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 of learning in the single-subject course “Genetic Engineering and Bioinformatics” is preferably carried out through projects to be completed during the final part of the course, as described below:

Module 2 (Prof. Barbara Bacci):
The exam consists of completing 3 image analysis projects.
For attending students: Each project is carried out and completed during the practical sessions. At the end of each session, the files and results related to the assigned task will be collected.
For non-attending students: The same projects must be completed independently and submitted to the instructor (complete instructions for completion and submission will be provided on virtuale.unibo.it). In this case, students must use their own computer and the free software QuPath https://qupath.github.io/
Assessment will be based on the quality and completeness of the projects.

Modules 1 (Dr. Vito Antonio Baldassarro) and 3 (Prof. Eleonora Iacono):
For attending students: During the last 4 hours of practical sessions, in a joint session between the two modules, students will be divided into working groups. Each group will be assigned a scientific study in genetic engineering. Each group must focus on the following points, which will then be discussed in class:

1. scientific concepts and experimental questions underlying the development of the study;
2. review of the study and possible implementations in the context of the methodologies covered during the course;
3. commentary on the pros and cons of genetic engineering using a science communication approach.
   During the discussion, knowledge of the methodologies used and the underlying theoretical principles covered in the course will also be evaluated.

For non-attending students or those unable to participate in the project: sit is possible to take an individual exam. This consists of an oral presentation of a scientific article, provided by the instructors on the virtual platform, supported by slides (10 minutes), and two questions related to each of the two modules (15 minutes).

Assessment results are communicated at the end of the project or exam. Each test is considered passed with a minimum score of 18/30.
The final grade will be the result of the weighted average between the exam of Module 2 and that of Modules 1 and 3.

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

 

A negative evaluation does not result in a numerical grade, but only a judgment (withdrawn or failed) recorded in the electronic register on AlmaEsami; therefore, it does not affect the student’s academic record.

The grade may be refused up to two times by informing the recording instructor during the exam session.

The responsible for recording grades for this course is Dr. Vito Antonio Baldassarro.

Students may register for exam sessions through AlmaEsami (http://almaesami.unibo.it/). Exam sessions are scheduled within the timeframes indicated in the academic calendar. Additional sessions are reserved for students who are out of course.

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