Interdisciplinary Core Courses

How to design and perform an experiment (12 hours)

Teacher: Prof. Graziano Martello

Schedule: 12th, 19th and 26th January 2024 - 2:30 to 5:30 PM

Description: The course comprises both lectures and practical activities, focused on how to design and perform experiments, and how to interpret and present results. I will draw parallels between how we make decisions in our everyday life and how we should perform experiments. We will discuss several examples, ranging from simple biological experiments to bioinformatic analyses.

Science Communication, Fundraising & Career Development (20 hours)

Teacher: Prof. Ralf Dahm

Schedule: May 2024

Description: This course explains the fundamentals of science communication and fundraising:

• The basic principles of good communication.

• How to prepare and deliver captivating scientific talks.

• How to design appealing posters.

• How to write clear and convincing scientific texts e.g. papers, applications.

• How to compile a compelling job application.

This course will comprise:

• Introductory lectures on the topics outlined above.

• Practical sessions during which participating students present their projects (in talks or on posters), grant proposals and job applications, and the tutors and other participants give feedback on a student’s presentation/other materials.

Fellowship and grant writing (30 hours)

Speaker: Prof. Luca Scorrano

Schedule: June-July 2024

Description This course aims at providing PhD students with basic principles on how to write convincing fellowship and grant applications. The course is organized in three intertwined blocks of lessons. The first block deals with the basic principles of the scientific method applied to biology, to provide a conceptual framework for grant applications. The second block of lessons uses hands-on examples of fellowships and grants to explain basic features of grantsmanship. Students are then asked to write a 2-page fellowship proposal on their topic of choice, using an EMBO fellowship like format. These proposals are due before the third block of lessons when we go through them and rank them as if we were a reviewing panel. The course is mostly flipped classroom and group work, except for the fellowship proposal that is of course individual.

Basics of Statistics and of R (8 hours)

Teacher: Prof. Mirko Pegoraro

Schedule: 11 March-12 April 2024 

Description: This workshop will introduce R. An initial description of basic concepts and principles develop into data manipulation and graphical representation using ggplot2. The workshop will also revisit basic statistical concepts and will include statistical analysis (ANOVA and post doc) and a simple loop. The workshop is hand-on so it requires students to have access to a PC/laptop installed with R (R studio is recommended but not strictly necessary). Access to the internet is necessary.

Thematic Courses

Gene Editing Part I: Basics of CRISPR-Cas Genome Editing (4 hours)

Instructors: Prof. Milena Bellin, Dott. Francesco Chemello

Schedule: March 2024

Description: CRISPR-Cas system has revolutionized the field of genome engineering. This course will give a broad overview of the different genome editing technologies, focusing on CRISPR-Cas, its discovery, applications, and the latest derived CRISPR-Cas based editing tools. Practical examples will be presented to show the advantages and limitations of the different strategies. Participation is recommended for PhD students that plan to follow the course “Advances in CRISPR-Cas Genome Editing” in the AY 2023/2024.

Teaching program:

1. History of genome editing: meganucleases, ZFN, TALEN, CRISPR-Cas9

2. Discovery of CRISPR-Cas system

3. CRISPR-Cas9 genome editing: DNA repair pathways, double-/single-cut editing

4. CRISPR-Cas based genome editing tools: CRISPRi, CRISPRa, base editing, prime editing.

Gene Editing Part II: Advanced gene editing (8 hours)

Instructors: Prof. Milena Bellin, Dott. Francesco Chemello

Schedule: April 2024

Description: The development of advanced CRISPR-Cas genome editing technologies has expanded the available gene editing strategies for treating various diseases. The course comprises both lectures and guided journal club activities, discussing the utilization of genome editing as possible treatment for human diseases, and focusing on the optimization of in vivo delivery and safety of the gene editing components. Participation in the course “Basics of CRISPR-Cas Genome Editing” is recommended.

Teaching program:

1. Novel advances in genome editing tools.

2. Delivery strategies of genome editing components.

3. Mitochondrial genome editing.

4. Safety challenges of genome editing.

Evolution under anthropogenic pressures and conservation (8 hours - one day in Chioggia)

Instructors: Prof. Carlotta Mazzoldi, Prof. Leonardo Congiu, Dott. Marco Munari

Schedule: March-April 2024

Description: The day will consist of a sequence of seminars on the topic mentioned in the title, a visit to the Fish market of Chioggia (with discussion on conservation and species vulnerability to exploitation), and a visit to the Museum of Adriatic Zoology (with discussion of consequences of exploitation on biodiversity, using the Adriatic Sea as an example).

Models in genetic disease research (15 hours)

Instructors: multiple speakers see file

Schedule: October 23rd, 24th, 25th, 26th, 2023. 

Description: The course is organized as a series of seminars in the framework of the ERASMUS+ week. The primary focus of the presentations will be around the benefits and advancements in utilizing model organisms for the study of complex diseases. 

Perspectives on fluorescence microscopy (8 hours)

Instructors: Prof. Marta Giacomello

Schedule:

Tuesday, January 23rd, 2024   

Wednesday, January 24th, 2024   

Tuesday, January 30th, 2024   

Wednesday, January 31st, 2024   

Description:

• Basic Principles of microscopy (2h): Diffraction, Resolution and Contrast, Optics of the microscope
• Fluorescence and Confocal Microscopy (2h):  Fluorescence microscopy (fluorophores, illumination), Basic Confocal microscopy (Lasers, multi-dimensional Image Recording)
• Fluorescent Probes (for fixed and live samples) (2h); Chemical and genetically encoded; Ratiometric - Non ratiometric
• Advanced techniques in fluorescence microscopy (2h): (FRET, TIRF, FRAP) and Super resolution microscopy

Microscope imaging analysis (8 hours) 

Instructors: Prof. Francesco Argenton, Dott.ssa Nicoletta Plotegher,

Schedule: June 25-26-27 and september 24th

Description: The aim of this course is to provide a formal understanding of what digital images are and how this makes them suitable to be mathematically handled in order to get more insights into our biological data. This will be done by means of a combination of traditional presentations on the topic, of exercises and discussion on data provided by the teachers or by the students. The course will be organized as follows:

• principles of image analysis, math on images, ImageJ/Fiji, n-dimensional images, image analysis: shape/density, ROIs, background. Examples and exercises based on what was discussed in class. (4 hours)
• most common errors in Image Analysis -> (1) sample preparation; (2) asking the right question; (3) image acquisition; (4) image analysis: automated vs manual analysis, machine learning applications. Discussion about the errors and how to avoid them. (2 hours)
• analysis of images provided by the students. (2 hours)

Molecular basis of neurodegeneration: from mechanisms to therapies (14 hours)

 Instructors: Prof. Elisa Greggio and Prof. Elena Ziviani (DiBio UNIPD)

Guest speaker: Dott.ssa Chiara Anselmi (Postdoctoral fellow, Stanford University)

Schedule:
May 14, 2024 - Hallmarks of neurodegenerative diseases: a focus on genetics 

May 16, 2024 - Mitochondrial dysfunction in neurodegenerative diseases 

May 21, 2024 - Protein aggregation in neurodegenerative diseases

May 23, 2024 - Mechanisms of mitochondrial quality control and neurodegeneration: lesson from genetics 

May 28, 2024 - Synaptic dysfunction in neurodegenerative diseases 

May 30, 2024 - Drosophila as a model in neurodegenerative disease research 

June 4, 2024 - Conserved features of neurodegeneration, evolutionary insight from a marine chordate

Description The human brain is by far the most complex structure existing in nature. The core component of the brain is the neuron, an electrically excitable cell that elaborates and transfers information by electro-chemical signaling to other neurons. Unlike other cells, the majority of neurons do not divide, lasting for the entire lifespan of one individual. Thus, neuronal loss equals information loss. Although neuronal degeneration is an inevitable process, which ultimately occurs in the aged brain, this process can be anticipated by a number of causes, of environmental nature, genetic origin or both. It is expected that 25% of the European population will be over 65 years of age by 2030, indicating how age-related disorders represent major medical and social challenges. This area of research is rapidly expanding and the discovery of novel molecular targets and diseases biomarkers is offering exciting therapeutics opportunities.  The course will offer a critical appraisal of the major themes in the study of neurodegenerative diseases, from genetics and protein aggregation to dysregulation of mitochondrial quality control, synaptic dysfunction and impaired proteostasis. The closing lecture will be held by a young researcher, Dr. Chiara Anselmi, former PhD student at DiBio, who will discuss how neurodegeneration can also be a physiological process in certain species.

Fundamentals of Evolutionary Biology (10 hours)

Instructors: Prof. Gil Rosenthal

Schedule:

Giov 19 Ott 17.30-19.15 Room: Residenza Nord Piovego

Mart 24 Ott 18.00-19.45 Room: Residenza Nord Piovego

Giov 26 Ott 17.30-19.15 Room: Residenza Nord Piovego

Mart 31 Ott 18.00-19.45 Room: Residenza Nord Piovego

Giov 2 Nov 17.30-19.15 Room: Residenza Nord Piovego

Description: The course focuses on a largely non-mathematical approach to the fundamentals of mathematical evolutionary theory as applied to modern evolutionary problems using next-generation approaches.  The course is designed to pair quantitatively oriented undergrad and LM students in the Galilean Academy with PhD level students focused in the life sciences.  Each lesson is paired with a problem set and readings from the primary literature. There are no formal prerequisites for the course, though some prior background in probability theory would be helpful.

Properties of adult stem cells across the animal kingdom – current concepts and future directions (10 hours)

Instructors: Prof. Bert Hobmayer

Schedule Nov 14-15-16-17 2023 Room 0G Botta Building

Description Main topic of the proposed course will be the properties of adult stem cells across the animal kingdom. While detailed knowledge about adult stem cells is present in vertebrate organ systems, invertebrate animal models exhibiting unparalleled capacities for regeneration, growth and immortality have obtained more attention only recently. As a result, we know their underlying adult stem cell lineages not nearly as well. This course aims at closing this gap, at uncovering the current open questions and the challenges lying ahead, and at addressing the available experimental approaches. Overall goal of this course is to raise awareness for the most up-to-date topics related to adult stem cells and their role in biological mechanisms and in medical applications.

Types of teaching units:

4 lecture and discussion units (one per day, each 90-120min):

• Introduction to animal adult stem cell lineages – properties and mechanisms of decision making

• Pluripotent interstitial cells in Hydrozoa as a case study of a prototypic adult stem cell lineage

• Epithelial stem cells in growth and morphogenesis

• An evolutionary perspective on adult stem cells – open questions and  future approaches

3 practical units (one per day, first three days, each 60-90min):

• How to recognize stem cells in light microscopy

• Life imaging of adult stem cells using transgenic animals

• Analysis of stem cell-specific gene expression in a single cell transcriptome database

NextGen DNAseq/RNAseq analysis (4 hours)

Instructors: Dott. Mirko Pegoraro

Schedule: 11 March-12 April 2024

Description: The workshop presents how to process next generation DNASeq/RNAseq data. The workshop consists of a lesson to understand the questions we are answering with Next gen seq and to understand the files generated by both the sequencing technology and data analysis. The lesson is then followed by a demonstration of the process of analysing and visualising RNA-Seq data. Required access to PC/laptop, internet linux.

Advanced Methods in Biochemistry (8 hours)

Instructors: Prof. Laura Cendron; Prof. Luigi Leanza

Schedule: June 2024

Description: 

The course aims at offering a general overview to the methods, approaches and novel technologies to develop a project based on biomolecular interactions, consisting of: 1) the capture of a network of interactions and the identification of interacting partners; 3) physical-chemical characterization of the interactions and 4) application of display technologies to the generation of libraries of high affinity and specificity binders.

Main topics in brief:

- Techniques to identify/study interactions:

o Co-immunoprecipitation/co-affinity purification coupled to quantitative mass spectrometry (w/o cross-linking)

o Label free Proximity Ligation assays techniques

- Techniques to measure interactions (HT and non-HT):

o Surface Plasmon Resonance- Principles and Assays: applications in protein research, Kinetic analysis of protein-protein interaction using SPR

o Interferometry techniques, Biomolecular interactions using Bio-Layer Interferometry (BLI): applications in protein research, Kinetic analysis of

protein-protein interaction using BLI

- Techniques to generate novel binders by libraries screenings:

o Naïve, immunization vs synthetic libraries, libraries diversity, main applications

o Introduction to Phage display

o Introduction to Yeast display

Cancer Metabolism (6 hours)

Instructors: Prof. Massimo Santoro

Schedule: May - June 2024

Description: The aim of this course is to give an overview of the most recent advances in cancer metabolism with a perspective on possible therapeutic interventions. Metabolism will be revisited as adaptations imposed by the activation of oncogenes, the loss of tumor suppressors, or the mutations of metabolic genes. We will become familiar with the concept of cancer heterogeneity related to metabolism, understand molecular, cellular and biochemical mechanisms leading to metabolism-guided cancer resistance, and acquire resistance to therapy. Specific aspects of cancer spreading and metastasis-related metabolic adaptation will be discussed.