BMB836: Application of CRISPR Genome Engineering in Cell Biology and Biomedicine

Study Board of Science

Teaching language: Danish or English depending on the teacher, but English if international students are enrolled
EKA: N210045102
Censorship: Second examiner: Internal
Grading: 7-point grading scale
Offered in: Odense
Offered in: Autumn
Level: Master's level course approved as PhD course

STADS ID (UVA): N210045101
ECTS value: 5

Date of Approval: 07-04-2021


Duration: 1 semester

Version: Approved - active

Comment

01016701 (former UVA) is identical with this course description. 
The course is aimed at master level and bachelor level students but can also be followed by students at Ph.D. level in which case the criteria for the written assignment are adjusted and evaluated accordingly.

A minimum number of participants (8) is required before the course is implemented and a maximum number can participate (36). The course has limited seats and in case of too many applications, priority is given to the timely registration by date of registration.

Entry requirements

Passed BMB507 and BMB508, or fully accepted to the master programme Molecular Bioscience, Biomedicine or Computational Biomedicine.

Academic preconditions

Students taking the course are expected to: 

  • Have knowledge corresponding to the curriculum presented in the courses BMB536, BMB507 and BMB508.
  • Be able to conduct basic laboratory experiments in cell and molecular biology.

Participant limit

36

Course introduction

The aim of the course is to provide an overview of the biological origin, the principles, and the use of the CRISPR/Cas9 system for genome engineering. Although the main focus of the course is on methodological approaches to alter genomic DNA sequences (gene editing), the course will also illustrate computational design of CRISPR reagents and how these can be used to modify the transcriptional and epigenetic regulation of gene expression to study the function of genes and proteins. In the experimental part, the student will learn how to design CRISPR targets using bioinformatics tools and how to generate gene knockouts/knock-ins, validate editing events, and analyse phenotypes using established technologies. The aim of the experimental part is to enable the students to apply these novel and efficient technologies in their own research projects.

The course builds on the knowledge acquired during the second-year courses BMB536, BMB507, and BMB508 and gives an academic basis for studying the causality between the genotype and phenotype relevant for BMB and Biomedical students.

In relation to the competence profile of the degree it is the explicit focus of the course to:
  • Give the competence to understand the biology and principles of the CRISPR/Cas9 system
  • Give the competence to utilize bioinformatic toolkits to design CRISPR/Cas9 reagents. 
  • Give experimental skills to apply CRISPR/Cas9 for gene editing
  • Give knowledge and understanding of genome engineering in life science research and medical applications.

Expected learning outcome

The learning objectives of the course is that the student demonstrates the ability to: 
  • Understand the evolution and biological relevance of CRISPR.
  • Understand the underlying principles, mechanism of action, and the potential as well as the limitations of genome editing using CRISPR/Cas9.
  • Design target specific CRISPR/Cas9 reagents and incorporate their use in own research projects.
  • Analyze and assess own results as well as those obtained by others using CRISPR/Cas9.
  • Explore other CRISPR-associated enzymes and systems for genome editing.
  • Discuss recent developments in the field of genome editing.

Content

The following main topics are contained in the course: 
  • The evolution and biological relevance of CRISPR
  • Design of CRISPR/Cas9 reagents (gRNAs) using bioinformatic tools
  • Understanding the structure of Cas-proteins and gRNA’s, their associated delivery systems and the principles behind gene targeting
  • Delivery methods (transfection/transduction) and associated vector systems
  • Basic rules for knockout, knock-in and base editing, including design of knock-in targeting constructs
  • The interplay between DNA repair pathways and CRISPR
  • Methods for detection of CRISPR/Cas9-induced editing and the establishment and validation of clonal cell lines
  • Consideration of on-target and off-target effects and rescue strategies to validate genotypes and phenotypes
  • Cell systems and model organisms
  • Targeted and genome-wide screens
  • Alternative genome editing tools
  • Application of the CRISPR/Cas9 system for genome engineering
  • Gene therapy and other biomedical applications of the CRISPR/Cas9 technology
  • Technology development
  • Ethical recommendation

Literature

The course literature will consists of review articles, research articles, exercises and protocols provided via e-learn at the start of the course.
See Blackboard for syllabus lists and additional literature references.

Examination regulations

Exam element a)

Timing

June

Tests

Oral exam based on an individual written assignment

EKA

N210045102

Censorship

Second examiner: Internal

Grading

7-point grading scale

Identification

Student Identification Card

Language

Normally, the same as teaching language

Examination aids

To be announced during the course

ECTS value

5

Additional information

The examination form for re-examination may be different from the exam form at the regular exam.

Indicative number of lessons

44 hours per semester

Teaching Method

At the faculty of science, teaching is organized after the three-phase model ie. intro, training and study phase.

  • Intro phase (lectures, classroom teaching) - Number of hours: 16
  • training phase: Number of hours: 28 hours, of which 16 hours examination and 12 hours laboratory 

Elaboration on the choice of teaching methods and their mutual coherence: The teaching methods for the theoretical part involve lectures based on review articles presented by the instructors and tutorials based on research articles presented by the students and discussed with the instructors. The teaching methods for the practical part involve computer exercise based on open-source software and laboratory exercises. The study phase includes preparations for the theoretical and practical parts and for a final assignment to be defended at an oral exam. The three phases provide progression of knowledge on how to design target specific CRISPR/Cas9 reagents and incorporate their use in the students own research project.

Educational activities 

  • Prepare for lectures by reading selected literature provided by the instructors.
  • Prepare presentations for tutorials, which are conducted in the format of a journal club, where developments in the field of genome editing are discussed by evaluating research publications.
  • Prepare small written assignments as part of the computer exercises.
  • Prepare a written assignment based on the laboratory exercises (group) and topics discussed during the course (individual).

Teacher responsible

Name E-mail Department
Jens S. Andersen jens.andersen@bmb.sdu.dk Institut for Biokemi og Molekylær Biologi
Kedar Nath Natarajan knn@d-ias.sdu.dk Institut for Biokemi og Molekylær Biologi

Timetable

35
Monday
30-08-2021
Tuesday
31-08-2021
Wednesday
01-09-2021
Thursday
02-09-2021
Friday
03-09-2021
08 - 09
09 - 10
10 - 11
11 - 12
12 - 13
13 - 14
14 - 15
Class f
Forelæsning
15 - 16
Class f
Forelæsning
Show full time table

Administrative Unit

Biokemi og Molekylær Biologi

Team at Registration & Legality

NAT

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