Dipartimento di Medicina e Chirurgia
Università degli Studi di Perugia

• The Research Doctorate represents a post-graduate advanced training course on research topics of high social impact and wide-ranging concerning pathologies which, epidemiologically, occupy the first places in terms of diffusion and, according to WHO projections, are destined to increase. Infectious and inflammatory diseases represent a serious public health problem and are among the main causes of mortality and morbidity worldwide. In these pathologies there is a failure or chronicity of the immune response, which instead would have the potential ability to successfully cope with their onset or progression. In order to treat or prevent inflammatory or infectious states it is necessary to understand in depth the mechanisms underlying the onset of the pathology, how the immune system controls inflammation, the strategies responsible for evasion from the immune system, the effects on the host following the activation of an immune response directed against itself (autoimmune disease) and the risk factors predisposing to the pathology. The Doctorate intends to attract young researchers with the aim of training and motivating a new generation of scientists by transferring to them knowledge and technical skills that will allow them to study infectious diseases and the activation of the immune response in innovative, exciting and productive ways. The doctoral course provides skills in strategic research areas at an international level, such as: i) the study of basic pathogenetic mechanisms that could lead to the identification of new diagnostic tools, the development of vaccines and other interventions for prevention and control of infectious diseases and the identification of new therapeutic targets; ii) the analysis of immune and metabolic responses in inflammatory and immune diseases as possible targets for new pharmacological therapies and for the development of personalized therapies; iii) the study of rare diseases; iv) the identification of risk factors for the prevention of chronic-degenerative diseases. The Doctorate promotes, also thanks to the countless international collaborations activated by the Doctorate teachers, a multidisciplinary approach that includes the omics sciences (transcriptomics, proteomics, metabolomics, lipidomics, metagenomics, secretomics) in association with the traditional biological sciences (immunology, molecular biology and cellular, microbiology, biochemistry, physiology, genomics, pathology, anatomy, pharmacology and public health), with the aim of evaluating the uses of research products for improving the health of the population. Infectious and immune-mediated diseases currently under study include malaria, toxoplasmosis, fungal (Candida and Aspergillus) and viral (coronavirus and other respiratory viruses) diseases, diabetes, obesity, cancer, autoimmune diseases, muscular dystrophy/atrophy and rare diseases. Further immunological studies focus on the genetic regulation of the immune response, the interaction between the innate immune system and gut microbial communities, and the function and regulation of cytokines involved in inflammation. The doctorate is divided into two different but interconnected curricula: Integrative biology of the host-pathogen relationship: The curriculum focuses on recent advances in the biology of infectious diseases and provides the basis for conducting research on these pathologies with both basic, translational or applicative implications. Integrated biological strategies in genetic, immuno-metabolic and oncological pathologies: The curriculum focuses on the acquisition of specific skills in the interface between immune and metabolic responses in oncological, autoimmune and genetic pathologies with the aim of developing innovative therapies. The approach to the various pathologies is translational and aims at the identification of biomarkers and possible therapeutic targets. The training project planned for the doctoral course has a high level of in-depth analysis and includes the following objectives: 1. Teaching activities and specific PhD seminars to acquire advanced knowledge in the biomedical field; training activities aimed at developing capabilities in the dissemination/communication of scientific results, technological transfer and entrepreneurship; multidisciplinary, transdisciplinary and interdisciplinary training activities; training activities aimed at gaining knowledge of European and international research frameworks. 2. Interaction with the national and international scientific community; 3. Acquisition of high professional level knowledge in the academic and industrial world.

• The main and specific objective of the Doctorate course is to train new generations of highly professional and multidisciplinary researchers in the field of inflammatory, immune and infectious diseases, capable of meeting and successfully tackling the scientific challenges represented by the knowledge of the human genome, inflammatory and infectious diseases, microorganisms and new and increasingly sophisticated technologies. In a transversal sense, the interdisciplinarity of the course and the important national and international collaborations of the Doctorate teachers will allow students to acquire knowledge in the field of innovative and cutting-edge preventive and therapeutic strategies (such as, for example, in the field of biopharmaceuticals and of personalized medicine) capable of counteracting the emerging challenges in the field of infectious diseases and inflammatory pathologies. The Doctorate will contribute to the creation of new links between Italian and foreign universities and the industrial world in a specialized scientific field, yet characterized by rapid evolution and multidisciplinarity. All doctoral students will be able to benefit from the interaction and participation/collaboration with the partner companies. In this context, students will have the opportunity to develop applied research projects and participate in the transfer of scientific results to the industrial world. The Doctorate course is divided into 2 curricula which provide for the development of complementary skills in the field of basic, pre-clinical and clinical research and in academic, national and international, and corporate contexts. The students themselves will become protagonists and collaborators of the Doctoral course, proposing and managing scientific research themselves and in collaboration with the course teachers. The Doctorate aims to broaden and deepen the scientific knowledge of doctoral students also through a structured training course developed in collaboration with teachers with a broad national and international scientific profile. At the end of the Doctorate, students will have acquired familiarity with the most innovative technologies of cellular and molecular biology. Furthermore, they will possess notions of a high professional level in the topics of biology of the host-pathogen relationship, inflammatory-based pathologies, immunogenetics and translational immunology and biostatistics, which will allow them to have a wide range of professional opportunities in the academic and industrial world.

At the end of the training course, doctoral students will have acquired high professional level knowledge regarding disciplines addressed during the Doctoral program and will be able to promote the advancement of scientific and technological knowledge, both in the academic and industrial fields. This will allow PhDs both access to a university career and placement in public and private research bodies, or in specialized companies (for example: pharmaceutical, biotechnological, nutraceutical companies and hospitals). The proposed training path and the international framework of the Doctorate will facilitate this process by providing students with the opportunity to access internationally prestigious post-doctoral scholarships, such as Marie-Curie grants and EMBO grants, or to national and international research programmes for young researchers (SIR, ERC starting grant, AIRC). Furthermore, the interaction and the study/research periods carried out at the partner companies will allow the PhD students to quickly come into contact with the industrial world and will provide a competitive advantage for possible hiring within the same companies. The Doctorate also lays the foundations for the possible creation of start-ups and spin-offs by young researchers. Finally, PhD students are regularly notified with calls for temporary or permanent positions issued by scientific associations, scientific journals, pharmaceutical industries and Italian and foreign universities. The implementation of a monitoring system for professional opportunities is envisaged and will be made available already during the PhD course.

Integrative biology of the host-pathogen relationship: The curriculum introduces students to recent advances in the biology of infectious diseases and provides the basis for conducting research on such diseases. The program focuses on the use of omics sciences (genomics, transcriptomics, proteomics, metagenomics, metabolomics, lipidomics, secretomics), traditional biological sciences such as molecular and cellular biology, immunology, genetics and epidemiological methodology. In particular, given the scientific expertise of several PhD supervisors, the research activities are focused on the study of fungi (Candida and Aspergillus), bacteria (with particular attention to drug-resistant bacteria), viral agents (coronaviruses and other respiratory viruses ) and protozoa (Plasmodium and Toxoplasma)..

Integrated biological strategies in genetic, immuno-metabolic and oncological pathologies: The curriculum focuses on the acquisition of specific skills in the interface between immune and metabolic responses in oncological, autoimmune and genetic pathologies, with the aim of developing innovative therapies. Great attention is paid to the immunosuppressive enzymes that catabolize amino acids and the role of immunometabolic genes in inflammatory and immune diseases. Moreover, the curriculum also focuses on understanding the cellular and molecular mechanisms involved in pathologies such as diabetes, obesity, cancer, autoimmune diseases, muscular dystrophy and atrophy, and diseases rare. The approach to the various pathologies is translational and aims at the identification of biomarkers and possible therapeutic targets.

The doctoral training path, aligned with the new guidelines: “Politiche di ateneo e programmazione dell’offerta formativa”, approved by the Academic Senate and the Board of Directors on 28 September 2023, is structured as follows:

• development of an INDIVIDUAL RESEARCH AND STUDY PROGRAMME under the guidance of multiple supervisors, referring to a specific disciplinary area among those on which the Course is focused;
• attendance of DOCTORAL LEVEL EDUCATIONAL ACTIVITIES, complementary to the research activity, for a minimum of 30 credits/three years, according to the indications of the College;
• attendance of OTHER TRAINING ACTIVITIES, which contribute to the student's education, but do not provide for the acquisition of credits.

RESEARCH AND INDIVIDUAL STUDY PROGRAM
Regarding the research program, the doctoral students are included in the activities of the research groups working in the facilities affiliated to the doctoral course (university departments and pharmaceutical companies). Doctoral students will follow a research program agreed with the professor responsible for the student's training and approved by the Doctoral Committee, and will actively participate in lab meetings and journal clubs. Furthermore, thanks to the extensive network of collaborations with other national and international universities and research bodies that the members of the Doctoral Committee maintain, doctoral students can participate in meetings for the definition of the various aspects of the research projects and for the evaluation of the accomplished results. In order to facilitate interactions and collaborations among doctoral students, regular meetings are also planned between doctoral students and researchers of the Department aimed at exchanging practical experiences and theoretical knowledge. The PhD student, in agreement with the supervisor, can participate in short internships and courses related to his/her the field of research, in other structures in Italy or abroad. Furthermore, the student can carry out the research project, for a maximum of 18 months, at prestigious international research laboratories.

DOCTORAL LEVEL EDUCATIONAL ACTIVITIES
Regarding the research program, the doctoral students are included in the activities of the research groups working in the facilities affiliated to the doctoral course (university departments and pharmaceutical companies). Doctoral students will follow a research program agreed with the professor responsible for the student's training and approved by the Doctoral Committee, and will actively participate in lab meetings and journal clubs. Furthermore, thanks to the extensive network of collaborations with other national and international universities and research bodies that the members of the Doctoral Committee maintain, doctoral students can participate in meetings for the definition of the various aspects of the research projects and for the evaluation of the accomplished results. In order to facilitate interactions and collaborations among doctoral students, regular meetings are also planned between doctoral students and researchers of the Department aimed at exchanging practical experiences and theoretical knowledge. The PhD student, in agreement with the supervisor, can participate in short internships and courses related to his/her the field of research, in other structures in Italy or abroad. Furthermore, the student can carry out the research project, for a maximum of 18 months, at prestigious international research laboratories.

DOCTORAL LEVEL EDUCATIONAL ACTIVITIES

The educational activities planned for the entire three-year cycle include:

The teaching activities are mainly delivered in English, even remotely in synchronous and asynchronous modes.

The details of the educational activities provided are reported in the reference cycle folder.

TRAINING ACTIVITIES

Le attività formative contribuiscono alla formazione del dottorando e includono le seguenti tipologie:

1. activity as an expert in the subject, with appointment pursuant to the current University Regulations on the subject;
2. tutoring activities by announcement, ascertained by the competent University Offices;
3. tutoring activity for students of first and second level degrees, ascertained and certified by the Tutor or the reference teacher of the course for which the tutoring is intended (up to a maximum of 30 hours);
4. active participation in Third Mission events organized by the relevant Department or the University (up to a maximum of 10 hours);
5. presentation by the doctoral student of scientific papers at conferences and seminars;
6. participation in journal clubs.

The training activities are recorded in the doctoral student's curriculum, but the achievement of credits is not expected for them and they do not contribute to meet the minimum requirements of the teaching activities. They contribute to the final evaluation of the doctoral student..

XXXIX ciclo

XXXVIII ciclo

XXXVII ciclo

XXXVI ciclo

PHD student representatives:

Florinda Apone  – XXXIX ciclo

Gianluca Vascelli  – XXXIX ciclo

Regolamento del Dottorato in Biologia dei Sistemi in Patologie Immunitarie ed Infettive

Regolamento di Ateneo dei corsi di Dottorato di Ricerca

Moduli per soggiorni all'estero

Modulo missioni

Modulo missione in paesi extra UE

Guidelines-for-preparation-of-PhD-thesis_new

Summary-of-Training-Activities-.Final