Model Organisms in Biological Research

Vakinformatie

Model Organisms in biological research

Taught by Dr. Lucas Mergan in '23-'24. Taught by Prof. Dr. Liesbet Temmerman in '24-'25.

The exam is oral and exists of questions about a self-chosen a research paper (4/20) and one bigger question based on the course content (9/20). You get no preparatory time. ‎
The remaining 7/20 points are received by participating in the practical sessions and making a presentation.

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0G43AE.htm

Examenvragen

29th January 2025

Article

• Same as previously mentioned

Theory

• Pronucleus injection and how is it used
• Explain a recombinase system in model organisms (e.g. Cre lox) → additional questions like: how it works, how the recombinase binds, why in the F2 generation, ...

17th January 2025

Self-chosen article (the first thing she asks is if you want to talk in Dutch or English):

1. explanation of experiments done with the model organism and article content (na een heel algemene uitleg zijn we door de figuren gegaan en wijst ze er aan die je moet uitleggen, het waren over het algemeen die met op het eerste zicht de mist duidelijke assen die ze kiest)
2. motivation of the use and choice of the model organism for a biological question
3. explanation of technologies used to address the research question (hier is bij mij niet echt iets over gevraagd, eerder bij de figuren ook uitleggen welke technieken zijn gebruikt, maar niet echt hoe ze werken)
4. motivation of alternative models or tools suited for testing the proposed hypotheses (bij mij was het eerder welke dingen kunnen ze nog verder onderzoeken en hoe, als er meerdere dingen zijn mag je kiezen. Ik heb ChIPseq gezegd, wat klopte en ik niet verder moest uitleggen, dus het moet niet met een techniek die we gezien hebben)
5. related content of the course as it pertains to the discussion (niet echt iets verder over gevraagd bij mij, maar ik had veel figuren dus vermoedelijk geen tijd meer voor)

Theory (she has a big stack of cards you need to pick from, at least 20 I would guess):

1. Tet-system (extra question: what kind of system = inducible/conditional. Ik had eerst binary system gezegd, wat niet is wat ze zocht maar in principe wel juist)

Other possible questions: optogenetics, QTL mapping, ablation in C. elegans

10th January 2025

Self-chosen article:

1. explanation of experiments done with the model organism and article content,
2. motivation of the use and choice of the model organism for a biological question,
3. explanation of technologies used to address the research question,
4. motivation of alternative models or tools suited for testing the proposed hypotheses,
5. related content of the course as it pertains to the discussion.

Theory:

Explain haploid screens. Extra question: What other screen can you do on a zebrafish + explain? (F2 genetic screen)

25th January 2024

Self-chosen article:

1. Globally explain the scientific paper (goal, findings, conclusions,...)
2. Why was this model organism chosen for this specific research?
3. They used cell lines created with targeted mutagenesis. What are the risks of using a cell line made with random mutagenesis? How can such cell lines still be useful in research?
4. Can other model organisms be used and why?

Theory:

• What is the TET system? Give an example of where it's useful.
• What are polytene chromosomes and what are they used for?
  • Extra question: How could you differentiate these easily under a microscope compared to normal chromosomes?
• Explain a recombinase system in model organisms (Cre lox)
  • Extra question: why would you do this

Other possible theory questions: Complementation system, forward screening C. elegans, ES cells, tetrad analysis,...

18th January 2024

Self-chosen article:

1. Globally explain the scientific paper (goal, findings, conclusions,...)
2. Why was this model organism chosen for this specific research?
3. They used cell lines created with targeted mutagenesis. What are the risks of using a cell line made with random mutagenesis? How can such cell lines still be useful in research?
4. Can other model organisms be used and why?

Theory:

• Cre lox system for a space and time specific expression in mice
  • Extra question: How can you get a specific loxP site into the DNA?
• Complementation assay
• How would you make a knock-out in a mouse?

21st January 2022

Self-chosen article:

1. Give two reasons as to why was a model organism was needed to answer the specific research question.
2. Give two reasons why it is model organism.
3. Could any of the other model organism taught in the course be used to answer this research question? Why (not)?
4. Is further research and sacrifice of the model organism required?

For theory based on lecture:

• A highly conserved gene is involved in axonal outgrowth in humans. You want to check if this gene is conserved in a model organism. Which model organism will you use for this? How will you do this (methods and approaches)? Also, you want to check which other genes are involved in this process. Which approaches and methods from the course will you use? If the function is not conserved, can you still study involved interactions in the model organism?

2022 Voorbeeld examen

Self chosen article (4/20):

1. Question A1. Give two (2) arguments why this organism is / these organisms are suited to tackle the specific research question at hand.
2. Question A2. Give two (2) arguments why it is a model organism / they are model organisms; as opposed to model systems, as per the distinction made in the course.
3. Question A3. Could any other model organism discussed during the course have been used to address the research question? Why (not)? Do you agree with the authors’ choice? Why (not)?
4. Question A4. Given the findings and conclusions of the article, propose one additional method or approach that was covered in the course, that may be of use for this research. Explain in sufficient conceptual detail why this would be useful or logical, and which insight would be gained from using this tool/method/approach.

THEORY - LECTURE-ONLY PART (9/20):

• Motor neuron injury can lead to loss of motor function (movement/locomotion) with poor recovery due to limited regeneration. The NICD protein is well conserved in animals and while it is upregulated after axonal injury, it is a negative regulator of axonal regeneration. You are tasked to find genes that through their effect on NICD levels may affect axonal regeneration, specifically so in the case of motor neuron injury. Explain how you would proceed to complete this task, making sure your answer contains clear arguments for considering the following elements:
  • Do you need live organisms to address this question? Do they need to be model organisms? Why (not)?
  • Which organism(s) discussed during the course would be suited to tackle this question? Would you use one or multiple ones?
  • How will you retrieve information that will allow you to correlate genetic interventions, NICD levels, axonal regeneration and motor function recovery? How will you probe for causality of interventions?
  • Next to proposing a research approach, provide at least one limitation that would need to be considered as well.

2021 August

Self chosen article:

• Why is this organism chosen for this research question
• Why is this organism chosen instead of another model organism
• Do you agree with the choice of the author
• Knowing the results, what technique or method would you add to this research
• Give 2 arguments why this organism is a model organisms.

Theoretical Question:

• What is QTL mapping? What is it used for? Which model organisms did we discuss QTL mapping strategies for and would it be suitable for other model organisms discussed in the course?

2021 January

Self chosen article:

• Why is this organism chosen for this research question
• Why is this organism chosen instead of another model organism
• Do you agree with the choice of the author
• Knowing the results, what technique or method would you add to this research
• Give 2 arguments why this organism is a model organisms.

Theoretical question:

• Explain terminator seeds
• After doing a forward screening in C. elegans, they found mutants with altered body length. Explain the strategy how you can know the causal mutations. Can you perform this stragety in other organisms and which step is important for causality?
• Explain morpholinos and compare with other similar technique.

2020 January

• What is a polytene chromosome and how is it used for genetics? (Extra questions: Why was it easier to have this to study genetics, answer because it is much bigger thanks to endoduplication which means that you can see it under a microscope. If you would have found a piece of the chromosome and you can sequence it, how can you find where it is located on the polytene chromosome, answer was in situ hybridisation [You can't answer CRISPR or something like that because it didn't exist back then].)
• ES technology, any alternatives?
• Give three tetrads
  • explain the Tet system
  • explain tetrad analysis
  • explain transformation in Arabidopsis thaliana.
  • Explain P elements
  • QTL mapping

2019 January

• ES technology mice
• QTL mapping
• Optogenetics
• Give examples of prokaryotes in biological research and explain their use
• What are terminator seeds, what is their use and given an example of how they work

2017-2018 January

• Wich primates are used as model organism and for which applications?
• Explain Tetrad analysis and the application.
• Explain Pronucleus injection in mice and the application.
• Explain foward genetics in C. elegans.
• Explain Cre recombinase system and how to use it giving examples