Biotechnologies PhD Course
- Details
Coordinator: Prof. Gianluigi Cardinali
Phone: +39.075.585.6478
E-Mail: This email address is being protected from spambots. You need JavaScript enabled to view it.
NEW Teaching 2024
Spring School on Biotechnologies 2024
A. Introduction
General aim of the PhD course in Biotechnologies is to provide a thorough background in biotechnological research, for purposes ranging from basic research to technology transfer. The programme comprises three curricula, namely “Medical Biotechnology”, “Molecular and Industrial Biotechnology” and “Biomaterials and Biodevices”.
B. Articulation in curricula
- Medical Biotechnologyis mainly focused on molecular and clinical diagnostics and development of innovative and customized therapies. The topics of the PhD program spans from the development of pharmacological tools to defeat a variety of diseases to the genetic processes that lead to organ regeneration. Active areas of research include molecular cell mechanisms in cancer, pharmacology of biotech drugs, cell biology (including stem cell biology), development of new medical devices. The educational objectives of the program encompass collaborative exchanges with national and international partners and internal classes on biotechnology disciplines.
- Molecular and Industrial Biotechnology focuses on active research areas such as: advanced genetic and microbial biotechnologies, cellular technologies for manipulation of stem cells, gene expression and cloning in prokaryotic and eukaryotic cells, biotechnological large scale production of useful bio-molecules, bio-based products, and recombinant cells; genetic, genomic, proteomic and cellular function analyses through technological approaches in silico, ex-vivo and in vivo; molecular and cellular technologies for biomedical application and for drug discovery, biotechnological strategies for industrial processes linked to chemistry, green-chemistry, biochemistry, supervision and quality control of biotechnological systems. Analysis and management of the biodiversity, environmental sustainability with special focus on the biotechnological productions.
- Biomaterials and Biodevicesis primarily concerned with the design and development of smart biomaterials that, together with the synthesis of nanostructured sensors, is opening new frontiers to biotechnology. Indeed, biomaterials and bio-devices represent an emerging research area applicable in all fields of biotechnology (red, green and white), playing a significant role in food and nutrition sciences, biomedicine, agriculture, imaging and many other technological fields.
C. Educational Objectives
The objectives integrated with the three-year teaching and research activities for the thesis, on site or abroad, are:
1st year: learning of theoretical and experimental knowledge with lessons and laboratory activities, under tutoring.
2nd year: development of the research project, participation in conferences, participation in teaching and training activities.
3rd year: research and continuous updating, drafting of the experimental thesis.
D. Learning Activities
Students are currently required to achieve a total of 50 credit forming units (CFU).
All students will present a yearly learning plan to the tutor and to the PhD faculty for approval.
Students can attend different types of courses and of experiences as listed below:
- Courses of the doctorate in Biotechnology (see Learning activities)
- Traineeship abroad: Students are requested to spend at least three months in foreigner institutions during the three years.
- Courses within the University of Perugia. Only courses at Master Degree level (Laurea Magistrale) are allowed and exclusively for topics lacking from the topics attended by the student prior to his/her enrolment in the PhD program.
- Linguistic, Information Technology and Soft Skills courses from the University of Perugia and other institutions
- Courses from other PhD programs
- Other external instruction programs out of the University of Perugia
- Seminars, meetings and congresses
Attribution of CFU for different learning activities
- Courses of the doctorate: 1 CFU / day
- Meetings, Congresses and Workshops on topics related to the PhD program: 0.5 CFU/day
- Seminars on topics related to the PhD program: 0.2 CFU
- Supporting teaching activity carried out by the student :1 CFU / 6 hrs
- Tutorship carried out by the student 1 CFU / 25 hrs.
- Traineeship and stages abroad: 5 CFU /month
Learning activities Archive:
Learning activities XXXVII Cycle
Learning activities XXXVI Cycle
Learning activities XXXV Cycle
Learning activities XXXIV Cycle
All materials are available in the Unistudium page of the doctorate.
Lectures in remote mode will be held in the Teams Room of the doctorate.
Round table: Biotecnologie e Società 2020
Round table: Biotecnologie e Società 2019
Winter School on Biotechnology 2018 (5 CFU)
E. Competences
E1. Linguistics
The Doctoral Course offers doctoral students the opportunity to participate to foreign language courses held at the University Language Canter (CLA). The levels of language courses offered at the CLA refer to the Common European Framework of Reference (CEFR). The language courses may have a six-month (10 ECTS) or an annual (13 ECTS) duration. At the end of the course the level achieved in the individual language skills will be assessed.
E2. Information technology
The Doctoral Course offers doctoral students the opportunity to participate in computer and labs already offered in other University study courses. Specific courses will also be organized in modules of 1 CFU (for example the use of software for data analysis, word processing programs, archiving and import programs for bibliographic data; in-depth study on databases and their consultation). For these courses, a verification of the level of knowledge acquired will be provided.
E3. Management of research, knowledge of research systems and funding systems.
The Doctoral Course offers the opportunity to participate to 1 CFU courses on research management, knowledge of research systems and funding systems. The courses will deal with: research design and development techniques; drafting and management of financial plans for research projects; project management by stages of work progress and their reporting; management of relations with lenders. The courses include a final check.
E4. Enhancement of research results and intellectual property
The PhD course offers the opportunity to participate to six 1-CFU courses on the enhancement of research and intellectual property. The 6 courses will cover: the transition from basic to applied research; research enhancement techniques; the funding of applied research; the protection of intellectual property; the intervention of universities in favour of patents; business creation and research spin-offs. The courses include a final verification.
F. Job and career opportunities
The aim of the doctorate is to develop skills and deep understanding in the experimental design, analyses and data management in order to achieve autonomy research and project management. This will allow:
1. Allocation in the field of research (universities and other public and private research institutes);
2. Allocation in biotechnological industries, in public and private companies / entities operating in the service sector and specifically: research and development laboratories and production and quality control departments in biotechnological companies and other companies interested in biotechnological innovation such as chemical companies (fine chemicals, bioenergetics, innovative materials), pharmaceuticals, agri-foodstuffs;
3. Allocation within the NHS.
G. Agreements and cooperation with third parties
G1. Foreign universities affiliated
- THE HEBREW UNIVERSITY OF JERUSALEM - Israel
- NICOLAUS COPERNICUS UNIVERSITY OF TORUN - Poland
G2. Other associated / affiliated Bodies / Companies
- ANGELANTONI LIFE SCIENCE
2.COSTA D'ORO S.P.A.
G3. Other bodies / companies with collaborations
- Brunner Tomas Universität - Konstanz, Germany
- Saarland University, Germany
- Libert Claude Universiteit Gent, Belgium
- Katholieke Universiteit Leuven, Belgium
- Jurga Stefan - Nanobiomed Center- Poland
- Ospedale Casa Sollievo della Sofferenza - Italy
Useful documents and links
Regolamento del Dottorato in Biotecnologie
Regolamento di Ateneo dei corsi di Dottorato di Ricerca
Training activities
- Details
Training activities scheduled in the academic year 2023/2024
Second semester
| Teaching module | hours | cfu | teacher | SSD | Year | Period | Date | |
| Lab safety: chemical and biological risks | 3 | 0.5 | Daniele Del Buono (docente del DSA3 UNIPG, corso mutuato) | AGR/13 | 1° | Second semester | 8-9 April, 14:30-17:30 |
|
| How to write a scientific paper | 3 | 0.5 | Antonio Michelucci (componente del Collegio dei docenti) | BIO/09 | 1° | Second semester | 10-May-24 | |
| MS Office | 6 | 1 | Massimo Lorenzoni (componente del Collegio dei docenti) | BIO/07 | 1° | Second semester | 16-18-23 April | |
| Statistics Using R with Biological Examples | 12 | 2 | Gianandrea La Porta (tecnico del DCBB UNIPG esperto di analisi statistica) | - | 1° | Second semester | September/October2024 | |
| LIFE Programme: the EU’s funding instrument for the environment | 6 | 1 | Matteo Pallottini (assegnista del DCBB UNIPG che fa parte del progetto LIFE IMAGINE ) | - | 1° | Second semester | 3, 10, 17 May 2024 | |
| Monitoring and Assessing Arctic Climate Change | 9 | 1.5 | David Cappelletti (docente esperto del DCBB UNIPG) | CHIM/07 | 2° | Second semester | 19-20-21 June | |
| Methodologies for the evaluation of the biological risk in the built environment | 6 | 1 | Ermanno Federici (componente del Collegio dei docenti) | BIO/19 | 2° | Second semester | 17-24 May | |
| Synergistic effects of climate change and biological invasions in Mediterranean freshwater ecosystems | 6 | 1 | Antonella Carosi (RTDA del DCBB UNIPG) | BIO/07 | 2° | Second semester | 18-21-25 March 9.00 - 11.00. |
|
| Microbial biofilms: biological and technological aspects | 6 | 1 | Donatella Pietrella (componente del Collegio dei docenti) | MED/07 | 2° | Second semester | 28 June, 5 e 8 July 15:00-17:00 |
|
| Phylogenetic reconstruction from uniparentally inherited genomes | 6 | 1 | Hovirag Lancioni (componente del Collegio dei docenti) |
BIO/18 |
2° | Second semester | 8 e 15 April |
First semester
| Teaching module | hours | CFU | teacher | SSD | Year | Period | Date | |
| Bibliographic databases, principles of bibliometrics and bibliography management | 3 | 0.5 | Gianandrea Salerno (docente del DSA3 UNIPG, corso mutuato) | AGR/11 | 1° | First semester | contact Lecturer | |
| Atomic simulations and multiscale modeling in the understanding of the structure-function relationship of biological macromolecules | 6 | 1 | Luigi Catacuzzeno (componente del Collegio dei docenti) | BIO/09 | 2° | First semester | November 27, Dicember 1 and 4, from 16.00 to 18.00 | |
| Ecology of zoonoses: environmental changes and emergence of new viruses | 6 | 1 | Barbara Camilloni (componente del Collegio dei docenti) | MED/07 | 2° | First semester | February 8 and 22, 2024 | |
| Methodologies for the evaluation of the biological risk in the built environment | 6 | 1 | Ermanno Federici (componente del Collegio dei docenti) | BIO/19 | 2° | First semester | February 15 and 29 2024 | |
LipidOne - an in-depth and user friendly lipidomic data analysis tool
- Details
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 (This email address is being protected from spambots. You need JavaScript enabled to view it.)
For problems with installation, operation, software compatibility contact Matteo Giulietti (This email address is being protected from spambots. You need JavaScript enabled to view it.)
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.
*) 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 (This email address is being protected from spambots. You need JavaScript enabled to view it.)
For problems with installation, operation, software compatibility contact Matteo Giulietti (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Organization
- Details
Director: Prof. Alceo Macchioni, +39.075.585.5579, This email address is being protected from spambots. You need JavaScript enabled to view it.
Vice-Director: Prof.ssa Carla Emiliani, +39.075.585.7436, This email address is being protected from spambots. You need JavaScript enabled to view it.
Administration: Dr. Cristina Mencolini, +39.075.585.5504, This email address is being protected from spambots. You need JavaScript enabled to view it.
Comitato dipartimentale VQR (C-Dip VQR):
Scientific Research Coordinator: Prof. David Michele Cappelletti
Third Mission: Prof. Luigi Vaccaro
Members: Proff. Cristiano Zuccaccia, Marco Paolantoni, Hovirag Lancioni, Silvana Piersanti
K-users: Dott.ssa Daniela Bonelli, Dott. Gianandrea La Porta
Administrative office: This email address is being protected from spambots. You need JavaScript enabled to view it.
Sig.ra Patrizia Celesti, +39.075.585.5700, This email address is being protected from spambots. You need JavaScript enabled to view it.
Sig.ra Silvana Tifi, +39.075.585.5700, This email address is being protected from spambots. You need JavaScript enabled to view it.
Sig.ra Nicoletta Tomassini, +39.075.585.5505, This email address is being protected from spambots. You need JavaScript enabled to view it.
Dr. Elisabetta Vescarelli, +39.075.585.5505, This email address is being protected from spambots. You need JavaScript enabled to view it.
Teaching office: This email address is being protected from spambots. You need JavaScript enabled to view it.
Dott.ssa Mariangela Aguzzi, +39.075.585.5635, This email address is being protected from spambots. You need JavaScript enabled to view it.
Sig.ra Lorena Canonico, +39.075.585.5633, This email address is being protected from spambots. You need JavaScript enabled to view it.
Sig.ra Claudia Mastroforti, +39.075.585.5643 This email address is being protected from spambots. You need JavaScript enabled to view it.
Reception (from Monday to Friday, from 7.30 to 19.30)
Elce (via Elce di Sotto, 8):
Sig. Leonardo Mortini, +39.075.585.5604, This email address is being protected from spambots. You need JavaScript enabled to view it.
Sig. Paolo Mazzola, +39.075.585.5604, This email address is being protected from spambots. You need JavaScript enabled to view it.
Sig. Marco Berta, +39.075.585.5604, This email address is being protected from spambots. You need JavaScript enabled to view it.
Giochetto (via del Giochetto):
Sig. Gianni Norgini, +39.075.585.7495, This email address is being protected from spambots. You need JavaScript enabled to view it.
Sig.ra Lidia Bucciferro, +39.075.585.7343, This email address is being protected from spambots. You need JavaScript enabled to view it.
Sig. Lucio Burani, +39.075.585.7495, This email address is being protected from spambots. You need JavaScript enabled to view it.
Sig.ra Flavia Passeri, This email address is being protected from spambots. You need JavaScript enabled to view it.
General Services:
Catalogo della ricerca IRIS - Supporto alla ricerca
Dr. Daniela Bonelli (Referente Area Chimica), +39.075.585.5550-5613, This email address is being protected from spambots. You need JavaScript enabled to view it.
Dr. Gianandrea La Porta (Referente Area Biologia), +39.075.585.5710, This email address is being protected from spambots. You need JavaScript enabled to view it.
Servizio smaltimento rifiuti - Laboratori chimici (SISTRI)
Dr. Antonio Cinti
Sig. Andrea Nicoziani
Servizio smaltimento rifiuti - Laboratori biologici (SISTRI)
Dr. Loretta Mancinelli
Servizi Informatici
Dr. Carlo Manuali, +39.075.585.5213, This email address is being protected from spambots. You need JavaScript enabled to view it.
Servizio Acquisto Alcooli per i Laboratori Biologici
Dr. Silvia Belia, +39.075.585.5761, This email address is being protected from spambots. You need JavaScript enabled to view it.
Sig. Antonello Sotgiu, +39.075.585.5721, This email address is being protected from spambots. You need JavaScript enabled to view it.
Servizio Acquisto Alcooli per i Laboratori Chimici
Sig. Remo Suriani, +39.075.585.5519, This email address is being protected from spambots. You need JavaScript enabled to view it.
Laboratorio Meccanico (piano 2° seminterrato edificio B)
Sig. Andrea Nicoziani, +39.075.585.5603, This email address is being protected from spambots. You need JavaScript enabled to view it.
Servizio Gas Centralizzati
Sig. Nicomede Pelliccia, +39.075.585.5571, This email address is being protected from spambots. You need JavaScript enabled to view it.
Teaching Activity – Offerta Formativa Prevista ed Erogata
- Details
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