Genome Engineering, 7.5 credits

Contents

Module 1: Theory, 3.5 credits

The lectures cover technologies used to modify genetic information in biological systems, with a focus on multicellular organisms.

The course includes classical and contemporary approaches, including transgenesis, recombinase-based systems, transposon-mediated integration, RNA interference, CRISPR/Cas-based genome editing, base editing, prime editing, CRISPR interference and activation, epigenome editing, reporter systems, optogenetic and chemogenetic tools, degron-based protein control, and functional genetic screens. The course also introduces gene delivery technologies, including microinjection, electroporation, viral vectors, transfection, lipid nanoparticle-based delivery, and organism-specific delivery strategies.

The course will examine how genome-engineering strategies are selected, designed, validated, and interpreted in different biological systems, including plants, invertebrate and vertebrate model organisms. The course also covers current opportunities and limitations in organelle genome engineering, as well as ethical, biosafety, regulatory, ecological, and societal aspects of genome engineering.

Module 2: Laboratory and design work, 3 credits

The laboratory sessions mainly focus on the application of genome engineering in genetic model organisms, primarily mouse, fly, and worm, to determine gene function.

Module 3; Paper presentation, 1 credit

Students will present key scientific papers, giving them an opportunity to understand experiments that lead to methods that are currently used.

Expected learning outcomes

After completing the course, students should be able to, with regard to:

Knowledge and Understanding

• Explain how genome engineering can be used to study gene function, control gene expression, and regulate cellular function, advancing the understanding of biological processes and disease.
• Describe the principles of genetic construct design, including sequence elements required for controlled gene expression or protein function.
• Summarize key methods for introducing genetic material into cells and organisms and for modifying endogenous genes
• Explain the mechanisms of RNA-based engineering techniques.
• Describe how genome-engineering technologies are used in functional genomics, including pooled screens, reporter-based assays, single-cell readouts, and perturbation-based experimental designs

Competence and Skills

• Design an engineering strategy for a defined biological objective, including construct design, guide RNA selection when relevant, delivery method, validation strategy, and appropriate controls.
• Select and justify suitable methods for introducing genetic material or genome-editing components into cells or organisms.
• Evaluate and apply appropriate genome editing strategies (e.g., CRISPR, TALENs, base editors) to address specific genetic questions.
• Choose and utilize reporter systems (e.g., fluorescent proteins) and functional manipulation tools (e.g., optogenetic actuators, toxins) to visualize, measure, or perturb cellular processes.
• Interpret and troubleshoot experimental outcomes from gene engineering techniques, identifying sources of error or inefficiency.
• Communicate a genome-engineering strategy orally and in writing, using appropriate terminology and logical justification.

Judgement and Approach

• Assess the suitability, limitations, and ethical implications of using specific organisms, cell systems, organoids, or genetic manipulation techniques for a given research objective.
• Critically evaluate the strengths, limitations, and potential off-target effects of genome editing and gene delivery technologies.
• Reflect on methodological choices in genome engineering experiments and propose improvements or alternative strategies based on biological rationale, technical feasibility, validation requirements, and responsible use.
• Demonstrate a responsible and scientifically rigorous approach when planning or interpreting gene manipulation experiments.
• Evaluate the importance of biological sex as a factor in the design, execution, and interpretation of genetic and biomedical research.
• Evaluate technical, ethical, biosafety, regulatory, and societal challenges involved in genome manipulation.

Required Knowledge

180 credits from completed courses, including at least 60 credits in biology (covering genetics, cell biology, molecular biology, and animal physiology), of which at least 7.5 credits must be in genetics; 20 credits in chemistry, of which at least 10 credits must be in biochemistry; and documented proficiency in experimental work corresponding to at least 30 credits.

Form of instruction

The course includes a combination of lectures and student-centered teaching formats, such as laboratory work in the form of dry and wet labs, and group assignments with oral presentations and discussions. Emphasis is placed on active learning, where students are encouraged to take responsibility for their own learning through exploration, collaboration, and critical reflection. All teaching components except lectures are mandatory.

The course is taught in English.

Examination modes

The theory module is assessed through an individual written exam. The written exam is assessed using the grades Fail (U), Pass (G), and Pass with Distinction (VG). The laboratory module is assessed by individual written lab reports. The paper presentation is done in a group but with individual assessment. The assessment includes both the presentation and active participation in the associated discussions. Students must submit written assignments in the prescribed format and actively participate in presentations and discussions. Active participation includes contributing reflections, questions, and attempts to answer questions posed to the individual or group. The paper presentation and the laboratory work are assessed using the grades Fail (U) or Pass (G).

The course grade is assigned only when all examinations have been completed and assessed. All examinations must be assessed with the grade Pass (G) to achieve the grade Pass (G) on the course. For the higher grade, Pass with Distinction (VG), all examination om module 2 and 3 must be assessed with the grade Pass (G) and the written exam assessed with the grade Pass with Distinction (VG). If any of the examinations have been assessed as Fail (U), the course grade will be Fail (U), provided that the student has completed all examinations for the module.

In case of absence from a mandatory teaching session, the examiner will decide whether the student should complete a replacement assignment or retake the component at a later date.
To pass the course, all assignments must be completed in accordance with the specified requirements.

The course coordinator may decide that active participation in specified activities will award bonus points to be added to the exam score, not exceeding 10% of the total exam points. It is the responsibility of the course coordinator to inform students at the start of the course which activities offer bonus points and the criteria for earning them.

For students who have not been approved at the regular exam, a new exam will be arranged in accordance with Umeå University's Rules for grades and examinations at undergraduate and advanced level (FS 1.1-574-22). The first re-exam is offered no later than two months after the regular exam. In the cases where the regular exam takes place in May or June, a first re-examination is offered instead within three months of the regular exam. In addition, at least one further re-examination is offered within one year from the regular exam date. If the result is Fail, the student is then referred to the exam the next time the course/module is given.

A student who has failed two examinations for a course or part of a course without a passing result, has the right to have another examiner appointed, unless there are special reasons against it (HF ch. 6 § 22). The request for a new examiner is made to the Deputy Head of the Department of Molecular Biology.

For students who have been granted recommended support due to a disability, the examiner may decide to make exceptions to the form of assessment specified in the course syllabus. Individual adaptations of the assessment method should be considered based on the student's needs and the intended learning outcomes of the course. For further information, please refer to the Procedures for support for students with disabilities and the Rules for grades and examination at first- and second-cycle studies.

Other regulations

The student has the right to be tested if previous education or corresponding knowledge and skills acquired in professional activities can be credited for the corresponding education at Umeå University. The application for credit is sent to the Studentcentrum. More information about credit transfer can be found on Umeå University's student website and in the Higher Education Ordinance (ch. 6).

The course cannot be included in a degree together with Transgene Technology N/T.

Transitional provisions

In the event that the syllabus ceases to apply or undergoes major changes, students are guaranteed at least three examinations (including the regular examination opportunity) according to the regulations in the syllabus that the student was originally registered on for a period of a maximum of two years from the time that the previous syllabus ceased to apply or that the course ended.