EXPERIMENTAL MODELS IN BIOLOGICAL AND BIOMEDICAL RESEARCH

Knowledge and understanding

On completion of the course, students know and understand:

•    the history of experimental biology and how the role of models in biological and biomedical research has evolved;

•    the concept of complexity of biological systems, the definition of an experimental model and the scientific contexts in which models are used;

•    the types of experimental model — in silico, in vitro and in vivo — with their respective characteristics, fields of application, advantages and limitations;

•    the quantitative and qualitative assessment parameters and the validation procedures of an experimental model, together with the concepts of scientific reproducibility and complementarity between models;

•    the relevance of phylogenetic relationships among model organisms and the features of the main prokaryotic and eukaryotic, animal and plant models;

•    the ethical and regulatory framework governing the selection and use of in vivo models;

•    the biotechnological and translational potential of the knowledge acquired, with reference to valorisation pathways (spinoffs, startups).

Applying knowledge and understanding

On completion of the course, students are able to:

•    select the experimental model best suited to a specific biological question or scientific objective, and justify that choice;

•    assess ex post, on papers drawn from the scientific literature, the appropriateness and validity of the model used and the soundness of the experimental design;

•    propose alternative or complementary modelling approaches to the same biological problem, specifying the experimental aspects involved and the expected advantages;

•    design the validation of a new experimental model, identifying the appropriate verification parameters;

•    recognise and apply the relevant ethical and regulatory constraints, including the 3R principle, when designing a study involving in vivo models;

•    organise and present the outcome of a modelling assessment in the form of a data report or a draft research project.

Making judgements

Students are able to form a critical, well-argued judgement on the model chosen in a published paper, to handle limited or conflicting information and to defend a position against opposing arguments. This ability is developed through the journal club, flipped classroom activities, case studies discussed in groups with pro/con debate, and the individual preparation of a research project.

Communication skills

Students are able to communicate complex scientific content in English, orally and in writing, clearly and unambiguously, to both specialist and non-specialist audiences. This ability is developed through in-class presentations of scientific papers, the journal club, the drafting of data reports and project outlines, and dissemination and grant-writing exercises.

Learning skills

Students are able to independently find, select and update the scientific sources needed to continue the study of experimental models in a self-directed way and to plan their own research activity. This ability is developed through independent literature searching for the presentations, guided participation in seminars, webinars, workshops and conferences, and individual in-depth study of specific models.

The course (6 CFU) comprises 47 hours of teaching activity, organised in 35 hours of lecture-based teaching (frontal lectures, 5 CFU) and 12 hours of interactive teaching (guided classroom and laboratory sessions, 1 CFU). All activities are delivered entirely in English.

Lecture-based teaching (35 hours)

Frontal lectures supported by slides, videos, webinars, documents and scientific papers provided in PDF format. Remote connections with experts on specific experimental models are also included.

Interactive teaching (12 hours)

•    journal club and flipped classroom activities, with students presenting and critically discussing scientific papers;

•    group work and case studies presented and discussed in active debate, with students arguing alternately for and against;

•    science communication exercises: dissemination, grant writing, drafting of a data report;

•    guided participation, in person or online, in seminars, webinars, meetings, workshops and conferences, also in collaboration with leading national and international research institutions.

Consistency between teaching methods and learning outcomes

Lecture-based teaching mainly serves the acquisition of knowledge about the types of model, their fields of application and their validation parameters (first descriptor). Interactive teaching is aimed at developing applied and transversal skills: justified model selection and the ex post assessment of published cases develop the ability to apply knowledge and understanding; pro/con debate and case discussion develop making judgements; presentations, the journal club and the grant-writing and data-reporting exercises develop communication skills; independent literature searching and participation in seminars and webinars develop learning skills.

If the course is delivered in blended or remote mode, appropriate adjustments may be made to the above, in order to ensure consistency with the syllabus.

Basic knowledge of cell and molecular biology, genetics and evolution is indispensable.

Knowledge of physiology, histology, anatomy, embryology and developmental biology — with particular reference to the central nervous system — and of epigenetics is important.

Basic familiarity with the critical reading of primary research articles and with elements of statistics applied to biological experimentation is useful.

A good command of written and spoken English is indispensable, as the course is delivered entirely in English and all teaching material is in English.

The knowledge listed above constitutes cultural prerequisites and is stated without reference to specific courses of this degree programme, so that students coming from other Italian or foreign institutions can assess whether their previous studies have provided it. The degree programme regulations set no formal prerequisites for this course.

Students who lack some of the knowledge indicated will be directed to textbooks or lecture notes useful for acquiring it.

Attendance is not compulsory but is strongly recommended.

A significant part of the expected learning outcomes is in fact achieved through the interactive teaching activities — journal club, group work, debates on case studies, seminars and connections with experts on specific experimental models — which take place through in-class discussion and cannot be fully replaced by individual study. Active participation also provides continuous feedback on the ability to critically analyse a scientific paper, which is the main object of the examination.

Students who are unable to attend are invited to contact the lecturer in order to agree on an individual study path; all teaching material is in any case made available on the University e-learning platforms.

1.     Models and the scientific method: The methodology of scientific research. History of experimental biology and its models. A historical and ontological pathway to the concept of complexity of biological systems.

2.     The experimental model: Concepts and contexts of an experimental model in scientific research. Representativeness, scale, reductionism and the limits of inference.

3.     Validation of an experimental model: Quantitative and qualitative assessment parameters. Construct, content and predictive validity. Scientific reproducibility and complementarity between models.

4.     Phylogeny and model choice: The relevance of phylogenetic relationships among model organisms. Main prokaryotic and eukaryotic models. Main plant models. Selection criteria according to the biological question.

5.     In silico models: Computational modelling, simulation and data analysis. Advantages, limitations and integration with experimental models.

6.     In vitro models: Normal and tumour cell cultures. Normal and tumour stem cells. iPS cells and cellular reprogramming.

7.     In vivo models: Laboratory animals. Models in developmental biology. Genetic and induced models.

8.     Humans as an experimental model: Controlled clinical studies: design, phases, limitations. The relationship between preclinical models and translational research.

9.     Evolution and future of experimental modelling: Embryoids, organoids, organ-on-chip, use of 3D printers.

10.   Ethics and regulation: Ethics in experimental modelling. The 3R principle. Regulatory constraints in the selection and use of in vivo models.

11.   Applied experimental modelling: Gene expression and function. Epigenetics. Sex determination. Ecotoxicology and the role of environmental parameters. Neurobiology and neuroscience: from the normal condition to neurodegenerative pathologies and experimental therapeutic approaches.

12.   From knowledge to valorisation: Science communication: dissemination, grant writing, data reporting, journal club. Biotechnological potential of scientific knowledge: spinoffs and startups. National and international research institutions.

Reference textbooks

1.     Striedter G.F., Model Systems in Biology: History, Philosophy, and Practical Concerns, The MIT Press, 2022 (ISBN 9780262046947). Available open access on the publisher's website.

2.     [to be defined — second reference textbook, easily available]

Recommended further reading

Reviews and research articles indicated by the lecturer for each topic of the syllabus, with particular reference to the case studies discussed in class.

Other teaching material

Copies of the material used during the lectures, lecture notes, scientific papers and further teaching material are provided by the lecturer and made available on the University e-learning platforms (Studium, http://studium.unict.it/). All teaching material is in English.

Learning is assessed through an oral examination held in English, lasting on average 40 minutes.

The examination is organised in two parts:

1.     an initial presentation of about 15 minutes, supported by slides, in which the student discusses one or more scientific papers agreed with the lecturer, critically analysing their modelling aspects, the suitability of the model with respect to the biological question and the validation parameters used, and proposing where possible alternative or complementary modelling approaches, specifying the experimental aspects involved and the expected advantages. Alternatively, the student may present and discuss a research project of their own, chosen from a list of topics suggested by the lecturer;

2.     a subsequent discussion, normally based on three questions, extended to the topics of the syllabus connected with the case presented.

During the course, formative assessment activities are carried out (journal club, group presentations, debates on case studies, short written reports). These do not produce a separate score and do not contribute directly to the final mark: their purpose is to allow both student and lecturer to monitor learning progress and to prepare for the final examination.

The following elements are taken into account in the examination: the relevance of the answers to the questions asked; the accuracy and depth of the content; the ability to connect the topic with other parts of the syllabus; the ability to provide examples; the independence and rigour of the critical judgement on model selection and validation; the command of technical English and overall clarity of expression.

The final mark, expressed out of 30, is awarded according to the following criteria:

•    Fail: the student does not possess the minimum required knowledge of the main experimental models and of the criteria for their validation; command of technical English is poor or absent and the student is unable to apply the knowledge acquired to the assessment of a case independently.

•    18–21: the student has minimal knowledge of the types of experimental model and of the related validation parameters; analyses the case presented in an essential way and with limited critical ability; presents the material sufficiently clearly, although command of language is underdeveloped.

•    22–25: the student has fair knowledge of experimental models and validation procedures, although limited to the main topics; integrates and critically analyses the case in a not always linear way; presents the material fairly clearly, with fair command of language.

•    26–28: the student has good knowledge of experimental models and of the criteria for their selection and validation; analyses the case critically and coherently, proposes alternative approaches fairly independently and presents the topics using appropriate language.

•    29–30 with distinction: the student has thorough knowledge of experimental models, of their limitations and of validation procedures; integrates and critically analyses the case promptly and rigorously, independently designs the validation of a new model and proposes original solutions; communication skills and command of language are excellent.

Learning assessment may also be carried out on-line, should the conditions require it.

To ensure equal opportunities and in compliance with current laws, interested students may request a personal interview in order to plan any compensatory and/or dispensatory measures based on educational objectives and specific needs. Students can also contact the CInAP (Centro per l'integrazione Attiva e Partecipata — Servizi per le Disabilità e/o i DSA) referring teacher within their department (https://www.cinap.unict.it/content/referenti).

1.     Main experimental models used in a given discipline (e.g. genetics, epigenetics, ecotoxicology) or to address a specific knowledge gap: describe their features, fields of application, advantages and limitations.

2.     Advantages and disadvantages of an experimental model of your choice, and criteria for selecting a model according to the biological question.

3.     How a new experimental model is created and validated: quantitative and qualitative assessment parameters, procedures and critical issues.

4.     Ethical limits and the regulatory framework for the use of in vivo models; the 3R principle and its implications for experimental design.

5.     The role of environmental parameters in biological research and in the reproducibility of experimental results.

6.     Iannielli et al., Pharmacological Inhibition of Necroptosis Protects from Dopaminergic Neuronal Cell Death in Parkinson's Disease Models. Cell Rep. 2018 Feb 20;22(8):2066-2079. doi: 10.1016/j.celrep.2018.01.089 — Present the paper and discuss the appropriateness of the model for the experiments proposed and the translational implications; propose modelling or experimental approaches alternative or complementary to those used.

7.     Esquerda-Canals et al., Mouse Models of Alzheimer's Disease. J. Alzheimer Dis. 2017;57(4):1171-1183. doi: 10.3233/JAD-170045 — Starting from this review and integrating it with further specific papers, present the animal models developed for genetically determined Alzheimer's disease, identifying the limitations, advantages and fields of application of each model.

8.     Hendrix et al., Reprogramming metastatic tumour cells with embryonic microenvironments. Nat Rev Cancer 2007 Apr;7(4):246-55. doi: 10.1038/nrc2108 — Starting from this review and integrating it with further specific papers, compare the chick and zebrafish models for the study of the tumour microenvironment and, where possible, propose alternative or complementary modelling or experimental approaches.