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Article ; Online: Spin studies via Drell-Yan processes at PANDA

Destefanis M.

EPJ Web of Conferences, Vol 73, p

2014 Volume 02012

Abstract: The nucleon structure is still not completely understood. A transverse momentum dependent description of the nucleon structure is a crucial milestone for several forthcoming studies in a wide range of experimental scenarios. By means of antiproton beams, ...

Abstract	The nucleon structure is still not completely understood. A transverse momentum dependent description of the nucleon structure is a crucial milestone for several forthcoming studies in a wide range of experimental scenarios. By means of antiproton beams, possibly polarized in a later stage of the project, with a beam momentum up to 15 GeV/c, which will be available at the future FAIR facility, the nonperturbative region of QCD is planned to be investigated. One of the main goals of the forthcoming experiments at FAIR is the study of Drell-Yan lepton pairs by means of proton-antiproton annihilations, taking also advantage of the expected high luminosity. The Drell-Yan production is a unique tool to access the spin dependent properties of the nucleon, and in particular its transverse degrees of freedom. Transverse Momentum Dependent (TMD) Parton Distribution Functions (PDFs), i.e. the Boer-Mulders function, the Sivers function, and the Transversity, could be deeply investigated by means of experimental angular asymmetries. In later stages of FAIR, single- and double-spin asymmetries could be investigated as well. The Drell-Yan physics program which could be accessed at FAIR with the PANDA experiment will be discussed in details, in the light of existing results in the field.
Keywords	Physics ; QC1-999 ; Science ; Q
Subject code	530
Language	English
Publishing date	2014-06-01T00:00:00Z
Publisher	EDP Sciences
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Diversity and detections of Phytophthora species from trade and non-trade environments in Ireland

O'Hanlon, R. / Choiseul, J. / Corrigan, M. / Catarame, T. / Destefanis, M.

Bulletin / Organisation Européenne et Méditerranéenne pour la Protection des Plantes

2016 Volume 46, Issue 3, Page(s) 594

Document type	Article
ZDB-ID	188103-6
ISSN	0071-2388 ; 0250-8052
Database	Current Contents Nutrition, Environment, Agriculture

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Article ; Online: Two new Nothophytophthora species from streams in Ireland and Northern Ireland: Nothophytophthora irlandica and N. lirii sp. nov.

O'Hanlon, Richard / Destefanis, Maria / Milenković, Ivan / Tomšovský, Michal / Janoušek, Josef / Bellgard, Stanley E / Weir, Bevan S / Kudláček, Tomáš / Horta Jung, Marilia / Jung, Thomas

PloS one

2021 Volume 16, Issue 5, Page(s) e0250527

Abstract: Slow growing oomycete isolates with morphological resemblance to Phytophthora were obtained from forest streams during routine monitoring for the EU quarantine forest pathogen Phytophthora ramorum in Ireland and Northern Ireland. Internal Transcribed ... ...

Abstract	Slow growing oomycete isolates with morphological resemblance to Phytophthora were obtained from forest streams during routine monitoring for the EU quarantine forest pathogen Phytophthora ramorum in Ireland and Northern Ireland. Internal Transcribed Spacer (ITS) sequence analysis indicated that they belonged to two previously unknown species of Nothophytophthora, a recently erected sister genus of Phytophthora. Morphological and temperature-growth studies were carried out to characterise both new species. In addition, Bayesian and Maximum-Likelihood analyses of nuclear 5-loci and mitochondrial 3-loci datasets were performed to resolve the phylogenetic positions of the two new species. Both species were sterile, formed chlamydospores and partially caducous nonpapillate sporangia, and showed slower growth than any of the six known Nothophytophthora species. In all phylogenetic analyses both species formed distinct, strongly supported clades, closely related to N. chlamydospora and N. valdiviana from Chile. Based on their unique combination of morphological and physiological characters and their distinct phylogenetic positions the two new species are described as Nothophytophthora irlandica sp. nov. and N. lirii sp. nov. Their potential lifestyle and geographic origin are discussed.
MeSH term(s)	DNA, Ribosomal Spacer/genetics ; Northern Ireland ; Phylogeny ; Phytophthora/genetics ; Phytophthora/isolation & purification ; Plant Diseases/microbiology ; Rivers/microbiology ; Sequence Analysis, DNA/methods ; Stramenopiles/genetics ; Stramenopiles/isolation & purification
Chemical Substances	DNA, Ribosomal Spacer
Language	English
Publishing date	2021-05-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0250527
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mitochondrial translocation of vitamin D receptor is mediated by the permeability transition pore in human keratinocyte cell line.

Silvagno, Francesca / Consiglio, Marco / Foglizzo, Valentina / Destefanis, Michele / Pescarmona, Gianpiero

PloS one

2013 Volume 8, Issue 1, Page(s) e54716

Abstract: Background: Vitamin D receptor (VDR) is a well known transcriptional regulator, active as heterodimer in association with coactivators and corepressors. In addition it has been described the extranuclear distribution of the receptor and in particular ... ...

Abstract	Background: Vitamin D receptor (VDR) is a well known transcriptional regulator, active as heterodimer in association with coactivators and corepressors. In addition it has been described the extranuclear distribution of the receptor and in particular the recently reported mitochondrial localization in platelets and megakaryocytes is intriguing because it appears to be a common feature of steroid receptors. Whereas for other members of the steroid receptor family the mitochondrial function has been explored, up to now nothing is known about a mitochondrial form of VDR in human proliferating cells. Methodology/principal findings: In this study we characterized for the first time the mitochondrial localization of VDR in the human keratinocyte cell line HaCaT. In proliferating HaCaT cells VDR was abundantly expressed in mitochondria in association with its binding partner RXRα and the import was ligand-independent. By immunoprecipitation studies we demonstrated the interaction of VDR with proteins of the permeability transition pore (PTP), VDAC and StAR. We then adopted different pharmacological and silencing approaches with the aim of hampering PTP function, either affecting PTP opening or abating the expression of the complex member StAR. By all means the impairment of pore function led to a reduction of mitochondrial levels of VDR. Conclusions: The results reported here demonstrate a ligand-independent mitochondrial import of VDR through the permeability transition pore, and open interesting new perspectives on PTP function as transporter and on VDR role in mitochondria.
MeSH term(s)	Cell Line ; Humans ; Keratinocytes/cytology ; Keratinocytes/metabolism ; Ligands ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/metabolism ; Mitochondrial Membrane Transport Proteins/physiology ; Mitochondrial Permeability Transition Pore ; Protein Transport ; Receptors, Calcitriol/metabolism ; Receptors, Calcitriol/physiology ; Retinoid X Receptors/metabolism
Chemical Substances	Ligands ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Permeability Transition Pore ; Receptors, Calcitriol ; Retinoid X Receptors
Language	English
Publishing date	2013-01-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0054716
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Article ; Online: Extremely low frequency electromagnetic fields affect proliferation and mitochondrial activity of human cancer cell lines.

Destefanis, Michele / Viano, Marta / Leo, Christian / Gervino, Gianpiero / Ponzetto, Antonio / Silvagno, Francesca

International journal of radiation biology

2015 Volume 91, Issue 12, Page(s) 964–972

Abstract: Purpose: To date, the effects of electromagnetic fields on cell metabolism have been overlooked. The objective of the present study was to investigate the influence of extremely low frequency electromagnetic fields (ELF-EMF) over mitochondrial ... ...

Abstract	Purpose: To date, the effects of electromagnetic fields on cell metabolism have been overlooked. The objective of the present study was to investigate the influence of extremely low frequency electromagnetic fields (ELF-EMF) over mitochondrial metabolism and the consequent impact on cancer cell growth. Materials and methods: The effects of ELF-EMF on cancer growth were investigated in several human cancer cell lines by crystal violet assay. The modulation of mitochondrial activity was assessed by cytofluorimetric evaluation of membrane potential and by real-time quantification of mitochondrial transcription. Moreover the expression of several mitochondrial proteins and their levels in the organelle were evaluated. Results: The long-term exposure to ELF-EMF reduced the proliferation of several cancer cell lines and the effect was associated to an increased mitochondrial activity without evident changes in ATP levels. The results of our experiments excluded a transcriptional modulation of mitochondrial respiratory complexes, rather suggesting that ELF-EMF increased the energy demand. The altered mitochondrial metabolism led to changes in mitochondrial protein profile. In fact we found a downregulated expression of mitochondrial phospho-ERK, p53 and cytochrome c. Conclusion: The results of the present study indicate that ELF-EMF can negatively modulate cancer cell growth increasing respiratory activity of cells and altering mitochondrial protein expression.
MeSH term(s)	Cell Count ; Cell Line, Tumor ; Cell Proliferation/radiation effects ; Electromagnetic Fields/adverse effects ; Electron Transport/radiation effects ; Gene Expression Regulation/radiation effects ; Humans ; Membrane Potential, Mitochondrial/radiation effects ; Mitochondria/metabolism ; Mitochondria/radiation effects ; Mitochondrial Proteins/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Transcription, Genetic/radiation effects
Chemical Substances	Mitochondrial Proteins ; RNA, Messenger
Language	English
Publishing date	2015
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3065-x
ISSN	1362-3095 ; 0020-7616 ; 0955-3002
ISSN (online)	1362-3095
ISSN	0020-7616 ; 0955-3002
DOI	10.3109/09553002.2015.1101648
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Article ; Online: PCR-based specific techniques used for detecting the most important pathogens on strawberry: a systematic review.

Mirmajlessi, Seyed Mahyar / Destefanis, Marialaura / Gottsberger, Richard Alexander / Mänd, Marika / Loit, Evelin

Systematic reviews

2015 Volume 4, Page(s) 9

Abstract: Background: Strawberry diseases are a major limiting factor that severely impact plant agronomic performance. Regarding limitations of traditional techniques for detection of pathogens, researchers have developed specific DNA-based tests as sensitive ... ...

Abstract	Background: Strawberry diseases are a major limiting factor that severely impact plant agronomic performance. Regarding limitations of traditional techniques for detection of pathogens, researchers have developed specific DNA-based tests as sensitive and specific techniques. The aim of this review is to provide an overview of polymerase chain reaction (PCR)-based methods used for detection or quantification of the most widespread strawberry pathogens, such as Fusarium oxysporum f.sp. fragariae, Phytophthora fragariae, Colletotrichum acutatum, Verticillium dahliae, Botrytis cinerea, Macrophomina phaseolina, and Xanthomonas fragariae. An updated and detailed list of published PCR protocols is presented and discussed, aimed at facilitating access to information that could be particularly useful for diagnostic laboratories in order to develop a rapid, cost-effective, and reliable monitoring technique. Methods: The study design was a systematic review of PCR-based techniques used for detection and quantification of strawberry pathogens. Using appropriate subject headings, AGRICOLA, AGRIS, BASE, Biological Abstracts, CAB Abstracts, Google Scholar, Scopus, Web of Knowledge, and SpringerLink databases were searched from their inception up to April 2014. Two assessors independently reviewed the titles, abstracts, and full articles of all identified citations. Selected articles were included if one of the mentioned strawberry pathogens was investigated based on PCR methods, and a summary of pre-analytical requirements for PCR was provided. Results: A total of 259 titles and abstracts were reviewed, of which 22 full texts met all the inclusion criteria. Our systematic review identified ten different protocols for X. fragariae, eight for P. fragariae, four for B. cinerea, six for C. acutatum, three for V. dahlia, and only one for F. oxysporum. The accuracy and sensitivity of PCR diagnostic methods is the focus of most studies included in this review. However, a large proportion of errors in laboratories occur in the pre-analytical phase of the testing process. Due to heterogeneity, results could not be meta-analyzed. Conclusions: From a systematic review of the currently available published literature, effective detection assays to detect the major strawberry pathogens have been developed. These assays can function as a basis for clinical labs, regulatory personnel, and other diagnosticians to adapt or implement for detection of these six important strawberry pathogens.
MeSH term(s)	Cost-Benefit Analysis ; Fragaria/microbiology ; Plant Diseases/microbiology ; Plant Leaves/microbiology ; Polymerase Chain Reaction ; Reproducibility of Results ; Sensitivity and Specificity
Language	English
Publishing date	2015-01-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review ; Systematic Review
ZDB-ID	2662257-9
ISSN	2046-4053 ; 2046-4053
ISSN (online)	2046-4053
ISSN	2046-4053
DOI	10.1186/2046-4053-4-9
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Article ; Online: The vitamin D receptor inhibits the respiratory chain, contributing to the metabolic switch that is essential for cancer cell proliferation.

Consiglio, Marco / Destefanis, Michele / Morena, Deborah / Foglizzo, Valentina / Forneris, Mattia / Pescarmona, Gianpiero / Silvagno, Francesca

PloS one

2014 Volume 9, Issue 12, Page(s) e115816

Abstract: We recently described the mitochondrial localization and import of the vitamin D receptor (VDR) in actively proliferating HaCaT cells for the first time, but its role in the organelle remains unknown. Many metabolic intermediates that support cell growth ...

Abstract	We recently described the mitochondrial localization and import of the vitamin D receptor (VDR) in actively proliferating HaCaT cells for the first time, but its role in the organelle remains unknown. Many metabolic intermediates that support cell growth are provided by the mitochondria; consequently, the identification of proteins that regulate mitochondrial metabolic pathways is of great interest, and we sought to understand whether VDR may modulate these pathways. We genetically silenced VDR in HaCaT cells and studied the effects on cell growth, mitochondrial metabolism and biosynthetic pathways. VDR knockdown resulted in robust growth inhibition, with accumulation in the G0G1 phase of the cell cycle and decreased accumulation in the M phase. The effects of VDR silencing on proliferation were confirmed in several human cancer cell lines. Decreased VDR expression was consistently observed in two different models of cell differentiation. The impairment of silenced HaCaT cell growth was accompanied by sharp increases in the mitochondrial membrane potential, which sensitized the cells to oxidative stress. We found that transcription of the subunits II and IV of cytochrome c oxidase was significantly increased upon VDR silencing. Accordingly, treatment of HaCaT cells with vitamin D downregulated both subunits, suggesting that VDR may inhibit the respiratory chain and redirect TCA intermediates toward biosynthesis, thus contributing to the metabolic switch that is typical of cancer cells. In order to explore this hypothesis, we examined various acetyl-CoA-dependent biosynthetic pathways, such as the mevalonate pathway (measured as cholesterol biosynthesis and prenylation of small GTPases), and histone acetylation levels; all of these pathways were inhibited by VDR silencing. These data provide evidence of the role of VDR as a gatekeeper of mitochondrial respiratory chain activity and a facilitator of the diversion of acetyl-CoA from the energy-producing TCA cycle toward biosynthetic pathways that are essential for cellular proliferation.
MeSH term(s)	Cell Line, Tumor ; Cell Proliferation ; Cellular Reprogramming ; Electron Transport ; G1 Phase Cell Cycle Checkpoints ; Humans ; M Phase Cell Cycle Checkpoints ; Metabolic Networks and Pathways ; Mitochondria/metabolism ; Neoplasms/metabolism ; Receptors, Calcitriol/genetics ; Receptors, Calcitriol/metabolism
Chemical Substances	Receptors, Calcitriol
Language	English
Publishing date	2014-12-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0115816
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Article: A disease resistance locus on potato and tomato chromosome 4 exhibits a conserved multipartite structure displaying different rates of evolution in different lineages

Destefanis, Marialaura / Brian Rigney / Dan Milbourne / Denis Griffin / Glenn J Bryan / Ingo Hein / Istvan Nagy / Karen McLean

BMC plant biology. 2015 Dec., v. 15, no. 1

2015

Abstract: BACKGROUND: In plant genomes, NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. R-gene sequences mostly differentiate by accumulating point mutations and gene conversion events. ... ...

Abstract	BACKGROUND: In plant genomes, NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. R-gene sequences mostly differentiate by accumulating point mutations and gene conversion events. Potato and tomato chromosome 4 harbours a syntenic R-gene locus (known as the R2 locus in potato) that has mainly been examined in central American/Mexican wild potato species on the basis of its contribution to resistance to late blight, caused by the oomycete pathogen Phytophthora infestans. Evidence to date indicates the occurrence of a fast evolutionary mode characterized by gene conversion events at the locus in these genotypes. RESULTS: A physical map of the R2 locus was developed for three Solanum tuberosum genotypes and used to identify the tomato syntenic sequence. Functional annotation of the locus revealed the presence of numerous resistance gene homologs (RGHs) belonging to the R2 gene family (R2GHs) organized into a total of 4 discrete physical clusters, three of which were conserved across S. tuberosum and tomato. Phylogenetic analysis showed clear orthology/paralogy relationships between S. tuberosum R2GHs but not in R2GHs cloned from Solanum wild species. This study confirmed that, in contrast to the wild species R2GHs, which have evolved through extensive sequence exchanges between paralogs, gene conversion was not a major force for differentiation in S. tuberosum R2GHs, and orthology/paralogy relationships have been maintained via a slow accumulation of point mutations in these genotypes. CONCLUSIONS: S. tuberosum and Solanum lycopersicum R2GHs evolved mostly through duplication and deletion events, followed by gradual accumulation of mutations. Conversely, widespread gene conversion is the major evolutionary force that has shaped the locus in Mexican wild potato species. We conclude that different selective forces shaped the evolution of the R2 locus in these lineages and that co-evolution with a pathogen steered selection on different evolutionary paths.
Keywords	coevolution ; disease resistance ; gene conversion ; genes ; genetic resistance ; genotype ; loci ; pathogens ; phylogeny ; Phytophthora infestans ; point mutation ; potatoes ; Solanum lycopersicum ; Solanum tuberosum ; tomatoes ; wild relatives
Language	English
Dates of publication	2015-12
Size	p. 255.
Publishing place	BioMed Central
Document type	Article
ISSN	1471-2229
DOI	10.1186/s12870-015-0645-8
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A disease resistance locus on potato and tomato chromosome 4 exhibits a conserved multipartite structure displaying different rates of evolution in different lineages.

Destefanis, Marialaura / Nagy, Istvan / Rigney, Brian / Bryan, Glenn J / McLean, Karen / Hein, Ingo / Griffin, Denis / Milbourne, Dan

BMC plant biology

2015 Volume 15, Page(s) 255

Abstract: Background: In plant genomes, NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. R-gene sequences mostly differentiate by accumulating point mutations and gene conversion events. ...

Abstract	Background: In plant genomes, NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. R-gene sequences mostly differentiate by accumulating point mutations and gene conversion events. Potato and tomato chromosome 4 harbours a syntenic R-gene locus (known as the R2 locus in potato) that has mainly been examined in central American/Mexican wild potato species on the basis of its contribution to resistance to late blight, caused by the oomycete pathogen Phytophthora infestans. Evidence to date indicates the occurrence of a fast evolutionary mode characterized by gene conversion events at the locus in these genotypes. Results: A physical map of the R2 locus was developed for three Solanum tuberosum genotypes and used to identify the tomato syntenic sequence. Functional annotation of the locus revealed the presence of numerous resistance gene homologs (RGHs) belonging to the R2 gene family (R2GHs) organized into a total of 4 discrete physical clusters, three of which were conserved across S. tuberosum and tomato. Phylogenetic analysis showed clear orthology/paralogy relationships between S. tuberosum R2GHs but not in R2GHs cloned from Solanum wild species. This study confirmed that, in contrast to the wild species R2GHs, which have evolved through extensive sequence exchanges between paralogs, gene conversion was not a major force for differentiation in S. tuberosum R2GHs, and orthology/paralogy relationships have been maintained via a slow accumulation of point mutations in these genotypes. Conclusions: S. tuberosum and Solanum lycopersicum R2GHs evolved mostly through duplication and deletion events, followed by gradual accumulation of mutations. Conversely, widespread gene conversion is the major evolutionary force that has shaped the locus in Mexican wild potato species. We conclude that different selective forces shaped the evolution of the R2 locus in these lineages and that co-evolution with a pathogen steered selection on different evolutionary paths.
MeSH term(s)	Chromosomes, Plant/genetics ; Conserved Sequence ; Disease Resistance/genetics ; Evolution, Molecular ; Genetic Loci ; Genotype ; Lycopersicon esculentum/genetics ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Plant Diseases/genetics ; Sequence Analysis, DNA ; Solanum tuberosum/genetics
Language	English
Publishing date	2015-10-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1471-2229
ISSN (online)	1471-2229
DOI	10.1186/s12870-015-0645-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Gene expression and sporophytic self-incompatibility in hazelnut

Torello Marinoni, D / Beltramo, C / Akkak, A / Destefanis, M.L / Boccacci, P / Botta, R

Acta horticulturae. 2009 Oct., no. 845 (1)

2009

Keywords	Corylus avellana ; hazelnuts ; gene expression ; sporophytes ; plant fertility ; selfing
Language	English
Dates of publication	2009-10
Size	p. 227-231.
Document type	Article
Note	Paper presented at the Seventh International Congress on Hazelnut, Volume 1, held June 23-27, 2008, Viterbo, Italy.
ISSN	0567-7572
Database	NAL-Catalogue (AGRICOLA)

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