Course Units

Teachings of the XL Doctoral Cycle

n.Denominazione dell’insegnamentoNumero di ore totali sull’intero cicloDistribuzione durante il ciclo di dottorato (anni in cui l’insegnamento è attivo)Descrizione del corso
1.Fondamental and methodology of applied Philogenetics  5  
first year 		The course will provide students with the tools to understand the evolutionary dynamics underlying complex phylogenetic relationships between organisms. The fundamentals to conduct and understand the main applied phylogenetic analyses will also be provided, with particular reference to the phenomena of speciation and differentiation between animal organisms in relation to space, time and environment.
At the end of the course, students will have acquired the necessary skills to interpret the results obtained from the analysis of molecular data in a biological key from a phylogenetic and phylogeographical perspective and will be able to reconstruct the evolutionary pathway of an organism on the basis of the data acquired.  
2.Advanced Immunology  5  
second year  		This course aims to deepen the study of the relationships and interactions between the cellular components of the immune system. In particular, the immunological mechanisms generating local and systemic damage and disease will be studied. The student will be provided with advanced knowledge on the pathophysiology of neoplasms of the human immune system. The most recent techniques for the production of monoclonal antibodies and their use as therapeutic diagnostic agents will be illustrated. Finally, the different types of vaccines (DNA, RNA, protein, inactivated etc.) will be illustrated, also in the light of the most recent post-pandemic developments.  
3.The gut microbiota and relationships with human pathophysiology. Basic and clinical research  5  
second year 		Microbial communities colonising the gastrointestinal tract are the subject of extraordinary interest in fundamental research and clinical trials. In healthy and non-diseased subjects, systematic analysis of the structure of these communities and the metabolic and immunomodulatory functions expressed has made it possible to hypothesise and, in some cases, validate, important relationships with the physiology and pathogenetic bases of numerous diseases. The objectives of the course are: the illustration of the main physiological axes that depend on intestinal microbial functions; knowledge of the main analytical methodologies used to study the microbiota; updating on the scientific evidence that identifies in the functions of the microbiota elements of susceptibility or resistance to non-diseases.  
4.Bioinformatic tecniques for data analysis of Next Generation Sequencing  5  
first year		The course aims to provide PhD students with the basics of analysing next-generation sequencing data. During the course, the different NGS techniques will be compared, highlighting the pros and cons and using real case studies as examples. The main software for quality control, removal of low-quality reads and assembly of reads (de novo or with reference) will also be used. For NGS methods that do not require assembly, data extraction software will be used.
It will be shown how to construct matrices for statistical data processing and preparation for final analysis according to the specific objectives of the case study.  
5.Hybridization in animals: occurrence, detection and consequences  5  
second year  		The course aims to provide an overview of the phenomenon of hybridisation, defined as reproduction between two distinct taxonomic units. The difference between natural and anthropogenic hybridisation will be emphasised. The former is a driver of evolution and source of new diversity in nature, the latter is mediated by humans and considered a risk to the conservation of many species. With respect to this we will provide the means to understand when hybridisation can be configured as introgressive and lead to the genomic extinction of a population or species. Through the analysis of case studies, the causes that may favour hybridisation in nature and its possible consequences, particularly in relation to its impact on wild species, will be brought into focus.  
6.From molecular cloning to in vivo experimental models  10  first year Module 1: Methods used to modify gene expression in complex eukaryotic organisms will be covered
complex eukaryotic organisms: knockout, transgenes, RNA interference, CRISPR-Cas. The practical part will cover the
simulation of molecular cloning for transgenic organisms in drosophila.
Module 2: The advantages and disadvantages of three in vivo experimental models will be evaluated: drosophila, zebrafish, mice. The practical part will cover phenotypic analysis of transgenic drosophila, recognition of balancing chromosome markers and making crosses between different drosophila lines.
7.Genetic applications for the conservation of aquatic fauna  5  first year  The main objective of this course is to illustrate to first-year PhD students how different molecular techniques can enable targeted conservation programmes on threatened or endangered aquatic fauna species in the Mediterranean basin and Atlantic coasts. Several case studies concerning the conservation of marine and dulcephalic fauna through DNA barcoding, integrated molecular taxonomy and conservation genetics techniques will be covered. At the end, the student will have to present a conservation project on an endangered fauna of his/her choice.
8.Construction of predictive models for assessing outcomes in clinical trials  5  
second year  		The aim of the course is to provide knowledge on the construction of multivariate statistical models for diagnostic and prognostic evaluation in clinical trials. In particular, the use of multiple logistic regression analysis models and survival analysis using Kaplan-Mayer curves for the prediction of adverse outcomes will be examined, through the in-depth study of concepts such as OR and HR, also obtained after correction for confounding factors.
9.Pathogenesis of atherosclerosis: searching for biomarkers in advanced lesions  5  
third year  		Cardiovascular disease is the leading cause of death and illness in developed countries, and atherosclerosis is the main culprit. Several genetic and environmental risk factors have been associated with the development of atherosclerotic lesions, including high levels of Apo B100-containing lipoproteins (i.e. LDL, VLDL and Lp(a)), low HDL levels, hypertension, diabetes, hyperlipidemic diet, smoking and lack of exercise. This chronic inflammatory disease is characterised by the accumulation of lipids and fibrous elements in the intimal layer of medium and large arteries. Erosion of the lesion surface can cause ulceration of the plaque leading to acute thrombosis and occlusion of the artery, resulting in major adverse clinical events. To date, many efforts have been made to elucidate the mechanisms underlying plaque formation and to identify reliable and specific markers of plaque susceptibility to rupture.  
10.Approaches and methodologies in the comparison of laboratory analytical methods  5  
third year		Evaluating the degree of agreement between the results obtained by measuring the same samples using a reference analytical method and one being validated is a key step, laid down by international standardisation bodies, in the process of developing a new analytical method. However, the available procedures present a continuous challenge both in the implementation of the available tests and in the interpretation of the generated outputs. Evidence of this is the diminished use of correlation analysis, which is certainly useful for establishing the strength of the relationship linking two variables, but totally unsuitable for producing an estimate of the degree of agreement between different analytical methods measuring the same variable. The aim of the course is to offer a historical perspective on the basis of the widespread use of correlation analysis for estimating the degree of agreement and to present an overview of the main tests and procedures available to analysts.
11.Advanced Topics in Signals Transduction  10  
first year  		Students enrolled in this course will gain knowledge on theoretical and experimental aspects at the cutting edge of biochemistry. The course will be based on the use of primary sources from the scientific literature to analyse experimental data, explain methodologies and introduce cutting-edge concepts. Emerging scientific topics such as epigenetics, exosomes and free radicals will be discussed in the context of basic and clinical science. Particular emphasis will be placed on the study of the biochemistry of specific cells and diseases. Intracellular signalling pathways of fundamental importance in biology and pathobiology will be discussed in a general context and in association with pathological conditions. Students will be involved in multiple activities (e.g. journal club, article evaluation, project writing) that require specific skills such as critical thinking, critical writing and critical evaluation.  
12.Infections and non transmissible diseases  5  
third year		The aim of the course is to provide a broad overview of the latest knowledge about the role of certain microorganisms (bacteria and viruses) in chronic, degenerative, autoimmune and oncological diseases. Examples include the role of the Epstein-Barr virus in multiple sclerosis, rheumatological diseases and Burkitt's lymphoma, infections caused by Streptococcus pyogenes and rheumatic fever as well as the role of endogenous human retroviruses on various chronic degenerative diseases.  
13.Progress Reports  20  
first, second and third year  		In the progress reports, doctoral students present their research activities during the year to their colleagues (from their own course and from other courses for interested students), and at the end of each presentation there is an active discussion moderated by the course coordinator.  

Other teaching activities

Seminars, laboratory and research activities, interdisciplinary, multidisciplinary and transdisciplinary training

n.Tipo di attivitàDescrizione dell’attività (e delle modalità di accesso alle infrastrutture per i dottorati nazionali)
1.Linguistic improvement

Linguistic improvement

Language skills will be promoted with a dedicated course in scientific English (10 CFU) held in cooperation with the University Language Centre. PhD students are also expected to reach level B2 of the European Certification Framework during their studies. Language skills will also be promoted by encouraging participation in lectures and seminars held in English by foreign lecturers. The doctoral students will also be encouraged, with the support of their tutor, to make presentations of their project and results in English in front of the College and to write their theses in English.  

2.Information technology further training

Further training in informatics

Computer skills applied to the biological sciences will be promoted with a course in Bioinformatics (6 CFU, Mapping and analysing DNA and protein sequences ; Rapid overview of microarray technologies. Introduction to different bioinformatic solutions related to microarrays; Software and tools: Open source bioinformatics software, Web services in bioinformatics). In addition,v depending on the methodologies used by the PhD student, lectures dedicated to specific software will be provided and seminar activities oriented towards the correct application of validation algorithms will be promoted.  

3.Valorisation and dissemination of results, intellectual property and open access to data and research products

Enhancement and dissemination of results, intellectual property and open access to data and research products


The doctoral programme has set up a Joint Teaching Commission, which will work on the coordination and rationalisation of teaching activities in order to ensure high quality and organisational standards. Each year, the students of the three active cycles present their research projects or results in 20-25 minutes for collective attention, discussion and evaluation, in the presence of the lecturers and their colleagues. The presentation of results at national and international congresses and their publication in international journals with external reviewers will be encouraged.  

4 - 14 november 2024

  • Massimo Ciccozzi
    Full Professor of Epidemiology and Health Statistics at the Campus Biomedico University in Rome
    Monday 4 November, Aula A of the Biomedical Complex h: 15.00
    Title: Epidemics and Pandemics
     
  • Vito De Pinto
    Full Professor of Molecular Biology at the University of Catania
    Thursday 7 November, Aula B of the Biomedical Complex h: 15.00
    Title: VDAC, the voltage-dependent anion-selective channel, gatekeeper of mitochondria, as a disease signalling hub and therapeutic target
     
  • Loris Zamai
    Associate Professor of Anatomy at the University of Urbino - Carlo Bo
    Monday 11 November, Lecture Hall C of the Biomedical Complex h: 16.30
     
  • Arturo Sala                     
    Full Professor of Translational Cancer Research presso la Brunel University of London
    Tuesday 12 November, Lecture Hall B of the Biomedical Complex h: 15.00
     
  • David Caramelli 
    Full Professor of Anthropology at the University of Florence
    Thursday 14 November, Aula A of the Biomedical Complex, h: 10.30 a.m.
    Title: Paleogenomics and Human Evolution