The PhD training will provide in-depth knowledge in the biomedical and biotechnological fields, enabling the PhD Doctor to plan and carry out research projects in the field of biotechnologies and the diagnosis, therapy, and prevention of diseases. During the PhD course, the PhD student will learn (i) the programming of scientific experiments including appropriate experimental controls, (ii) the analysis and interpretation of the obtained data, and (iii) the presentation of the data to a specialized audience at national and international conferences and/or through publication in scientific journals. The presence of state-of-the-art instrumentation within the research facilities of the PhD program will allow the PhD student to acquire highly marketable knowledge and generate robust and multidimensional data. The PhD student will thus learn the statistical and bioinformatic fundamentals of data analysis obtained during the research project. The acquisition of “soft skills” by the PhD student will facilitate the application, development, and transfer of functional scientific knowledge both to research activities and to entry into the workforce. The achievement of educational objectives will be obtained thanks to the presence in the Medical Biotechnology doctoral course of members of the faculty involved in various national and international research projects. During the three-year course, the doctoral candidate will be assigned an individual research project to be carried out within the framework of funded projects in the hosting institutions. Consequently, the doctoral candidate will be inserted into an already consolidated scientific context where they can mature scientifically through interaction with other researchers. Furthermore, the doctoral candidate will be assigned a tutor with whom they will periodically discuss the research results obtained and report on the planning of subsequent experiments
The PhD training includes some planned educational activities which includes:
- Bacterial genomics and animal models in bacteriology: The knowledge of the whole sequence of a microbe is the first step of its characterization, since this allows the prediction of gene and protein sequences. A modern study of bacterial genetics needs adequate sequencing technologies (i.e. long reads allowing genome completion) and bioinformatic analysis tools which help the conceptualization of data and their integration with previously generated knowledge. The knowledge of the bacterial genome is a fundamental prerequisite for the set up of animal models to study bacterial physiology and pathogenicity. In this course the fundamentals of bacterial genomics will be explained, together with the current genome sequencing technologies and analysis tools. An emphasis will be also put on the laboratory preparation of bacterial cultures to be used for animal studies and on the design of animal models and experiments.
- Environmental carcinogens and cancer: Overview of naturally occurring and man-made carcinogens: the known and the new. Molecular mechanisms underlying cancer onset. The role of scientific research in early diagnosis, prevention, and treatment of environmental-induced cancers. Asbestos, the best-known man-made tragedy; the past, new asbestos-like substances and the future. The time required for a substance to be recognized as a carcinogen: implications for health, the environment and the economy. Research models for the prevention and treatment of environmentally induced tumors. Common molecular mechanisms underlying the onset of tumors related to environmental pollutants: basic scientific research, the “omic” era and its role in improving therapies for cancer patients
- Immune response elicited by infection and vaccination in clinical and pre-clinical studies: Profiling the induction and the persistence of immune responses upon infection or vaccination, particularly with novel vaccine platforms such as RNA vaccines, is a priority. Methods for profiling the adaptive immune responses include antigen-specific antibody assessment and their functionality testing, antigen-specific B and T cells immunophenotyping by multidimensional flow cytometry and subsequent computational analysis of data, multiplex detection of cytokine/chemokines, B memory or T ELISPOT assays. Immune responses can be characterized in human blood collected before and after vaccination, and in draining lymph nodes, bone marrow and spleen in animal studies. The dissection of the host immune mechanisms elicited by pathogens or vaccines, is fundamental for guiding vaccination or therapeutic strategies.
- Designing and implementing a clinical trial: The main objective of the course is to learn how to design and implement a clinical trial. The course will be structured to implement the following steps in clinical trials design: define the hypothesis; review the literature; develop eligibility criteria; sample size calculation; trial protocol (with steps taken to minimize bias); ethical approval; outcome measures; data interpretation and sources of bias/errors. Moreover, an overview of all the possible clinical trials design will be provided. Another objective of the course will be the design and implementation of a systematic review protocol.
- Functional and structural properties of proteins (theory and practice): The objective of this course is to illustrate how optical methods can be used to study protein folding, dynamics and stability. A basic theoretical knowledge of spectroscopic methods (i.e. UV-visible absorption, fluorescence, infrared and circular dichroism) is an advantage but not mandatory. The course will start with a review of the optical properties of proteins. Then, concrete examples (e.g. β-lactamases, single-domain antibody fragments, lysozymes) will be analysed in details, on the basis of theoretical background (shortly reviewed during the course) and data found in the literature.
- Computational biology for the study of protein structure and function: Teaching will be in the area of structural bioinformatics. Structural bioinformatics belongs to computational biology studying the relationship between structure and function with the help of computational tools. These tools can be as simple as a protein sequence analysis to find homologous proteins in different organisms, or more complex tools to determine the tertiary structure of a whole protein. The course will introduce the field, covering the principles and tools for protein sequence analysis, and secondary and tertiary structure prediction through different methodologies. Students will learn about useful webservers and software used by scientists in the field, and the theory behind them.
- Antibacterial discovery and development in the era of resistance: This course will allow the PhD students in Medical Biotechnologies to better understand the problem of antibiotic resistance, and the implications for the development of novel effective antibacterial therapies. After a short introduction presenting the current panorama of antibiotic resistance and underlying biochemical mechanisms, the course will showcase several strategies allowing the successful discovery and development of innovative antibacterial drugs, including beta-lactamase inhibitors, molecules targeting peptidoglycan synthesis, the biosynthesis and transport of lipopolysaccharide. Furthermore, additional novel approaches, such as the inhibition of virulence or the prevention of antibiotic-induced dysbiosis, will also be discussed.
- Molecular Biotechnologies: From Research to Anatomical Pathological Diagnosis: Paraffin embedding has enabled the establishment of a bio-banking facility within the realm of research. This course aims to provide students in medical biotechnology with both theoretical knowledge and practical skills for the management and analysis of biological tissue samples used in applied research: FFPE, formalin-fixed paraffin embedded. The program will delve into routine techniques (Immunostaining, IF and IHC, qPCR) and progress to more sensitive molecular investigation methods (RNAScope, BaseScope, ddPCR, DEParray, NGS, Nanostring technologies).
- Pathological Anatomy Methodologies for the Study of Predictive Therapeutic Response Markers: Liquid Biopsy in the Context of NSCLC: Precision medicine has revolutionized the treatment for patients with NSCLC, particularly those affected by lung adenocarcinoma. This course will cover the following topics. Patient identification relies on the search for biomarkers (EGFR, ALK, ROS-1, and PDL-1), ideally performed on tissue biopsy or surgical specimens. When invasive procedures are not feasible, liquid biopsy serves as a valuable alternative resource, enabling the identification of somatic mutations and monitoring disease progression and response to therapy.
- Early Diagnosis of Cervical Carcinoma: New Frontiers in Characterizing HPV-Associated Cervical Lesions: Genital HPV infection is quite common and in rare cases can lead to the development of cervical neoplasia. Diagnosis of HPV infection is primarily done through Pap smear, although in recent years HPV-DNA testing has been added alongside Pap smear, which is a molecular analysis that identifies the types of HPV most commonly associated with tumor development. The objective of the course is to provide doctoral students with updates on the characterization of HPV infections and the role of genotyping in cervical carcinoma screening.