Dettagli

Pubblicato: 10 Giugno 2021

Please visit the new version of LipiOne 2.0 at lipidone.eu.

Description

GENERAL DESCRIPTION

LipidOne, a freely available software that processes lipidomics data to help researchers to find new relationships between lipid profile and the activity of enzymes/genes involved.

LipidOne, automatically highlights all qualitative and quantitative changes in lipid building blocks both among all detected lipid classes and among experimental groups.  Thanks to LipiOne, the discovered differences in lipid building blocks can be easily linked to the activity of specific enzyme classes and or gene expression.

CITATION

Please, cite our work as:

Roberto Maria Pellegrino, Matteo Giulietti, Husam B R Alabed, Sandra Buratta, Lorena Urbanelli, Francesco Piva, Carla Emiliani, LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario, Bioinformatics, 2021; btab867, https://doi.org/10.1093/bioinformatics/btab867

CONTACT

For general questions concerning the use of the software please contact Roberto Maria Pellegrino (Questo indirizzo email è protetto dagli spambots. È necessario abilitare JavaScript per vederlo.)

For problems with installation, operation, software compatibility contact Matteo Giulietti (Questo indirizzo email è protetto dagli spambots. È necessario abilitare JavaScript per vederlo.)

Download

Click here to download

LipidOne is an executable file that does not require installation. Follow the instructions below and try working with our example datasets.

Instruction:

a) For the first time only, the user must install the Gnuplot graphics libraries. They can be downloaded free of charge from: https://sourceforge.net/projects/gnuplot/files/gnuplot/5.4.2;

b) Download LipidOne and place it in a folder of the user's choice.

c) Double click on the icon to start LipidOne.

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*) We would like to thank Dmitry Karasik and colleagues for the development of the Perl Prima library (http://www.prima.eu.org/), which we used for the development of the Graphical User Interface of LipidOne.

**) We also thank Thomas Williams and colleagues for their GNUPLOT graphical library (http://www.gnuplot.info/), useful for the creation of the LipidOne bar graphs.

Dataset

Try and explore some example datasets with LipidOne.

RETINA: Trzeciecka, A. et al. (2019) Comparative lipid profiling dataset of the inflammation-induced optic nerve regeneration. Data in Brief, 2352-3409.

FUNGUS: Lipid profiling of fungus (our internal, unpublished results).

ALGAE: Lipid profiling of algae from Riken Demonstration Files (http://prime.psc.riken.jp/compms/msdial/main.html).

Note: If the lipid annotation of your dataset does not comply with the LSI guidelines*, you can convert your data with LipidLynxX Converter.

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*) Liebisch,G. et al. (2020) Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures. Journal of Lipid Research, 61, 1539-1555.

How to use

Three-step LipidOne workflow

1) Data upload: the user must select a data matrix (txt or csv tab delimited file) containing the names and concentrations in each lipid sample detected (see example dataset). The accepted lipid nomenclature is the "molecular species level" or "sn-position level" as reported by the Lipidomics Standards Initiative (LSI) Guidelines.

2) Query selection: The user starts to explore the dataset using seven types of analysis and dynamic context-dependent menus.

3) Get results: all graphs and tables can be exported.

Click here to download the quick guide 

License

GENERAL STATEMENT

LipidOne is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

DISCLAIMER

LipidOne is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

CONTACT

For general questions concerning the use of the software please contact Roberto Maria Pellegrino (Questo indirizzo email è protetto dagli spambots. È necessario abilitare JavaScript per vederlo.)

For problems with installation, operation, software compatibility contact Matteo Giulietti (Questo indirizzo email è protetto dagli spambots. È necessario abilitare JavaScript per vederlo.)

Dettagli

Pubblicato: 20 Luglio 2023

The group of Integrated Physiology and Preclinic took its first steps in October 2015 with the SIR funded project “Novel nanoparticles-based approach to brain cancer therapy”. The group consists of six units that interact synergistically with the aim of research, teaching, third mission and service to companies. The related laboratories are equipped with instruments that have been purchased starting from 2015, in relation to the funded projects, while some are on loan for free use, made available by companies with which the group collaborates through third mission and service activities. The personnel belonging to the group consists of Associate Professor Bernard Fioretti, three post-doc researchers, five PhD students and a variable number of graduate and undergraduate students from the master’s degree courses in biology and biotechnology, Food Economy and Culture (ECOCAL) and Agricultural Food Science and Technology (STAGAL).

Research areas

The areas of interest are the study of ion channels through the patch-clamp technique and functional imaging on the themes of fertility, anti-tumor therapy study and nanomedicine, and for the development of nutraceutical products.

Unit of Electrophysiology. The electrophysiology unit aims to study the electrical activity of ion channels and how they are influenced by interaction with external agents such as molecules and nanoparticles.

Unit of Functional Imaging. The functional imaging unit aims to study the electrical activity of cells using calcium indicators through microscopy techniques.

Unit of Cellular and Molecular Biology. The cellular and molecular biology unit deals with the culture and preparation of cells to be used for electrophysiology and functional imaging studies. It also deals with proteomics and metabolomics as support activities for the interpretation of results obtained from electrophysiology and functional imaging units.

Unit of Nanocompounds. The nanocompounds unit deals with the synthesis of organic molecules and nanoparticles and their conjugation with organic molecules of biomedical interest.

Unit of Food Analytical Chemistry. The analytical chemistry unit performs analysis of nutraceutics and provides support activities to the group research lines, using chromatography techniques, mass spectrometry and UV-Vis spectrophotometry.

Unit of Molecular Dynamics and modeling. The molecular dynamics and modeling unit deals with the development of models for the analysis and processing of data produced by other units. It also deals with the study of chemical properties related to the systems studied by electrophysiology and functional imaging units through classical, quantum-chemical and molecular dynamics techniques.

Staff

Prof. Bernard Fioretti, Associate Professor

Dr. Federico Palazzetti, Senior Scientist

Dr. Francesco Ragonese, Post-Doc

Dr. Paola Sabbatini, Post-Doc

Dr. Andrea Biagini, PhD Student

Dr. Concetta Caglioti, PhD Student

Dr. Elko Gliozheni, PhD Student

Dr. Paola Quellari, PhD Student

Dr. Luana Sallicandro, PhD Student

Funded Projects

2023 - “Valorizzazione del potenziale terapeutico del resveratrolo nella medicina personalizzata mediante combinazione con altri principi attivi in formulazioni innovative – VAPORE”. Funded by Ministero per le Imprese e il Made in Italy (MIMIT). (Local coordinator: Bernard Fioretti)

2023 – “Ruolo della eccitabilità sensoriale ovarica nella fisiopatologia della follicologenesi - The Nova Study” Supported by Ministero per l’Università e la ricerca (MUR) by PRIN 2022 program (202294JF88). (Principal investigator: Bernard Fioretti)

2021-2022 “Studio del rapporto struttura-funzione della proteina E di SARS-CoV-2 per lo sviluppo di agenti terapeutici nel trattamento del Covid-19” Supported by Ministero per l’Università e la ricerca (MUR) by PRIN 2020 program (FISR2020IP_03461). (Principal investigator: Bernard Fioretti)

2021- “Studio dell’impatto delle radiazioni nelle missioni spaziali e del potenziale terapeutico del resveratrolo sulla fisiologia della riproduzione femminile” Supported by Agenzia Spaziale Italiana (ASI). Eligible for funding, pending ranking list update. (Principal investigator: Bernard fioretti).

2019 – “Accordo quadro con S&R Farmaceutici S.p.A.” (Third mission activity).

2018-2022 “Exploring novel approaches to NOTCH1 targeting as therapy for chronic lymphocytic leukemia” Supported by AIRC (External collaborator).

2015-2019 “Novel nanoparticles-based approach to brain cancer therapy” Supported by Ministero dell’Istruzione, dell’Università e della Ricerca (MIUR) SIR, Scientific Independence of young Researchers, 2014 (RBSI144EUA) Principal Investigator: Bernard Fioretti.

2015-2019 “Origin of Chiral Discrimination” Supported by Ministero dell’Istruzione, dell’Univeristà e della Ricerca (MIUR) SIR, Scientific Independence of young Researchers, 2014 (RBSI14U3VF) Principal Investigator: Federico Palazzetti.

 Recent Publications

1. Adamo, F.M.; Silva Barcelos, E.C.; De Falco, F.; Dorillo, E.; Rompietti, C.; Sorcini, D.; Stella, A.; Del Papa, B.; Baldoni, S.; Esposito, A.; Geraci, C.; Arcaleni, R.; Pennetta, C.; Ragonese, F.; Moretti, L.; Mameli, M.; Di Ianni, M.; Rosati, E.; Fioretti, B. and Sportoletti, P.
Therapeutic Targeting Potential of Novel Silver Nanoparticles Coated with Anti-CD20 Antibody against Chronic Lymphocytic Leukemia. Cancers (2023) 15 3618.
DOI: 10.3390/cancers15143618

2. Caglioti, C., Iannitti, R., Ceccarelli, G., Selan, L., Artini, M., Papa, R., Malvasi, A., Gentile, R., Del Bianco, D., Apone, F., Angelini, P., Palazzetti, F. and Fioretti B.
Cranberry/Chondroitin Sulfate Co-precipitate as a New Method for Controlling Urinary Tract Infections, Antibiotics (2023) 12 (6) 1053.
DOI: 10.3390/antibiotics12061053

3. Zucchi, A., Claps, F., Pastore, A.L., Perotti, A., Biagini, A., Sallicandro, L., Gentile, R., Caglioti, C., Palazzetti, F., Fioretti, B.
Focus on the Use of Resveratrol in Bladder Cancer, International Journal of Molecular Sciences(2023) 24 (5), art. no. 4562, . Cited 1 time.
DOI: 10.3390/ijms24054562

4. Bachmann, M., Rossa, A., Varanita, T., Fioretti, B., Biasutto, L., Milenkovic, S., Checchetto, V., Peruzzo, R., Ahmad, S.A., Patel, S.H., Lukowski, R., Edwards, M.J., Ceccarelli, M., Gulbins, E., Zoratti, M., Mattarei, A., Szabo, I.
Pharmacological targeting of the mitochondrial calcium-dependent potassium channel KCa3.1 triggers cell death and reduces tumor growth and metastasis in vivo, Cell Death and Disease (2022) 13 (12), art. no. 1055, .
DOI: 10.1038/s41419-022-05463-8

5. Caglioti, C., Monarca, L., Pennetta, C., Ragonese, F., Palazzetti, F., Fioretti, B.
Exploring the potential energy surface of interacting pairs of Ag dimers
AIP Conference Proceedings(2022) 2611, art. no. 020012, .
DOI: 10.1063/5.0119913

6. Battaglia, R., Caponnetto, A., Caringella, A.M., Cortone, A., Ferrara, C., Smirni, S., Iannitti, R., Purrello, M., D’amato, G., Fioretti, B., Di Pietro, C.
Resveratrol Treatment Induces Mito-miRNome Modification in Follicular Fluid from Aged Women with a Poor Prognosis for In Vitro Fertilization Cycles, Antioxidants
(2022) 11 (5), art. no. 1019, .
DOI: 10.3390/antiox11051019

7. Caglioti, C., Palazzetti, F., Monarca, L., Lobello, R., Ceccarini, M.R., Iannitti, R.G., Russo, R., Ragonese, F., Pennetta, C., De Luca, A., Codini, M., Fioretti, B.
LY294002 Inhibits Intermediate Conductance Calcium-Activated Potassium (KCa3.1) Current in Human Glioblastoma Cells, Frontiers in Physiology (2022) 12, art. no. 790922, .
DOI: 10.3389/fphys.2021.790922

8. Ceccarini, M.R., Codini, M., Cataldi, S., Fioretti, B., Brecchia, G., Albi, E., Beccari, T.
Licium Barbarum cultivated in Italy: Chemical characterization and nutritional evaluation, Italian Journal Food of Science (2022) 34 (3), pp. 59-65.
DOI: 10.15586/ijfs.v34i3.2242

9. Caglioti, C., De Luca, A., Pennetta, C., Monarca, L., Ragonese, F., Sabbatini, P., Lago, M.N.F., Lombardi, A., Palazzetti, F., Fioretti, B.
A Theoretical Study on trans-Resveratrol - Cu(I) Complex, Lecture Notes in Computer Sciences (2022) 13382 LNCS, pp. 237-248.
DOI: 10.1007/978-3-031-10592-0_18

10. Gerli, S., Della Morte, C., Ceccobelli, M., Mariani, M., Favilli, A., Leonardi, L., Lanti, A., Iannitti, R.G., Fioretti, B.
Biological and clinical effects of a resveratrol-based multivitamin supplement on intracytoplasmic sperm injection cycles: a single-center, randomized controlled trial, Journal of Maternal-Fetal and Neonatal Medicine (2022) 35 (25), pp. 7640-7648.
DOI: 10.1080/14767058.2021.1958313

11. Ragonese, F., Monarca, L., De Luca, A., Mancinelli, L., Mariani, M., Corbucci, C., Gerli, S., Iannitti, R.G., Leonardi, L., Fioretti, B.
Resveratrol depolarizes the membrane potential in human granulosa cells and promotes mitochondrial biogenesis, Fertility and Sterility (2021) 115 (4), pp. 1063-1073.
DOI: 10.1016/j.fertnstert.2020.08.016

12. Illiano, E., Trama, F., Zucchi, A., Iannitti, R.G., Fioretti, B., Costantini, E.
Resveratrol‐based multivitamin supplement increases sperm concentration and motility in idiopathic male infertility: A pilot clinical study, Journal of Clinical Medicine (2020) 9 (12), art. no. 4017, pp. 1-10.
DOI: 10.3390/jcm9124017

13. Iannitti, R.G., Floridi, A., Lazzarini, A., Tantucci, A., Russo, R., Ragonese, F., Monarca, L., Caglioti, C., Spogli, R., Leonardi, L., De Angelis, M., Palazzetti, F., Fioretti, B.
Resveratrol Supported on Magnesium DiHydroxide (Resv@MDH) Represents an Oral Formulation of Resveratrol With Better Gastric Absorption and Bioavailability Respect to Pure Resveratrol, Frontiers in Nutrition (2020) 7, art. no. 570047.
DOI: 10.3389/fnut.2020.570047

14. Menchetti, L., Curone, G., Andoni, E., Barbato, O., Troisi, A., Fioretti, B., Polisca, A., Codini, M., Canali, C., Vigo, D., Brecchia, G.
Impact of goji berries (Lycium barbarum) supplementation on the energy homeostasis of rabbit does: Uni‐ and multivariate approach, Animals (2020) 10 (11), art. no. 2000, pp. 1-19.
DOI: 10.3390/ani10112000

15. Cataldi, S., Arcuri, C., Lazzarini, A., Nakashidze, I., Ragonese, F., Fioretti, B., Ferri, I., Conte, C., Codini, M., Beccari, T., Curcio, F., Albi, E.
Effect of 1α,25(OH)2 vitamin D3 in mutant P53 glioblastoma cells: Involvement of neutral sphingomyelinase1, Cancers(2020) 12 (11), art. no. 3163, pp. 1-15.
DOI: 10.3390/cancers12113163

16. Menchetti, L., Brecchia, G., Branciari, R., Barbato, O., Fioretti, B., Codini, M., Bellezza, E., Trabalza-Marinucci, M., Miraglia, D.
The effect of Goji berries (Lycium barbarum) dietary supplementation on rabbit meat quality, Meat Science (2020) 161, art. no. 108018.
DOI: 10.1016/j.meatsci.2019.108018

17. Naureen, Z., Perrone, M., Paolacci, S., Maltese, P.E., Dhuli, K., Kurti, D., Dautaj, A., Miotto, R., Casadei, A., Fioretti, B., Beccari, T., Romeo, F., Bertelli, M.
Genetic test for the personalization of sport training, Acta Biomedica (2020) 91, art. no. e2020012, pp. 1-15.
DOI: 10.23750/abm.v91i13-S.10593

18. Dionigi, L., Ragonese, F., Monarca, L., Covino, S., de Luca, A., Iannitti, R.G., Bastioli, F., Moulas, A.N., Allegretti, M., Fioretti, B.
Focus on the use of resveratrol as an adjuvant in glioblastoma therapy, Current Pharmaceutical Design (2020) 26 (18), pp. 2102-2108.
DOI: 10.2174/1381612826666200401085634

19. Manfroni, G., Ragonese, F., Monarca, L., Astolfi, A., Mancinelli, L., Iannitti, R.G., Bastioli, F., Barreca, M.L., Cecchetti, V., Fioretti, B.
New insights on kca3.1 channel modulation, Current Pharmaceutical Design (2020) 26 (18), pp. 2096-2101.
DOI: 10.2174/1381612826666200316152645

Dettagli

Pubblicato: 21 Aprile 2020

XXXVIII cycle - A.A. 2022/23, 2023/24 and 2024/2025 (also valid for XXXVI and XXXVII cycles)

List of the ad-Hoc Courses Offered

List of the scientific Seminars offered for the PhD cycles XXXVIII, XXXVII and XXXVI

Dettagli

Pubblicato: 21 Aprile 2020

XXXIX cycle - A.A. 2023/24, 2024/25 and 2025/2026 (also valid for XXXVII and XXXVIII cycles)

List of the ad-Hoc Courses Offered