TEACHING ACTIVITY COMMITTEE FOR Ph.D. COURSE

Prof. Alberto Barausse
Dott. Francesco Dal Grande
Prof. Marta Giacomello
Prof. Lucia Manni
Prof. Graziano Martello
Prof. Natascia Tiso
Prof. Elena Ziviani
Prof. Michela Zottini

ORGANIZATION OF THE TEACHING ACTIVITY

1) Obligatory attendance of 10 seminars/year. Signature of speaker or college member is required.
2) Obligatory attendance of 3 courses in 3 years.
3) Obligatory attendance of 1 course/years paid by the Department of Excellence Project.
4) The seminars will be held ALWAYS on Thursday of the week, preferentially starting at 14.00.

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TEACHING ACTIVITY 2023

1. Models in genetic disease research.
Dates: 24, 25, 26, 27, October 2022.
Program

2. Deadly Sins in Scientific Research (8 hours) – Seminar Room, second floor south, Polo Vallisneri.
Dates: 16, 23 February – 2, 9 March 2023, 14.00 p.m.
Speaker: Lucio Bonato, University of Padova.
Aim: stimulating PhD students to become aware of frequent “faults” in the practice of scientific research (in planning studies, in performing the research and interpreting results, and publishing the results), with the general aim of strengthening scientific integrity, accuracy and effective scientific advancements.

3. High content imaging (8 hours) – Room H, mezzanine floor, Polo Vallisneri.
Dates: 1, 7, 8, 14 March 2023, h. 9.30-11.30 a.m.
Speaker: Marta Giacomello, University of Padova.
High content imaging (HCI) is an approach that combines automated fluorescence microscopy and multiparametric image analysis. The main aim of HCI is to extract high content data (including morphological, texture, intensity parameters) from an image of a biological sample.
HCI is a three-steps process, including: (i) image acquisition; (ii) image processing; (iii) image analysis. HCI can be used for both medium and high throughput screens, based on fluorescent assays suitable for live 2D/3D biological models or multiplex cell painting.
Besides providing fundamental knowledge and skills for the design and analysis of HCI experiments.

4. Basics of CRISPR-Cas Genome Editing (4 hours) – Room H, mezzanine floor, Polo Vallisneri.
Dates: 28, 29 March 2023, h. 9.30-11.30 a.m.
Speakers: Milena Bellin, Francesco Chemello, University of Padova.
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.

5. R101 (4 hours) – Room M, mezzanine floor, Polo Vallisneri
Dates: 4, 5 April 2023, h. 10.00-12.00 p.m.
Speaker: Mirko Pegoraro, Liverpool John Moores University, (UK).
This workshop introduces R. An initial description of basic concepts and principles develop into the use of some data manipulation and graphical representation using ggplot2. The workshop also includes 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 internet is necessary.

6. NextGen DNAseq/RNAseq analysis (4 hours) – Room H, mezzanine floor, Polo Vallisneri.
Dates: 4, 5 April 2023, h. 13.00-15.00 p.m.
Speaker: Mirko Pegoraro, Liverpool John Moores University, (UK).
The workshop presents how to process next generation DNASeq/RNAseq data. Required access to PC/laptop, internet linux.

7. Science Communication, Fundraising & Career Development (18 hours) - Room G, mezzanine floor, Polo Vallisneri.
Speakers: Ralf Dahm (Institute of Molecular Biology, Germany), Natascia Tiso (University of Padova).
· 2  May 2023, 5:00-6:30 pm: Effective Science Communication I
· 8  May 2023, 5:00-6:30 pm: Effective Science Communication II
· 9  May 2023, 5:00-6:30 pm: Effective Science Communication III
· 15 May 2023, 5:00-6:30 pm: Giving Convincing Oral Presentations

· 16 May 2023, 4:30-6:30 pm: How to Apply for Jobs in Science I
· 5  June 2023, 4:30-6:30 pm: How to Apply for Jobs in Science II

· 6  June 2023, 4:30-6:30 pm: Presentations by students, session I
· 19 June 2023, 4:30-6:30 pm: Presentations by students, session II

· 20 June 2023, 4:30-6:30 pm: Discussion of applications by students I
· 26 June 2023, 4:30-6:30 pm: Discussion of applications by students II

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, such as papers, grant/fellowship 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.

8. Fellowship and grant writing (30 hours) – Room: to be defined
Dates: May - June - September 2023.
Speaker: Luca Scorrano, University of Padova.
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 grantmanship. 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.

9. OMICS approaches in biomedicine: paving the way toward Personalised Medicine (8 hours).
Speaker: Alberto Sola-Leyva, University of Granada.
- 14 June 2023, h. 16.30-18.30 p.m. - Room G, mezzanine floor, Polo Vallisneri;
- 15 June 2023, h. 9.30-12.00 p.m. - Room H, mezzanine floor, Polo Vallisneri;
- 16 June 2023, h. 9.30-12.30 p.m. - Room G, mezzanine floor, Polo Vallisneri.
 

The identification of biomarkers is a key element for medicine, in terms of less invasive and more effective procedures. Integrative approaches of different molecular biology comet techniques are a key element for personalised medicine. In this course we will approach the analysis of transcriptomics, meta-transcriptomics, microbiome, proteomics and metabolomics.

10.  Microscope imaging analysis (8 hours) – Room: to be defined
Dates: September 2023.
Speakers: Francesco Argenton, Nicoletta Plotegher, University of Padova.
The course will provide a set of principles of quantitative imaging.

11. Artificial Intelligence (4 hours) – Room: to be defined
Dates: September 2023.
Speakers: Stefania Bortoluzzi, Gabriele Sales, University of Padova.
Biology is a wide subject that offers many possibilities to apply AI and machine learning. This course will be theoretical and practical, and will provide an introduction on the potential offered by the application of AI in biology and biomedicine. There will be a test/questionnaire at the end of each block of lectures.

12. How to design and perform an experiment (8 hours) – Room: to be defined
Dates: October/November 2023,
Speaker: Graziano Martello, University of Padova.
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.