Bioengineering en - omics
Bioengineering is a broad area of activities. It is a discipline that combines many aspects of traditional engineering fields such as chemical, electrical and mechanical engineering. Within the spectrum of activities of bioengineering CRISPR CAS9 (genome editing technique) takes the lead in e.g. CRISPR edited immune cells for cancer therapy, improving IVF (in vitro fertilization), creating seedless tomatoes or creating biofuel. Genetic manipulation of microorganisms, plants and mammalian cells can be used to let these cells produce new molecules and/or knocking out genes encoding for proteins and allowing thus to obtain knowledge about these proteins and consequent metabolic pathways. Targeted knock-outs can be also used to manipulate biological processes in so called metabolic engineering. Manipulating the cell genome brings along changes in transcriptome and metabolome. The holistic approach of -omics (genomics, transcriptomics and metabolomics) allows to shed a light on the consequences of such genetic changes.
This minor focuses on learning and applying the techniques of CRISPR CAS9 and exploring the consequences of genome editing in silico using -omics approach. Depending on the student choice, students will experience the use of CRISPR CAS9 technology to:
- knock-out genes in yeast genome with the aim to prepare genetically modified yeast producing more bioethanol and thus offer sustainable biotechnology method to reduce greenhouse gases,
- knock-out genes in mammalian cells in order to study and develop the therapy for the diseases caused by mutated genes,
- engineer immune cells for cancer immunotherapeutic applications.
To obtain desired result, cloning strategy will be first designed and further carried out in the laboratory. Students will analyse the consequences of the genetic manipulation with respect to the genome, transcriptome and metabolome using various software tools during computer practicums.
This course is intended to mimic the practice of a research group. Students are responsible for their own research and reporting the results by weekly meetings/presentations to the rest of the research groups (students) and their group leaders (lecturers). Additionally, students are motivated to discuss with their the class mates current findings in the bioengineering and -omics field via presenting selected research articles.
- Students will be able to orientate in the field of biomolecular engineering and genomic research.
- Students will be able to set up a cloning strategy and execute it in the laboratory.
- Students will be able to generate and process “big data”.
- Students will be able to use various genomic software and online tools to investigate functional regions of genetic elements and analyse amino acid sequence regarding composition, properties, homology, structure and function.
- Students will be able to interpret and report data obtained from molecular cloning and genomic software tools.
- Students will be able to interpret and report data obtained from research articles.
- Students will be able to link the use of several genomic techniques to the practical aspects of laboratory experiments.
In case of a low number of applications for the minor, the minor may not be offered. After closing the registration period, you will be informed as soon as possible (no later than 20 December 2019).
To start the minor student has to have minimum of 75 EC related to Life Sciences & Technology and successfully completed courses of Molecular Biology, including the basic skills in molecular cloning.
The following documents must be send:
Overview of current status of obtained EC's together with the list of courses from which the EC's were obtained.
Students are graded based on six assessments.
Assessment A: Theory knowledge is assessed by written exam (open and multiple choice questions) – individual grading. Grading 0.1 – 10.
Assessment B: The practical instruction in the laboratory are assessed by the attendance (mandatory), commitment, lab journal and a report (grade 0.1 - 10) – group grading.
Assessment C: The research design for cloning experiment (for laboratory assignment) is assessed by written plan of approach (Go/NoGo moment) and attendance and active participation during realization of the plan of approach – group grading.
Assessment D: The practical performance of the course assignment is assessed by the attendance and active participation in the laboratory, at tutor meetings and work discussions (minimum 80%). Data interpretation is assessed by the poster presentation (grade 0.1 – 10) – individual grading.
Assessment E: The computer practicums are assessed by the attendance at computer practicums and presentations (mandatory), commitment and a report (grade 0.1 - 10) – individual grading.
Assessment F: An important feature of an HBO-skilled biotechnology analyst is the ability of self-reflection, even more when we work as a team. The student writes a reflection on his/her function/role in the minor Bioengineering and -omics. Individual grading, assessed as sufficient/insufficient.
No mandatory literature
Thomas A., Thrive in Genetics, Oxford University Press, 2013, ISBN: 9780199694624
Primrose S.B. and Twyman R.M., Principles in Gene Manipulation and Genomics, John Wiley And Sons Ltd, 2006, seventh edition, ISBN: 9781405135443
Students get 30 EC when successfully finalizing the course. Course consists of six parts (A, B, C, D, E, F):
Part A (Theory): 160 hours
Lectures 46 hours
Self-study 110 hours
Exams 4 hours
Part B (Practical instructions in the laboratory): 64 hours
Preparation/self-study 16 hours
Practical instruction 32 hours
Report 16 hours
Part C (Research design): 66 hours
Literature study 40 hours
Tutor meetings 6 hours
Plan of approach 20 hours
Part D (Laboratory assignment): 262 hours
Self-study/preparation 97 hours
Tutor meetings 15 hours
Practical work in the lab 96 hours
Work discussions/presentations 46 hours
Poster presentation 8
Part E (Computer practicums): 260 hours
Self-study/implementation 143 hours
Practical instructions 28 hours
Work discussions/presentations 66 hours
Report 22 hours
Part F (Self-reflection): 28 hours
Preparation 22 hours
Report 6 hours