B8794 - Genetic Engineering and Bioinformatics

Learning outcomes

The student understands the principles underlying the manipulation of genetic material for the creation of in vitro and in vivo models, as well as for gene therapy. They learn the main techniques for the generation of Knock-out and Knock-in cells and animals, and for the expression of reporter genes. The student is also familiar with the main analytical methods and the related bioinformatics tools. Furthermore, the student understands the applications and potential of the main image analysis systems. They are able to perform basic analyses using open-source software applied to microscopic preparations for the evaluation and quantification of cellular and tissue structures.

Course contents

SPECIFIC PREREQUISITES FOR THIS COURSE:

To better understand the topics covered in this course, students are advised to have already acquired knowledge in the following areas: molecular and cellular biology.

 

SPECIFIC CONTENTS:

MODULE 1 – Dr. Vito Antonio Baldassarro

The syllabus is structured as follows:

Lectures (16 h):

· Introduction to genetics applied to transgenesis (2h)

· Main strategies for genetic material manipulation (2h)

· In vivo Knock-out and Knock-in constitutive and conditional models (2h)

· Humanized animal models and their applications (2h)

· Reporter genes (2h)

· Genome and transcriptome in vitro manipulation and application examples (4h)

· Gene therapy in veterinary and human medicine (2h)

Laboratory Sessions (16h):

· Principles of bioinformatics analysis applied to the genome and transcriptome (4h)

· Bioinformatics analysis pipeline: from raw data to pathway analysis (4h)

· Principles of image analysis and main open-source software (4h)

 

 

MODULE 2 – Prof. Barbara Bacci

The syllabus is structured as follows:

Lectures (16 h):

· Digitization and quality assessment of microscopic slides for image analysis (2h)

· Principles open-source image analysis software (QuPath) (2h)

· Basic principles of image analysis: recognition of cellular and tissue structures – classification, segmentation (2h)

· Quantification methods of cellular and tissue structures in digital microscopic slides (2h)

Laboratory Sessions (16h):

· Quantification of cellular and tissue structures in histological microscopic slides (4h)

· Quantification of cellular and tissue structures in immunohistochemical and in situ hybridization slides (4h)

· Presentation of a project with final dataset and results

 

MODULE 3 – Prof. Eleonora Iacono

The syllabus is structured as follows:

Lectures (8 h):

· Advantages and disadvantages of using genetic engineering in livestock animals (1h)

· Improvement of productive performance (1h)

· Genetic engineering and the welfare of farm animals (1h)

· Use of genetically engineered livestock animals in biomedical fields (1h)

 

At the end of the theoretical and practical lessons of all three modules, a shared 4-hour session is planned, during which students will discuss the pros and cons of genetic engineering using a case study as an example.

Readings/Bibliography

The teaching materials for this course are available on the Virtuale Learning Environment (https://virtuale.unibo.it/?lang=en).

The reference updated bibliography will be uploaded on the online platform for each topic.

Teaching methods

The course includes both theoretical lectures and laboratory sessions: lectures will be delivered as frontal lessons, while the laboratory sessions will take place in the computer lab and through group work.

Considering the types of activities and teaching methods adopted, attendance for this course requires the successful completion of Modules 1 and 2 via e-learning, and Module 3 on health and safety training in study environments. Information about the schedule and access to Module 3 is available in the dedicated section of the Degree Program website.

Participation in practical and laboratory sessions requires wearing a lab coat and appropriate footwear. Suitable personal protective equipment (PPE), such as disposable latex gloves, will be provided as needed.

Assessment methods

The assessment for the Monodisciplinary Course “Genetic Engineering and Bioinformatics” consists of an oral presentation of a scientific article supported by slides (10 minutes), and three questions related to each of the three modules of the course (15 minutes).

The project-based assessment consists of a group discussion on the pros and cons of genetic engineering, using a case study as an example. The discussion will also be evaluated based on the methods used and the theoretical principles involved.

The final grade is communicated at the end of the project. The exam is considered passed with a minimum score of 18 out of 30.

 

In evaluating the oral exam, the instructor will use the following grading scale:

- Basic understanding of only a few course topics; analysis skills emerge only with the instructor’s help; generally correct language → 18–22

- Limited knowledge of several topics; independent analysis only on procedural issues; correct language use → 23–26

- Broad knowledge of course topics; ability to make autonomous critical judgments; mastery of discipline-specific terminology → 27–29

- Comprehensive understanding of course content; fully independent critical analysis and connections; excellent command of terminology and argumentation skills → 30–30 with honors

 

The result of the oral exam will be communicated at the end of the session. The minimum passing grade is 18/30. Based on the level of student participation during the final discussion day on the proposed topics, up to 1 extra point may be awarded.

Negative results are not graded numerically but recorded as “withdrawn” or “failed” in the electronic transcript on AlmaEsami, and do not affect the student’s academic record.

Grades for individual parts and the final grade will be published on the Virtuale Learning Environment (https://virtuale.unibo.it/?lang=en ) by the designated course contact within 5 working days of the exam.

Students may reject the final grade 3 times, by informing the course examiner via email within 5 working days.

The designated course contact for this course is Vito Antonio Baldassarro

Students can register for exams through the AlmaEsami platform (http://almaesami.unibo.it/). Exams are scheduled during the designated periods in the academic calendar. Additional sessions are available for students beyond the standard program duration.

 

Students with learning disorders and/or temporary or permanent disabilities: please, contact the office responsible (https://site.unibo.it/studenti-con-disabilita-e-dsa/en/for-students) as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, taking into account the teaching objectives.

Teaching tools

Power Point presentations, videos, and dedicated softwares will be used.

In case of difficulty understanding the course content, the instructor is available for clarification meetings, which must be scheduled via email.

Office hours

See the website of Vito Antonio Baldassarro

See the website of Barbara Bacci

See the website of Eleonora Iacono