Videos and dissemination initiatives promoted by the University of Eastern Piedmont's PhD in Chemistry and Biology at DiSIT Alexandria (https://www.disit.uniupo.it/it) can be viewed on the UPO PhD in Chemistry and Biology YouTube channel.
Course materials will be available on the DIR Higher Education Platform, via authentication.
The following types of courses have been programmed:
- basic courses, established to acquire generic skills useful in all laboratory activities (they are designed for first-year PhD students when fully operational, but currently everyone can take them)
- internal teacher course
- visiting professor course
- courses borrowed from other learning activities
VISITING PROFESSOR COURSE: Structural perspectives on reading, writing and repairing DNA FA0334
Prof. David Jeruzalmi
2 ECTS
This course encompasses a series of lectures at the nexus of structural biology, biochemistry, and cell biology. An important goal of these lectures, and that of structural molecular biology, is to understand biology in terms of the atoms that carry out its various functions: carbon, nitrogen, and oxygen, phosphorous, sulfur, etc. The so-termed central dogma of molecular biology: DNA makes RNA makes protein serves as the organizing principle of this course. Biological information flows from DNA to RNA to protein. And information in DNA is also replicated. The central importance of the flow of information in biology is indicated by the rigorous control that cells exercise over the underlying biochemical reactions. This course will be implemented in so-termed ‘flipped’ mode. Prior to each class meeting, students will review reading material, listen to lecture videos. Class time will be devoted to discussion/questions about the lecture, review of selected portions of the lecture, problems sets.
Luminescent hybrids emitting red light for bioimaging applications and thermometry
Prof. Sergio Lima
0.25 ECTS
This seminar will address the design and preparation of nano- and submicron-scale luminescent hybrid materials incorporating rare-earth ions, with a focus on their application in cellular imaging and nanothermometry. Emphasis will be placed on how structural and compositional engineering at the nanoscale enables precise control over optical response and functionality. Three distinct material platforms will be presented, each based on a different light-generation strategy. Key optical processes—including downshifting emission, plasmon-enhanced luminescence, and upconversion—will be examined. Selected examples demonstrating the performance of these systems in bioimaging and temperature sensing, will be provided to highlight the potential application of these luminescent hybrids for biomedical applications.
Deuterated and tritiated compounds play pivotal roles across diverse disciplines, including Chemistry, Biology, and Material Science.[1a] Tritiated molecules serve as indispensable radiotracers in drug discovery, facilitating crucial Absorption, Distribution, Metabolism, and Excretion (ADME) studies.[1b] Conversely, deuterated compounds are instrumental in metabolomics, enabling precise quantification through internal standardization. Moreover, strategic incorporation of deuterium into specific molecular positions can modulate metabolism rates, mitigate toxic metabolite formation in-vivo, and enhance the performance and stability of emitters essential in OLED devices and bioimaging. Therefore, the development of efficient and selective methods for the late-stage incorporation of hydrogen isotopes into complex molecules is of paramount importance.[1c-d] In this context, the development of nanocatalyzed hydrogen isotope exchange (HIE) reactions[1e] allowing the labelling of numerous substructures (alkylamines[2a-b], thioethers[2c], heterocycles[2a, 2d-e]) in complex molecules through selective C-H activation processes using Ru nanoparticles will be summarized. These reactions find practical utility in synthesizing deuterated LC-MS/MS reference materials, including oligonucleotides[2e], and tritiated pharmaceuticals with high molar activities. Fundamentally, theoretical calculations elucidate the role of dimetallacycles as key intermediates, dictating the regioselectivities of C-H activation processes at the Ru nanocluster surface. Then the possibility to tune the reactivity of Ru nanoparticles in the context of C-H deuteration reactions with organic ligands[3] and to generate catalytically active nanoclusters (Ir[4] and Rh[5]) in-situ from air-stable and commercially available precatalysts will be discussed. To conclude, a novel approach to accessing deuterated compounds with maximized isotopic enrichments using the concept of recirculation in continuous-flow technology[6] and a Ni catalyzed transformation allowing the precise deuterium incorporation on the α-position of the azine’s nitrogen[7] will be presented.
Basic course: A toolbox for biological data exploration, wrangling, and analysis in R
Dr. Giacomo Assandri
1 ECTS
The course is structured into two 4-hour modules and aims to provide participants with basic knowledge for the exploration, preparation, and analysis of biological data, using tools that are also applicable to other disciplines, through the open-source statistical software R. The first, introductory module presents the main procedures for data visualization and restructuring, as well as the production of exploratory graphs useful for setting up subsequent analyses, and includes an example of multivariate linear regression. The second, advanced module focuses on the analysis of datasets that do not meet the assumptions of linear regression, introducing Generalized Linear Models as a framework for dealing with more complex data.
Not Just Plastic and Garbage: The New Life of Polymers in Microelectronics
Dr. Riccardo Chiarcos
0.5 ECTS
The course presents emerging applications of polymers in microelectronics. These new perspectives could keep alive future interest in polymeric materials in a world where there is an ever-increasing effort to reduce the daily use of plastics.
The class will focus on the study of energy metabolism in different models. The first part will regard the importance of studying cellular metabolism, along with some examples. Furthermore, in this section, key molecules and the most popular approaches/techniques used in research to assess the energy status in in vitro and in vivo models will be examined. The second part will provide an overview on the adipose tissue and its metabolism. It will focus on the current research involving this tissue as a target for the amelioration of different pathological conditions.
Do stem cells truly exist as a distinct cellular entity, or are they cells transiently occupying a particular regulatory state?
Multicellular life emerged under a fundamental constraint: increasing complexity requires specialization, yet long-term survival demands renewal. Differentiation creates function, but it limits plasticity. Stemness may therefore represent evolution’s solution to this tension — not as a fixed cell type, but as a dynamic state that reconciles commitment with reversibility.
In this seminar, stemness will be reframed as a property emerging from gene regulatory networks and cellular context. Traveling across evolutionary time — from early multicellular organisms to mammalian tissues — we will explore how cells navigate identity, fate, and plasticity.
The ability to experimentally reprogram differentiated cells back to pluripotency has profoundly challenged classical hierarchies, revealing that cellular identity is more fluid than once imagined.
Rather than a rigid lineage tree, cell fate may resemble a landscape of accessible states.
Finally, we will discuss how the reactivation or destabilization of stem-like states contributes to disease, particularly in cancer, where cellular plasticity becomes a driver of adaptation and therapeutic resistance.
Stemness will thus be presented not as a category of cells, but as a dynamic strategy embedded in the logic of multicellular life.
Disinformation can be very harmful. AI provides us with tools to mitigate these harms, such as methods to detect inauthentic accounts and coordinated information operations. Large language models (LLMs) can also help rate the reliability of information sources and aid in fact-checking tasks. However, attempts to scale up these AI-supported interventions must account for unintended consequences when people interact with AI. In some cases, fact-checking information generated by an LLM can actually decrease news discernment. In the hands of bad actors, AI can become a dangerous weapon. Aside from much-discussed deepfakes, generative AI can be used to easily and cheaply create fake but credible profiles and content at scale. These capabilities enable the infiltration and manipulation of vulnerable online communities. Given the near-impossibility of detecting AI-generated content, research is needed to develop new ways of challenging the provenance of content before wide exposure through distribution channels like social media and search engines.
This course provides an overview of the CRISPR-Cas landscape, beginning with the evolutionary origins and molecular logic of prokaryotic immunity. We will explore the expansion of the CRISPR toolset beyond simple double-strand breaks, including base editing, prime editing, and epigenetic modulation. Participants will evaluate delivery strategies for mammalian systems -ranging from viral vectors to lipid nanoparticles- and conclude with practical frameworks for experimental design.
Portable spectroscopic techniques for the characterization of solid materials: FORS and XRF analysis
Prof. Maurizio Aceto
0.25 ECTS
The workshop illustrates the potentialities of the FORS technique as a preliminary survey method for the characterisation of coloured solid materials, and of the XRF technique as a method of elemental analysis for the characterisation of solid materials. Practical examples of analysis will be shown using materials of different nature (e.g. pigments, minerals and stones, metals, glasses, ceramics, etc). PhD students are invited to bring their own samples for the analysis.
We will examine the logic of pooled CRISPR screens as a tool for dissecting complex biological pathways and identifying novel therapeutic targets. The course covers the entire experimental pipeline: from the construction of gRNA libraries to the practical execution of selective pressure in cell populations and data analysis. Significant focus is placed the diverse applications of screening in identifying molecular target for drug discovery and modeling diseases.
Case examples of conflicts relating to authorship and data ownership – a workshop on common issues concerning scientific integrity in academic research
Prof. Rainer Schulin
0.5 ECTS
This workshop will examine various cases that illustrate typical conflicts that can arise in research regarding the authorship of publications and ownership of research data and materials. In the first part of the workshop the participants will work in small groups. Each group will work on a different case. Thereafter the groups will present their case and their answers to the questions posed to the whole group for discussion.
Targeted Therapy and Immunotherapy in tumors: drug resistance mechanisms
Prof. Valentina Audrito
0.5 ECTS
The course provides an in-depth overview of the two major cutting-edge therapeutic strategies in oncology: (i) molecularly targeted therapies aimed at inhibiting key oncogenic drivers and deregulated signaling pathways in cancer cells, and (ii) immunotherapeutic approaches designed to restore and potentiate anti-tumor immune responses. Metastatic melanoma will be presented as a paradigmatic tumor model to critically examine these treatment modalities, with particular emphasis on the molecular and cellular mechanisms underlying therapeutic resistance and tumor adaptation.
Honey Fraud in the Age of Modern Analytics: Why Current Standards Are Not Enough
Prof. Juray Majtan
0.5 ECTS
Honey is among the most complex and most frequently adulterated food commodities in the world. Yet the parameters used to assess its quality in the current EU and Codex Alimentarius frameworks were largely established decades ago — long before modern adulteration techniques, sophisticated analytical tools, and the concept of medical-grade honey. This interactive workshop challenges PhD students and early-career researchers to move beyond standard compositional thinking and engage critically with the science of honey authentication. Through a short lecture on the global honey fraud landscape followed by a structured group design exercise, participants will construct and defend multi-parameter authentication panels tailored to real-world regulatory, commercial, and research scenarios. The workshop introduces the concept of functional authenticity — the idea that measuring what honey does, not only what it contains, is essential for meaningful quality assessment.
Marker identification with multivariate methods: applications in biomedicine, the environment, and food
Prof. Elisa Robotti
0.25 ECTS
The course aims to provide the foundations of multivariate methods for identifying biomarkers from chemical, omic, and spectral data, based on classification and machine learning methods. Examples from the biomedical, environmental, and food fields will be provided.
Integrated biophysical approach for the analysis of protein-protein and protein-ligand interactions
Prof. Riccardo Miggiano
0.25 ECTS
Protein-protein and protein-ligand interactions play essential roles in many biological processes, including signaling pathways, transcriptional regulation, and numerous other metabolic reactions. To understand the role of these interactions in biological processes, it is important to study the interaction dynamics that describe the stoichiometry of complexes, the free binding energy, and their binding cooperativity as intermolecular communication. These biochemical parameters are complementary to structural biology studies. In particular, the enthalpic and entropic components of free binding energy are related to the mechanistic aspects of interaction and have been widely exploited in drug discovery studies.
The aim of this course is to describe the practical and theoretical aspects of biophysical methods used to measure the stoichiometry and affinity of interactions involving proteins. In particular, the course will focus on the potential application of the following techniques in the field of biochemistry and structural biology: i) SAXS; ii) calorimetry (ITC); iii) differential scanning fluorimetry (DSF); iv) surface plasmon resonance (SPR); and v) microscale thermophoresis (MST).
Combining biophysical methods for the analysis of protein-protein and protein-ligand interaction
Prof. Riccardo Miggiano
0.25 ECTS
Protein crosstalks as well as protein-ligand interactions play essential roles in many biological processes including signaling pathways, transcriptional regulation and numerous other metabolic reactions. In order to understand the role of such protein interactions in biological processes it is important to investigate the interaction dynamics describing the stoichiometry of the complexes, the binding free energy and their binding cooperativity as inter-molecular communication. These biochemical parameters are complementary to structural biology studies. In particular, the enthalpic and entropic components of the binding free energy directly refer to the mechanistic aspects of the binding and have been widely exploited in drug discovery research pipeline. The aim of this course is the description of practical and theoretical aspects of biophysical methods used for measuring the stoichiometry and affinity of many protein interactions. In particular, the course will focus on the application potential of the following techniques in the field of biochemistry and structural biology: i) small-angle X-ray scattering; ii) isothermal titration calorimetry (ITC); iii) differential scanning fluorescence (DSF); iv) surface plasmon resonance (SPR) and v) microscale thermophoresis (MST).
What are semiconductors? Why are they so important in modern technology? In this short course, you will gain fundamental knowledge about these materials, emphasizing the properties that make them highly desirable for current microelectronics. A brief historical overview will elucidate how fundamental studies led to the synthesis of the first transistors. Semiconductor properties will be discussed and elucidated based on their atomic structure, and an overview of experimental techniques to address carrier transport in semiconductors will be provided.
Course of the LM in Chemical Sciences, open to PhD students and teachers of Chemistry/Sciences, with the aim of identifying teaching strategies based on the active involvement of the student, by exploiting the discussion between teachers and undergraduates/PhD students interested in a career as teachers about the problems associated with the teaching/learning of Chemistry at school and university.
Course of the LM in Chemical Sciences, open to PhD students and teachers of Chemistry/Sciences, with the aim of identifying teaching strategies based on the active involvement of the student, by exploiting the discussion between teachers and undergraduates/PhD students interested in a career as teachers about the problems associated with the teaching/learning of Chemistry at school and university.
Teacher training course open to PhD students. The course aims to show simple chemistry experiments that can be replicated in schools to raise students' awareness of current issues. Specifically, the course is divided into four days covering topics related to sustainability, recycling, green chemistry, and the environment.
The course (48 hours, 6 ECTS) combines lectures and applied activities to provide methodological tools for designing educational pathways in the life sciences. Topics include taxonomy, evolution, biodiversity, and ecology, with a focus on the experimental method. The course aims to develop skills in planning lessons and activities for secondary school and includes practical exercises and a visit to a Natural History Museum.
Crystallographic methods for the structural analysis of molecules, materials, and proteins
Prof. Marco Milanesio
0.25 ECTS
The seminar will summarize the fundamentals and applications of the crystallographic and not crystallographic methods of structural characterization. In details, investigation methods devoted to small molecules and materials and to macromolecules of biologica interest will be described.
Epigenetic Mechanisms and Chromatin Architecture: From Cellular Identity Maintenance to Tumor Reprogramming
Prof. Filippo Cernilogar
0.5 ECTS
Questo corso esplora i meccanismi epigenetici e l’architettura della cromatina come pilastri fondamentali della regolazione dell’identità cellulare, analizzando come uno stesso genoma possa dare origine a fenotipi diversi in contesti fisiologici e patologici. Attraverso l’esame di processi chiave, quali la metilazione del DNA e le modifiche istoniche, verrà approfondito il modo in cui la cellula “scrive”, “legge” e “cancella” le informazioni regolatorie necessarie al mantenimento della propria memoria funzionale.
Verranno inoltre esaminate alcune delle più avanzate tecnologie di Next-Generation Sequencing — tra cui ChIP-seq, CUT&RUN, ATAC-seq e Hi-C — che consentono di mappare l’accessibilità della cromatina e l’organizzazione tridimensionale del genoma con elevata risoluzione. Infine, analizzeremo come la riprogrammazione degli enhancer e dei super-enhancer possa guidare la progressione tumorale e la plasticità metastatica, discutendone le implicazioni per la medicina di precisione e per l’editing dell’epigenoma tramite sistemi CRISPR.
Nella seconda parte del corso verranno trattati i principi e le principali metodologie bioinformatiche per l’analisi dei dati NGS, illustrando il workflow che conduce dall’allineamento delle sequenze al genoma di riferimento fino all’identificazione delle regioni arricchite (“peaks”) e alla loro visualizzazione mediante genome browsers. Il livello di approfondimento tecnico di questa sezione sarà calibrato in base alle conoscenze di base dei partecipanti.