Pietro Franceschi

Pietro Franceschi
Fondazione Edmund Mach - Istituto Agrario San Michele All'Adige | Fondazione Mach · Department of Computational Biology (CBC)

PhD - Physics

About

169
Publications
22,049
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Introduction
Pietro Franceschi obtained a PhD in Physics at the University of Trento in 2004. From the field of molecular and plasma physics, he moved to mass spectrometry and its biological applications. At present his research interests range from biostatistical treatment of omics data to metabolomics and MS based metabolic Imaging
Additional affiliations
January 2007 - August 2016
Fondazione Edmund Mach - Istituto Agrario San Michele All'Adige
Position
  • Researcher
January 2004 - January 2007
Università degli Studi di Trento
Position
  • Research Associate

Publications

Publications (169)
Article
Full-text available
For the extraction of spatially important regions from mass spectrometry imaging (MSI) data, different clustering methods have been proposed. These clustering methods are based on certain assumptions and use different criteria to assign pixels into different classes. For high-dimensional MSI data, the curse of dimensionality also limits the perform...
Conference Paper
Full-text available
As product mislabeling in wine industry remains a significant problem in the recent years, leading to significant losses in sales, employment, and revenue for this important component of food industry. Therefore, effective control measures require the assistance of the more advanced and precise analytical techniques for wine authentication to root...
Conference Paper
Full-text available
In recent years, the interest of consumers in high-quality food products has been increased remarkably. One of the most imitated products is the Grana Padano PDO cheese, one of the most renowned Italian cheeses. Grana Padano PDO cheese can be mislabeled regarding its aging, because the quality and consequently the price of the cheese increases acco...
Article
Full-text available
Juglans regia (L.) is cultivated worldwide for its nutrient-rich nuts. In Italy, despite the growing demand, walnut cultivation has gone through a strong decline in recent decades, which led to Italy being among the top five net importing countries. To promote the development of local high-quality Italian walnut production, we devised a multidiscip...
Article
Full-text available
Microbial communities in agricultural soils are fundamental for plant growth and in vineyard ecosystems contribute to defining regional wine quality. Managing soil microbes towards beneficial outcomes requires knowledge of how community assembly processes vary across taxonomic groups, spatial scales, and through time. However, our understanding of...
Article
Secretory immunoglobulin A (SIgA) interaction with commensal bacteria conditions microbiota composition and function. However, mechanisms regulating reciprocal control of microbiota and SIgA are not defined. Bacteria-derived adenosine triphosphate (ATP) limits T follicular helper (Tfh) cells in the Peyer’s patches (PPs) via P2X7 receptor (P2X7R) an...
Conference Paper
PDO (Protected Designation of Origin) cheeses are products recognized as having higher quality and therefore can claim higher prices on the market. For this reason, in the last years there has been a flourishing of similar products that try to imitate PDO hard cheeses since when the cheese is sold in grated or shredded form, easy economic gain can...
Article
Full-text available
Potatoes (Solanum tuberosum L.) are one of the most valuable agricultural crops, and the flesh of these tubers provides various classes of healthy compounds important for human nutrition. This work presents the results of a joint analysis of different chemical classes of compounds which provided insights on the metabolic characterization of pigment...
Article
Full-text available
Detector and column saturations are problematic in comprehensive two-dimensional gas chromatography (GC×GC) data analysis. This limits the application of GC×GC in metabolomics research. To address the problems caused by detector and column saturations, we propose a two-stage data processing strategy that will incorporate a targeted data processing...
Article
Full-text available
Lipids play many essential roles in living organisms, which accounts for the great diversity of these amphiphilic molecules within the individual lipid classes, while their composition depends on intrinsic and extrinsic factors. Recent developments in mass spectrometric methods have significantly contributed to the widespread application of the liq...
Article
Full-text available
Naturally occurring stable isotope ratios in animal tissues allow estimation of species trophic position and ecological niche. Measuring multiple isotopes of migratory species along flyway bottlenecks offers the opportunity to sample multiple populations and species whose tissues carry information at continental scales. We measured δ 2 H, δ 18 O, δ...
Article
Full-text available
One of the most economically important grapevine diseases is Downy mildew (DM) caused by the oomycete Plasmopara viticola. A strategy to reduce the use of fungicides to compensate for the high susceptibility of V. vinifera is the selection of grapevine varieties showing pathogen-specific resistance. We applied a metabolomics approach to evaluate th...
Conference Paper
Full-text available
With wine fraud, being a widespread problem, the need for more sophisticated and precise analytical methods of its detection remains ever persistent. Nuclear magnetic resonance (NMR) spectroscopy has been widely used for analysis of wine in recent years, but wine musts were much less studied; in fact, only one paper dealt with the NMR spectra of ac...
Article
Full-text available
Direct lung administration of budesonide in combination with surfactant reduces the incidence of bronchopulmonary dysplasia. Although the therapy is currently undergoing clinical development, the lung distribution of budesonide throughout the premature neonatal lung has not yet been investigated. Here, we applied mass spectrometry imaging (MSI) to...
Article
Full-text available
Corticosteroids as budesonide can be effective in reducing topic inflammation processes in different organs. Therapeutic use of budesonide in respiratory diseases, like asthma, chronic obstructive pulmonary disease, and allergic rhinitis is well known. However, the pulmonary distribution of budesonide is not well understood, mainly due to the diffi...
Preprint
Naturally occurring stable isotope ratios in animal tissues allow estimation of species trophic position and ecological niche. Measuring multiple isotopes of migratory species along flyway bottlenecks offers the opportunity to sample multiple populations and species whose tissues carry information at continental scales. We measured δ ² H, δ ¹⁸ O, δ...
Article
The meadow spittlebug Philaenus spumarius, vector of the bacterium Xylella fastidiosa, relies on vibrational communication to accomplish mating: the female calls to establish a duet with a male. A deeper knowledge of the species’ reproductive biology and behaviour would provide useful information for developing control techniques based on principle...
Article
In preterm infants, InSurE (Intubation–Surfactant–Extubation) and LISA (less invasive surfactant administration) techniques allow for exogenous surfactant administration while reducing lung injury associated with mechanical ventilation. We compared the acute pulmonary response and lung deposition of surfactant by LISA and InSurE in surfactant-deple...
Article
Full-text available
Background Drug mass spectrometry imaging (MSI) data contain knowledge about drug and several other molecular ions present in a biological sample. However, a proper approach to fully explore the potential of such type of data is still missing. Therefore, a computational pipeline that combines different spatial and non-spatial methods is proposed to...
Article
Full-text available
Plasmopara viticola is the causal agent of grapevine downy mildew (DM). DM resistant varieties deploy effector-triggered immunity (ETI) to inhibit pathogen growth, which is activated by major resistance loci, the most common of which are Rpv3 and Rpv12. We previously showed that a quick metabolome response lies behind the ETI conferred by Rpv3 TIR-...
Article
Scope To identify reliable biomarkers of food intake (BFIs) of pulses. Methods and results A randomized crossover postprandial intervention study was conducted on 11 volunteers who consumed lentils, chickpeas and white beans. Urine and serum samples were collected at distinct postprandial time points up to 48 h, and analyzed by LC‐HR‐MS untargeted...
Article
Full-text available
Background: Apples are rich in bioactive polyphenols and fiber. Evidence suggests that consumption of apples or their bioactive components is associated with beneficial effects on lipid metabolism and other markers of cardiovascular disease (CVD). However, adequately powered randomized controlled trials are necessary to confirm these data and expl...
Article
Casein δ34S of 725 samples of cheese from all over the world were measured using IRMS. δ34S alone made it possible to establish characteristic ranges of values for two types of Italian cheese (Grana Padano PDO and Parmigiano Reggiano PDO) and also for the different regions and provinces of both the Grana Padano PDO and the Parmigiano PDO zones. Mor...
Article
Full-text available
Background: The amount of surfactant deposited in the lungs and its overall pulmonary distribution determine the therapeutic outcome of surfactant replacement therapy. Most of the currently available methods to determine the intrapulmonary distribution of surfactant are time-consuming and require surfactant labelling. Our aim was to assess the pot...
Conference Paper
The cultivated Eurasian grapevine (Vitis vinifera L.) is highly susceptible to downy mildew (DM) – caused by the biotrophic oomycete Plasmopara viticola (Berk. & M.A. Curtis) Berl. & De Toni – the major disease of temperate-humid climates among various pathogen threats. DM control relies mainly on the massive use of fungicides leading to environmen...
Article
Sea fennel is an herbaceous aromatic and edible halophyte, naturally occurring in coastal areas of the Mediterranean basin. Besides its scientific interest as salt-tolerant species it exhibits considerable nutritional value and economical potential. As sea fennel is distributed in maritime areas, where natural iodine is available in high concentrat...
Article
Full-text available
Introduction Current markers of Parkinson’s disease (PD) fail to detect the early progression of disease state. Conversely, current omics techniques allow the investigation of hundreds of molecules potentially altered by disease conditions. Based on evidence previously collected by our group in a mouse model of PD, we speculated that a particular s...
Article
Chymosin is a protease that curdles the milk casein. Animal rennet was the first discovered source of chymosin and its use is mandatory for the production of PDO cheeses such as Parmigiano Reggiano and Grana Padano. Of the alternatives, fermentation-produced chymosin is the most competitive because it functions in a similar way, but is much cheaper...
Article
Full-text available
The development of new resistant varieties to the oomycete Plasmopara viticola (Berk.& Curt) is a promising way to combat downy mildew (DM), one of the major diseases threatening the cultivated grapevine (Vitis vinifera L.). Taking advantage of a segregating population derived from “Merzling” (a mid-resistant hybrid) and “Teroldego” (a susceptible...
Article
Enhancing drug penetration in solid tumors is an interesting clinical issue, of considerable importance. In pre-clinical research mass spectrometry imaging is a promising technique to visualize drug distribution in tumors in different treatment conditions and its application in this field is rapidly increasing. However, in view of the huge variabil...
Article
Full-text available
Compound identification is the main hurdle in LC-HRMS-based metabolomics, given the high number of ‘unknown’ metabolites. In recent years, numerous in silico fragmentation simulators have been developed to simplify and improve mass spectral interpretation and compound annotation. Nevertheless, expert mass spectrometry users and chemists are still n...
Article
European law requires a designation of origin for virgin and extra virgin olive oils (at least in terms of EU/non-EU provenance). Stable isotope ratios have been successfully applied to determine the geographical origin of olive oils, but never to distinguish EU and non-EU oils. In this study ²H/¹H, ¹³C/¹²C and ¹⁸O/¹⁶O ratios were analysed in bulk...
Article
Full-text available
The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional s...
Article
Mass spectrometry imaging is a valuable tool for visualizing the localization of drugs in tissues, a critical issue especially in cancer pharmacology where treatment failure may depend on poor drug distribution within the tumours. Proper preprocessing procedures are mandatory to obtain quantitative data of drug distribution in tumours, even at low...
Article
Full-text available
Background The multidisciplinary nature of nutrition research is one of its main strengths. At the same time, however, it presents a major obstacle to integrate data analysis, especially for the terminological and semantic interpretations that specific research fields or communities are used to. To date, a proper ontology to structure and formalize...
Chapter
Liquid chromatography-mass spectrometry (LC-MS) untargeted experiments require complex chemometrics strategies to extract information from the experimental data. Here we discuss “data preprocessing”, the set of procedures performed on the raw data to produce a data matrix which will be the starting point for the subsequent statistical analysis. Dat...
Article
Full-text available
Background The ability of finding complex associations in large omics datasets, assessing their significance, and prioritizing them according to their strength can be of great help in the data exploration phase. Mutual Information based measures of association are particularly promising, in particular after the recent introduction of the TICe and M...
Article
Multivariate techniques based on projection methods such as Principal Component Analysis and Partial Least Squares (PLS) regression are widely applied in metabolomics. However, the effects of confounding factors and the presence of specific clusters in the data could force the projection to produce inefficient representations in the latent space, p...
Preprint
Full-text available
Background: The ability of finding complex associations in large omics datasets, assessing their significance, and prioritizing them according to their strength can be of great help in the data exploration phase. Mutual Information based measures of association are particularly promising, in particular after the recent introduction of the TICe and...
Article
Full-text available
Downy mildew (Plasmopara viticola) is one of the most destructive diseases of the cultivated species Vitis vinifera. The use of resistant varieties, originally derived from backcrosses of North American Vitis spp., is a promising solution to reduce disease damage in the vineyards. To shed light on the type and the timing of pathogen-triggered resis...