3 is obviously essential to ensure both safety and therapeutic efficacy, and in recent years, the low-dose O 3 concept has led to a significant reduction in the administered O 3 concentrations. However, the molecular events triggered by such low concentrations in the blood still need to be fully elucidated. In this basic study, we analysed the molecular modifications induced ex vivo in sheep blood by 5 and 10 µg O 3 /mL O 2 by means of a powerful metabolomics analysis in association with haemogas, light microscopy and bioanalytical assays. This combined approach revealed increased oxygenation and an increased antioxidant capacity in the O 3 -treated blood, which accorded with the literature. Moreover, original information was obtained on the impact of these low O 3 concentrations on the metabolic pathways of amino acids, carbohydrates, lipids and nucleotides, with the modified metabolites being mostly involved in the preservation of the oxidant–antioxidant balance and in energy production.
Keywords	low-dose ozone ; oxidative stress ; antioxidant response ; antioxidant capacity ; interleukins ; metabolomics ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	290
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Non-Invasive Paleo-Metabolomics and Paleo-Proteomics Analyses Reveal the Complex Funerary Treatment of the Early 18th Dynasty Dignitary NEBIRI (QV30)

Elettra Barberis / Marcello Manfredi / Enrico Ferraris / Raffaella Bianucci / Emilio Marengo

Molecules, Vol 27, Iss 7208, p

2022 Volume 7208

Abstract: Biochemical investigations were carried out on the embalmed head of Nebiri (Museo Egizio, Turin; S-5109)—an 18th Dynasty Ancient Egyptian dignitary—and on the canopic jar containing his lungs (Museo Egizio, Turin; S. 5111/02) with the aim of ... ...

Abstract	Biochemical investigations were carried out on the embalmed head of Nebiri (Museo Egizio, Turin; S-5109)—an 18th Dynasty Ancient Egyptian dignitary—and on the canopic jar containing his lungs (Museo Egizio, Turin; S. 5111/02) with the aim of characterizing the organ’s (lung) specific paleo-proteins and of identifying the compounds used in his embalming “recipe”. The application of a functionalized film method allowed us to perform a non-invasive sampling. Paleo-proteomics confirmed the presence of lung tissue-specific proteins (organ specific) as well as the presence of proteins linked to severe inflammation. Paleoproteomics and paleometabolomics further allowed the identification of the main components of Nebiri’s embalming recipe: animal fats and glue, balms, essential oils, aromatic plants, heated Pistacia, and coniferous resins. Both the use of Pistacia and coniferous resins in an early 18th Dynasty individual confirm Nebiri’s high social status. The technique applied offers a targeted approach to the chemical characterization of human tissues, embalming compounds, and organic materials layering in pottery. The ability of the functionalized film method to harvest all types of compounds, from macromolecules (i.e., proteins) to small molecules (i.e., organic acids) opens a new path in the study of ancient material culture; furthermore, it allows to perform untargeted analysis, which is necessary when no a priori information is available.
Keywords	non-invasive chemical analyses ; paleo-proteomics ; paleo-metabolomics ; New Kingdom ; Nebiri ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2022-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: New Non-Invasive Method for the Authentication of Apple Cultivars.

Barberis, Elettra / Amede, Elia / Dondero, Francesco / Marengo, Emilio / Manfredi, Marcello

Foods (Basel, Switzerland)

2021 Volume 11, Issue 1

Abstract: Food authentication is very important to protect consumers, sellers, and producers from fraud. Although several methods have been developed using a wide range of analytical techniques, most of them require sample destruction and do not allow in situ ... ...

Abstract	Food authentication is very important to protect consumers, sellers, and producers from fraud. Although several methods have been developed using a wide range of analytical techniques, most of them require sample destruction and do not allow in situ sampling or analysis, nor reliable quantification of hundreds of molecules at the same time. To overcome these limitations, we have developed and validated a new noninvasive analytical workflow for food authentication. The method uses a functionalized strip to adsorb small molecules from the surface of the food product, followed by gas chromatography-mass spectrometry analysis of the desorbed analytes. We validated the method and applied it to the classification of five different apple varieties. Molecular concentrations obtained from the analysis of 44 apples were used to identify markers for apple cultivars or, in combination with machine learning techniques, to perform cultivar classification. The overall reproducibility of the method was very good, showing a good coefficient of variation for both targeted and untargeted analysis. The approach was able to correctly classify all samples. In addition, the method was also used to detect pesticides and the following molecules were found in almost all samples: chlorpyrifos-methyl, deltamethrin, and malathion. The proposed approach not only showed very good analytical performance, but also proved to be suitable for noninvasive food authentication and pesticide residue analysis.
Language	English
Publishing date	2021-12-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704223-6
ISSN	2304-8158
ISSN	2304-8158
DOI	10.3390/foods11010089
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Article ; Online: Kohonen Artificial Neural Network and Multivariate Analysis in the Identification of Proteome Changes during Early and Long Aging of Bovine

Brandi, Jessica / Robotti, Elisa / Manfredi, Marcello / Barberis, Elettra / Marengo, Emilio / Novelli, Enrico / Cecconi, Daniela

Journal of agricultural and food chemistry

2021 Volume 69, Issue 38, Page(s) 11512–11522

Abstract: To study proteomic changes involved in tenderization ... ...

Abstract	To study proteomic changes involved in tenderization of
MeSH term(s)	Animals ; Cattle ; Female ; Male ; Mass Spectrometry ; Meat/analysis ; Multivariate Analysis ; Muscle, Skeletal ; Neural Networks, Computer ; Proteome ; Proteomics
Chemical Substances	Proteome
Language	English
Publishing date	2021-09-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	241619-0
ISSN	1520-5118 ; 0021-8561
ISSN (online)	1520-5118
ISSN	0021-8561
DOI	10.1021/acs.jafc.1c03578
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Article ; Online: Multi-Omics Approaches for Freshness Estimation and Detection of Illicit Conservation Treatments in Sea Bass (

Benedetto, Alessandro / Robotti, Elisa / Belay, Masho Hilawie / Ghignone, Arianna / Fabbris, Alessia / Goggi, Eleonora / Cerruti, Simone / Manfredi, Marcello / Barberis, Elettra / Peletto, Simone / Arillo, Alessandra / Giaccio, Nunzia / Masini, Maria Angela / Brandi, Jessica / Cecconi, Daniela / Marengo, Emilio / Brizio, Paola

International journal of molecular sciences

2024 Volume 25, Issue 3

Abstract: Fish freshness consists of complex endogenous and exogenous processes; therefore, the use of a few parameters to unravel illicit practices could be insufficient. Moreover, the development of strategies for the identification of such practices based on ... ...

Abstract	Fish freshness consists of complex endogenous and exogenous processes; therefore, the use of a few parameters to unravel illicit practices could be insufficient. Moreover, the development of strategies for the identification of such practices based on additives known to prevent and/or delay fish spoilage is still limited. The paper deals with the identification of the effect played by a Cafodos solution on the conservation state of sea bass at both short-term (3 h) and long-term (24 h). Controls and treated samples were characterized by a multi-omic approach involving proteomics, lipidomics, metabolomics, and metagenomics. Different parts of the fish samples were studied (muscle, skin, eye, and gills) and sampled through a non-invasive procedure based on EVA strips functionalized by ionic exchange resins. Data fusion methods were then applied to build models able to discriminate between controls and treated samples and identify the possible markers of the applied treatment. The approach was effective in the identification of the effect played by Cafodos that proved to be different in the short- and long-term and complex, involving proteins, lipids, and small molecules to a different extent.
MeSH term(s)	Animals ; Bass ; Multiomics
Language	English
Publishing date	2024-01-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25031509
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Article ; Online: Precision Medicine Approaches with Metabolomics and Artificial Intelligence.

Barberis, Elettra / Khoso, Shahzaib / Sica, Antonio / Falasca, Marco / Gennari, Alessandra / Dondero, Francesco / Afantitis, Antreas / Manfredi, Marcello

International journal of molecular sciences

2022 Volume 23, Issue 19

Abstract: Recent technological innovations in the field of mass spectrometry have supported the use of metabolomics analysis for precision medicine. This growth has been allowed also by the application of algorithms to data analysis, including multivariate and ... ...

Abstract	Recent technological innovations in the field of mass spectrometry have supported the use of metabolomics analysis for precision medicine. This growth has been allowed also by the application of algorithms to data analysis, including multivariate and machine learning methods, which are fundamental to managing large number of variables and samples. In the present review, we reported and discussed the application of artificial intelligence (AI) strategies for metabolomics data analysis. Particularly, we focused on widely used non-linear machine learning classifiers, such as ANN, random forest, and support vector machine (SVM) algorithms. A discussion of recent studies and research focused on disease classification, biomarker identification and early diagnosis is presented. Challenges in the implementation of metabolomics-AI systems, limitations thereof and recent tools were also discussed.
MeSH term(s)	Algorithms ; Artificial Intelligence ; Machine Learning ; Precision Medicine/methods ; Support Vector Machine
Language	English
Publishing date	2022-09-24
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms231911269
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