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Article ; Online: High genetic diversity suggests a long evolutionary history of plum pox virus‐M in Turkey

Teber, Saffet / Gürcan, Kahraman / Brevet, Marie / Palmisano, Francesco / Candresse, Thierry / Dallot, Sylvie

Plant Pathology. 2023 Feb., v. 72, no. 2 p.300-311

2023

Abstract: The genetic diversity and evolutionary history of the epidemic plum pox virus strain M (PPV‐M) have been poorly studied. We sequenced the genomes of 69 PPV‐M isolates selected from different Turkish regions. These new nearly full‐length genomic sequences ...

Abstract	The genetic diversity and evolutionary history of the epidemic plum pox virus strain M (PPV‐M) have been poorly studied. We sequenced the genomes of 69 PPV‐M isolates selected from different Turkish regions. These new nearly full‐length genomic sequences were analysed together with 21 previously reported Turkish sequences of the PPV‐MIs clade and with 50 sequences of other PPV‐M isolates collected worldwide, including four sequences of Albanian isolates. Major genomic features were maintained in all new PPV‐M genomic sequences, with the highest divergence detected in the PIPO, P1 and CP proteins. Turkish PPV‐M isolates displayed a high genetic diversity and grouped into two sister clades, one formed by PPV‐MIs isolates only and a second clade consisting of the previously described PPV‐Ma and PPV‐Mb subclades. The combined diversity for PPV‐M isolates (Europe, Japan and Turkey) reached to 0.022 ± 0.001, which is slightly higher than the diversity of the globally distributed PPV‐D strain (0.017 ± 0.001). Likewise, the genetic diversity of PPV‐M (0.020 ± 0.001) in Turkey was found to be comparable to that observed for PPV‐M isolates from other countries (0.021 ± 0.001) and even marginally higher if considering partial genomic sequences that allow the inclusion of a much larger number of isolates and countries. Overall, the original distribution of PPV‐MIs, which seems to be almost specific to Turkey, and the high genetic diversity of PPV‐MIs and other Turkish PPV‐M isolates suggest a long evolutionary history of M isolates in Turkey and position this country as a centre of diversity of PPV‐M.
Keywords	Japan ; Plum pox virus ; center of diversity ; genetic variation ; genome ; genomics ; plant pathology ; sharka disease ; Europe
Language	English
Dates of publication	2023-02
Size	p. 300-311.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	415941-x
ISSN	1365-3059 ; 0032-0862
ISSN (online)	1365-3059
ISSN	0032-0862
DOI	10.1111/ppa.13663
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Article ; Online: Understanding neurodegenerative disorders by MS-based lipidomics.

Calvano, Cosima D / Palmisano, Francesco / Cataldi, Tommaso Ri

Bioanalysis

2018 Volume 10, Issue 11, Page(s) 787–790

MeSH term(s)	Biomarkers/metabolism ; Humans ; Lipid Metabolism ; Mass Spectrometry ; Metabolomics ; Neurodegenerative Diseases/metabolism
Chemical Substances	Biomarkers
Language	English
Publishing date	2018-06-04
Publishing country	England
Document type	Journal Article
ISSN	1757-6199
ISSN (online)	1757-6199
DOI	10.4155/bio-2018-0023
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Article ; Online: Analysis of Phospholipids, Lysophospholipids, and Their Linked Fatty Acyl Chains in Yellow Lupin Seeds (

Calvano, Cosima Damiana / Bianco, Mariachiara / Ventura, Giovanni / Losito, Ilario / Palmisano, Francesco / Cataldi, Tommaso R I

Molecules (Basel, Switzerland)

2020 Volume 25, Issue 4

Abstract: Hydrophilic interaction liquid chromatography (HILIC) and electrospray ionization (ESI) coupled to either Fourier-transform (FT) orbital-trap or linear ion-trap tandem mass spectrometry (LIT-MS/MS) was used to characterize the phospholipidome of yellow ... ...

Abstract	Hydrophilic interaction liquid chromatography (HILIC) and electrospray ionization (ESI) coupled to either Fourier-transform (FT) orbital-trap or linear ion-trap tandem mass spectrometry (LIT-MS/MS) was used to characterize the phospholipidome of yellow lupin (
MeSH term(s)	Chromatography, Liquid/methods ; Fatty Acids/analysis ; Lupinus/chemistry ; Lysophospholipids/analysis ; Phosphatidylcholines/analysis ; Phospholipids/analysis ; Spectrometry, Mass, Electrospray Ionization ; Tandem Mass Spectrometry/methods
Chemical Substances	Fatty Acids ; Lysophospholipids ; Phosphatidylcholines ; Phospholipids
Language	English
Publishing date	2020-02-13
Publishing country	Switzerland
Document type	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/molecules25040805
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Article ; Online: Targeted analysis of ceramides and cerebrosides in yellow lupin seeds by reversed-phase liquid chromatography coupled to electrospray ionization and multistage mass spectrometry.

Bianco, Mariachiara / Calvano, Cosima Damiana / Losito, Ilario / Palmisano, Francesco / Cataldi, Tommaso R I

Food chemistry

2020 Volume 324, Page(s) 126878

Abstract: Ceramides (Cer) and cerebrosides are important sphingolipids (SL) involved in many biological processes. Herein, the SL content of yellow lupin seeds (Lupinus luteus) was determined by liquid-liquid extraction, mild alkaline hydrolysis (1 h at 37 °C) and ...

Abstract	Ceramides (Cer) and cerebrosides are important sphingolipids (SL) involved in many biological processes. Herein, the SL content of yellow lupin seeds (Lupinus luteus) was determined by liquid-liquid extraction, mild alkaline hydrolysis (1 h at 37 °C) and reversed-phase liquid chromatography with negative electrospray ionization coupled to either an orbital-trap (Fourier-transformed, FT) or linear ion-trap (LIT) mass spectrometry (RPLC-ESI/MS). The chemical identity of SL including the sugar residues and sphingoid backbone (SB) was inferred by collision-induced dissociation multiple-stage mass spectrometry (MS
MeSH term(s)	Ceramides/analysis ; Cerebrosides/analysis ; Chromatography, High Pressure Liquid ; Chromatography, Reverse-Phase ; Fatty Acids/analysis ; Fatty Acids/chemistry ; Lupinus/chemistry ; Lupinus/metabolism ; Seeds/chemistry ; Seeds/metabolism ; Spectrometry, Mass, Electrospray Ionization/methods ; Sphingosine/analogs & derivatives ; Sphingosine/analysis
Chemical Substances	Ceramides ; Cerebrosides ; Fatty Acids ; phytosphingosine (GIN46U9Q2Q) ; behenic acid (H390488X0A) ; Sphingosine (NGZ37HRE42) ; lignoceric acid (RK3VCW5Y1L)
Language	English
Publishing date	2020-04-21
Publishing country	England
Document type	Journal Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2020.126878
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Article ; Online: Development of a mass spectrometry immunoassay for unambiguous detection of egg allergen traces in wines.

Pilolli, Rosa / Chaudhari, Ravindra / Palmisano, Francesco / Monaci, Linda

Analytical and bioanalytical chemistry

2017 Volume 409, Issue 6, Page(s) 1581–1589

Abstract: A mass spectrometry immunoassay (MSIA) specifically designed for the detection of egg allergens in wines is described. MSIA is based on an immunoaffinity enrichment procedure combined with targeted MS/MS detection of selected egg peptide markers. ... ...

Abstract	A mass spectrometry immunoassay (MSIA) specifically designed for the detection of egg allergens in wines is described. MSIA is based on an immunoaffinity enrichment procedure combined with targeted MS/MS detection of selected egg peptide markers. Polyclonal antibodies raised against native ovalbumin, chosen as the target protein tracing for egg powder, were immobilized onto low backpressure monolithic MSIA customized disposable tips. Ovalbumin-free wine samples were fortified with standard protein at different concentrations in the low microgram-per-milliliter range. A simple protocol was devised consisting of a 1:4 dilution of the wine sample with a basic solution for pH adjustment, followed by a semi-automated purification/enrichment step on MSIA customized disposable tips fitted on a multichannel electronic pipette. Among the main figures of merit, LOD and LOQ values as low as 0.01 and 0.03 μg/mL, respectively, and within-day precision of 18% should be noticed. Noteworthy, the developed assay outperformed current MS-based methods for the detection of allergenic protein in wine matrices, thanks to the immunoaffinity enrichment. In addition, compared to other immunoassays, the present approach boasts the unquestionable advantage of providing an unambiguous identification of the target protein by simultaneous detection of three unique peptide markers each giving three specific MS/MS transitions.
Language	English
Publishing date	2017-02
Publishing country	Germany
Document type	Journal Article
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-016-0099-3
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Article ; Online: MALDI matrices for low molecular weight compounds: an endless story?

Calvano, Cosima Damiana / Monopoli, Antonio / Cataldi, Tommaso R I / Palmisano, Francesco

Analytical and bioanalytical chemistry

2018 Volume 410, Issue 17, Page(s) 4015–4038

Abstract: Since its introduction in the 1980s, matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has gained a prominent role in the analysis of high molecular weight biomolecules such as proteins, peptides, oligonucleotides, and ... ...

Abstract	Since its introduction in the 1980s, matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has gained a prominent role in the analysis of high molecular weight biomolecules such as proteins, peptides, oligonucleotides, and polysaccharides. Its application to low molecular weight compounds has remained for long time challenging due to the spectral interferences produced by conventional organic matrices in the low m/z window. To overcome this problem, specific sample preparation such as analyte/matrix derivatization, addition of dopants, or sophisticated deposition technique especially useful for imaging experiments, have been proposed. Alternative approaches based on second generation (rationally designed) organic matrices, ionic liquids, and inorganic matrices, including metallic nanoparticles, have been the object of intense and continuous research efforts. Definite evidences are now provided that MALDI MS represents a powerful and invaluable analytical tool also for small molecules, including their quantification, thus opening new, exciting applications in metabolomics and imaging mass spectrometry. This review is intended to offer a concise critical overview of the most recent achievements about MALDI matrices capable of specifically address the challenging issue of small molecules analysis. Graphical abstract An ideal Book of matrices for MALDI MS of small molecules.
Language	English
Publishing date	2018-07
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-018-1014-x
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Article ; Online: Glycosphingolipidomics of donkey milk by hydrophilic interaction liquid chromatography coupled to ESI and multistage MS.

Calvano, Cosima Damiana / Glaciale, Marco / Palmisano, Francesco / Cataldi, Tommaso R I

Electrophoresis

2018 Volume 39, Issue 13, Page(s) 1634–1644

Abstract: Hydrophilic interaction liquid chromatography coupled to negative-ion electrospray linear ion-trap multiple-stage MS (HILIC-ESI- ... ...

Abstract	Hydrophilic interaction liquid chromatography coupled to negative-ion electrospray linear ion-trap multiple-stage MS (HILIC-ESI-MS
MeSH term(s)	Animals ; Ceramides/analysis ; Chromatography, High Pressure Liquid ; Equidae ; Fatty Acids/analysis ; Glycosphingolipids/analysis ; Hydrophobic and Hydrophilic Interactions ; Milk/chemistry ; Monosaccharides/analysis ; Sphingosine/analogs & derivatives ; Sphingosine/analysis ; Tandem Mass Spectrometry
Chemical Substances	Ceramides ; Fatty Acids ; Glycosphingolipids ; Monosaccharides ; phytosphingosine (GIN46U9Q2Q) ; Sphingosine (NGZ37HRE42) ; safingol (OWA98U788S)
Language	English
Publishing date	2018-03-12
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	619001-7
ISSN	1522-2683 ; 0173-0835
ISSN (online)	1522-2683
ISSN	0173-0835
DOI	10.1002/elps.201700475
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Article: Sesquiterpene Fingerprinting by Headspace SPME–GC–MS: Preliminary Study for a Simple and Powerful Analytical Tool for Traceability of Olive Oils

Damascelli, Anna / Palmisano, Francesco

Food analytical methods. 2013 June, v. 6, no. 3

2013

Abstract: Solid-phase microextraction combined with gas chromatography–mass spectrometry is employed to characterise the head space composition of extra virgin olive oil with particular emphasis on some sesquiterpenes useful for oil classification. It is ... ...

Abstract	Solid-phase microextraction combined with gas chromatography–mass spectrometry is employed to characterise the head space composition of extra virgin olive oil with particular emphasis on some sesquiterpenes useful for oil classification. It is demonstrated that α-muurolene and α-farnesene contents (normalised to α-copaene), besides discriminating between Apulian and foreign oils, is even capable of differentiating between different sub-brands of Terra di Bari (protected denomination of origin) oils, produced in neighbouring, very restricted areas of the Apulian region.
Keywords	extra-virgin olive oil ; gas chromatography ; headspace analysis ; mass spectrometry ; microextraction ; traceability
Language	English
Dates of publication	2013-06
Size	p. 900-905.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	2429656-9
ISSN	1936-976X ; 1936-9751
ISSN (online)	1936-976X
ISSN	1936-9751
DOI	10.1007/s12161-012-9500-9
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Article ; Online: Identification of neutral and acidic glycosphingolipids in the human dermal fibroblasts.

Calvano, Cosima Damiana / Ventura, Giovanni / Sardanelli, Anna Maria / Losito, Ilario / Palmisano, Francesco / Cataldi, Tommaso R I

Analytical biochemistry

2019 Volume 581, Page(s) 113348

Abstract: Skin fibroblasts are recognized as a valuable model of primary human cells able of mirroring the chronological and biological aging. Here, a lipidomic study of glycosphingolipids (GSL) occurring in the easily accessible human dermal fibroblasts (HDF) is ... ...

Abstract	Skin fibroblasts are recognized as a valuable model of primary human cells able of mirroring the chronological and biological aging. Here, a lipidomic study of glycosphingolipids (GSL) occurring in the easily accessible human dermal fibroblasts (HDF) is presented. Reversed-phase liquid chromatography with negative electrospray ionization (RPLC-ESI) coupled to either orbitrap or linear ion-trap multiple-stage mass spectrometry was applied to characterize GSL in commercially adult and neonatal primary human fibroblast cells and in skin samples taken from an adult volunteer. Collision-induced dissociation in negative ion mode allowed us to get information on the monosaccharide number and ceramide composition, whereas tandem mass spectra on the ceramide anion was useful to identify the sphingoid base. Nearly sixty endogenous GSL species were successfully recognized, namely 33 hexosyl-ceramides (i.e., HexCer, Hex
MeSH term(s)	Acidic Glycosphingolipids/analysis ; Acidic Glycosphingolipids/metabolism ; Adult ; Cells, Cultured ; Dermis/cytology ; Dermis/metabolism ; Fibroblasts/cytology ; Fibroblasts/metabolism ; Humans ; Neutral Glycosphingolipids/analysis ; Neutral Glycosphingolipids/metabolism
Chemical Substances	Acidic Glycosphingolipids ; Neutral Glycosphingolipids
Language	English
Publishing date	2019-06-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2019.113348
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Article: The first phlebo‐like virus infecting plants: a case study on the adaptation of negative‐stranded RNA viruses to new hosts

Navarro, Beatriz / Minutolo, Maria / De Stradis, Angelo / Palmisano, Francesco / Alioto, Daniela / Di Serio, Francesco

Molecular plant pathology. 2018 May, v. 19, no. 5

2018

Abstract: A novel negative‐stranded (ns) RNA virus associated with a severe citrus disease reported more than 80 years ago has been identified. Transmission electron microscopy showed that this novel virus, tentatively named citrus concave gum‐associated virus, is ...

Abstract	A novel negative‐stranded (ns) RNA virus associated with a severe citrus disease reported more than 80 years ago has been identified. Transmission electron microscopy showed that this novel virus, tentatively named citrus concave gum‐associated virus, is flexuous and non‐enveloped. Notwithstanding, its two genomic RNAs share structural features with members of the genus Phlebovirus, which are enveloped arthropod‐transmitted viruses infecting mammals, and with a group of still unclassified phlebo‐like viruses mainly infecting arthropods. CCGaV genomic RNAs code for an RNA‐dependent RNA polymerase, a nucleocapsid protein and a putative movement protein showing structural and phylogenetic relationships with phlebo‐like viruses, phleboviruses and the unrelated ophioviruses, respectively, thus providing intriguing evidence of a modular genome evolution. Phylogenetic reconstructions identified an invertebrate‐restricted virus as the most likely ancestor of this virus, revealing that its adaptation to plants was independent from and possibly predated that of the other nsRNA plant viruses. These data are consistent with an evolutionary scenario in which trans‐kingdom adaptation occurred several times during the history of nsRNA viruses and followed different evolutionary pathways, in which genomic RNA segments were gained or lost. The need to create a new genus for this bipartite nsRNA virus and the impact of the rapid and specific detection methods developed here on citrus sanitation and certification are also discussed.
Keywords	Citrus ; Phlebovirus ; RNA ; RNA-directed RNA polymerase ; arthropods ; case studies ; certification ; genome ; genomics ; hosts ; mammals ; new genus ; nucleocapsid proteins ; phylogeny ; plant diseases and disorders ; plant viruses ; sanitation ; transmission electron microscopy ; viruses
Language	English
Dates of publication	2018-05
Size	p. 1075-1089.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2020755-4
ISSN	1364-3703 ; 1464-6722
ISSN (online)	1364-3703
ISSN	1464-6722
DOI	10.1111/mpp.12587
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