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Bioengineering en - omics

The CRISPR Cas9 technique enables you to change genetic material in a way that some people describe as copy and paste. Apart from being hot and exiting this technique has several great possibilities and unquestionable benefits. Like editing 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. And targeted knock-outs can be used to manipulate biological processes in so called metabolic engineering.

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 student choice, students will experience the use of CRISPR CAS9 technology to e.g. knock-out genes in the yeast genome in order to produce more bioethanol and thus reduce greenhouse gases. They could use the method to knock-out genes in mammalian cells in order to study and develop the therapy for the diseases caused by mutated genes. Or to engineer immune cells for cancer immunotherapeutic applications.

In the minor cloning strategy will be studied and students will analyse the consequences of the genetic manipulation with respect to the genome, transcriptome and metabolome using various software tools during computer practicums.

The course mimics the practice of a research group. Students are responsible for their own research. They report the results to the rest of the research groups (students) and their group leaders (lecturers). Additionally, students are motivated to discuss with their class mates current findings in the bioengineering and –omics field.

Leerdoelen

- Students will be able to orientate in the field of biomolecular engineering and genomic research; both in aspects of biotechnology and biomedicine.

- 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.

Aanvullende informatie

Target group:

This course is suitable for motivated students having an interest in learning latest techniques of molecular cloning (CRISPR CAS9) and in learning holistic approach of molecular cloning involving the use of various software for genome/transcriptome and metabolome analysis.

Students have to have successfully completed basic courses either in Molecular Biology, Molecular Detection, Molecular Medicine or similar courses involving topics of cell, biochemistry, molecular biology and basic cloning techniques.

Added value:

Students will obtain the expertise of independent design and execution of molecular cloning experiments, big data interpretation and reporting. They will also experience working in a research group as biotechnology analysts. It gives them advantage when job requests are focused on molecular cloning techniques using CRISPR CAS9 technology. Investigating molecular cloning and its influence on the metabolism of the cell will deepen their knowledge in molecular biology.

Ingangseisen

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. Foreign students are asked to deliver the proof of successfully completed course of safety work in biology/microbiology laboratories.

Following documents must be send to email martina.sura@hvhl.nl in electronical version:

- Overview of current status of obtained ECs together with the list of courses from which the ECs were obtained.

Toetsing

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.

Literatuur

No mandatory literature.

Recommended 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

Rooster

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