Chemika Examenwiki - Gebruikersbijdragen [nl]

Applied Medical Biotechnology

2026-01-16T12:51:21Z

R0895938: /* 15 January 2026 */

[[Categorie: Mabb]]
==Vakinformatie==
Given by Philippe Van den Steen, Diether Lambrechts and Jan Cools. Each professor gave 4 classes. Each part has the same weight on the exam and one part is oral with written preparation. At the end of each chapter of the classes of professor Lambrechts are possible exam questions (questions are guaranteed to be from that list). This is a subject from the faculty of bioscience engineering. (2024-2025)

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/I0I27AE.htm#activetab=doelstellingen_idp1519328

==Exam questions==

===15 January 2026===
Oral parts were with Cools or Van der Steen

Cools:
# In a whole genome study on 100 patients they found the following mutations: What can you conclude from this? Wat advise would you give these patients? What risks do these patients have?
#* 3 patients with DNMT3A mutants: VAF=0.02, VAF = 0.01, VAF = 0.05
#* 1 patient with a TET2 mutant: VAF = 0.01
#* 1 patient with mutations in DNMT3A (VAF = 0.49), TET2 (VAF = 0.38) and P53 (VAF = 0.26)
# 4 Concepts to explain
#* PROTAC
#* CAR-T cell therapy
#* Irreversible vs reversible kinase inhibitor
#* How can you know lung cancer is caused by smoking?

Van der steen:
# Type one interferons. How are they used to treat disease? We saw two examples. Explain them both. On what mechanism do they work? In case of INF-beta, does it work better glycosylated or non-glycosylated and why?
# A group of researchers want to make a small biological against sequestration of malaria. Why could such a drug be useful? We saw to types of drug screens. Describe the differences and (dis)advantages. When developping the anti-sequestration drug, would you go for an intracellular or extracellular target?

Lambrechts:
# Give 2 examples of an inducible gene expression system. Describe them schematically.
# Somatic copy number alterations are frequent in solid tumors. We discussed 2 examples of how these copy number alterations can be used as biomarkers: 1/ to tailor PARP inhibitors to ovarian cancer patients or 2/ to aid in the pre-symptomatic detection of cancer in pregnant women. Give the name of both genetic tests and briefly describe how they work (give their underlying principle).

===09 January 2026===
Lambrechts was present for the oral exam

Cools:
# Explain PROTAC and molecular glues. Compare. Give an example in cancer-context. Which technique do you use for measuring if your PROTAC worked?
# Explain 4 definitions/concepts
#* Bispecific antibodies
#* Effect deamination on mutations
#* Why does clonal hematopoiesis increase with aging
#* How can we change a transcriptional repressor into an activator

Lambrechts:
# Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
# Describe schematicaly how i) chemical and ii) transposon insertional mutagenesis screens work in zebrafish and explain. How would you use a CRISPR screen in the zebrafish (discuss the example highlighted) and would this result in comparable data as in i) and ii). Finally, describe which system you use to induce gene expression in the zebrafish.

Van den Steen:
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

===09 January 2026 AM===
Cools and Lambrechts were present for the oral exam

Cools:
# Explain Clonal hematopoeisis (what it is). Why it is different from Leukemia. To what other disease/complications it is linked. Something about the expected VAF of CH.
# Explain 4 definitions/concepts
#* PROTAC
#* mutation signature
#* CAR T-cell
#* How can we change a transcriptional repressor into an activator

Lambrechts:
# Describe the Cre-recombinase system. Cre recombinase is used to generate 5 types of transgenic mice. Describe each type briefly.
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types

Van den Steen:
# What vaccination strategy should you use against leishamania polysaccharides, why do you think this would (not) be effective?
# Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?

===17 Januari 2025 AM===
Van Den Steen and Lambrechts were present for the oral exam

Cools:
# What is CAR T cell therapy? How can there be resistance against CAR T cell therapy? How can we improve the CAR T cell therapy to prevent resistance?
# Explain 4 definitions/concepts
#* H3K4me3
#* Effect deamination on mutations
#* siRNAs
#* Irreversible kinase inhibitors

Lambrechts:
# We discussed the usage of three model organisms. Can you describe their advantages and disadvantages that you would take into account when designing your laboratory experiments?
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.

Van den Steen:
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# monoclonal antibody (called malarimab) with high affinity for circum-sporozoite protein was designed: explain how this can be used in the fight against malaria - effector mechanisms, compare with vaccination and with antimalarial drugs chloroquine and artemisinine, how can there be optimisation of the monoclonal antibody and should the monoclonal antibody be sialylated to have good anti-malarial activity?

===16 Januari 2025 PM===
Cools and Lambrechts were present for the oral exam

Cools:
# What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
# Four questions:
#* What is the difference between bulk CRISPR screens and single cell CRISPR screens?
#* What is PROTAC?
#* What are CAR-T cells?
#* H3K27me3

Lambrechts:
#Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
#After quality control , scRNAseq can be analyzed in different ways. Please describe some of the methods typically used to assess differences between 2 conditions by scRNAseq.

Van den Steen:
#Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?
#Develop a vaccine against specific saccharide of T. Cruzi. Which vaccine do you use, how to adapt it, what process is used and how can T. cruzi acquire resistance?

===16 Januari 2025 AM===
Oral exam by one of the professors (we had the oral exam from Lambrechts)

Cools:
# Give the 3 ways to do immunotherapy on cancer cells, describe them, give their advantages and dis-
# Explain 4 definitions/concepts
#* PROTAC
#* H3K4me3
#* ChIP seq
#* Clonal hematopoeisis

Lambrechts:
# Question about somatic number mutations (PARP inhibitors etc)
# Question about Cre recombinase and the 5 applications (transgenic mice)

Van den Steen
# mRNA vaccin: explain design, mechanism and immunology of this concept
# explain malaria sequestration, if you would use small molecule inhibitors and explain difference between phenotype and targetting screening and explain how you could use targetting screens.

===10 Januari 2025 PM===
You had an oral exam by one of the professors (post-it note on exam paper which one)

Cools (oral: he read your answer and asked extra questions, do not need to explain again what you wrote down):
# What is CAR T cell therapy? How to detect if it worked (answer: PCR of TCR DNA)? What are some problems (at least 3) and how to solve these?
# Four questions:
#* genome instability
#* PROTAC
#* ChIPseq
#* bivalent antibodies (bijvraag: advantages and disadvantages compared to CAR T)

Lambrechts:
# scRNAseq can be complemented by CITEseq, scTCRseq and ATACseq. Can you explain how and what these 3 methods measure?
# How is zygote injection used to generate transgenic mice ? Which are the 5 potential applications in brief ?

Van den Steen (oral):
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# vaccination strategy against leishamania polysaccharides, why do you think this would (not) be effective?

===10 Januari 2025 AM===
Cools and Van den Steen were present for the oral exam
Cools:
# What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
# Four questions:
#* What is the difference between bulk CRISPR screens and single cell CRISPR screens?
#* What is PROTAC?
#* What are CAR-T cells?
#* H3K27me3

Lambrechts:
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
# Can you (schematically) describe the technology used by the scientist Jiankee He. Can you describe what Jiankee He did to upset the international scientic community. And why is there less controversy around the authorised use of Casegevy in humans - describe ?

Van den Steen:
# Give two examples of therapeutics of type 1 interferon. Also describe the underlying mechanism. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
# A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

===6 september 2024===
Cools:
# Whole-exome sequencing data of white blood cells of individuals given including the VAF of the mutations. The mutations that were found were DNMT3A, JAK2, TET2 and ASXL1: what is going on in these individuals, what can you conclude from the data, what would you recommend these individuals?
# Describe 3 different types of immunotherapy for cancer treatment in detail, compare these different types and give their advantages and disadvantages, also explain the main problems with these types of immunotherapy

Van Den Steen:
# What are the biological therapeutics for TNF-alfa. Compare, give advantages and disadvantages. What is the main therapeutic that is used? What is the main problem with it? Would you sialylate this biological therapeutic?
# Design a vaccination strategy against Trypanosoma cruzi

Lambrechts:
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
# Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?

===18 januari 2024===
Cools:
# what is clonal hematopoiesis? How to detect? Consequences/implications?
# a) CAR-T cell b) single-cell CRISPR screen c) ATAC sequencing d) PROTAC

Van den Steen:
# IFN-alfa: give the different types + their (dis)advantages, their application, should they be sialylated?
# Explain placental malaria + which type of vaccine would you make + would it be effective?

Lambrechts:
# PARP inhibitors and pre-symptomatic tumor detection; name of the two tests and how they work.
# Cre recombinase system + 4 types of mouse models

===12 januari 2024===
Cools:
# Ik heb 10 kankercellijnen waarvan er 4 een puntmutatie hebben op een non-coded region. De puntmutatie bevindt zich voor de promotor van een gekend oncogen. Hoe controleer ik of de puntmutatie invloed heeft op de expressie van dit oncogen? Beschrijf de methodes die je zou toepassen (ChIP sequencing + ATAC)
# a) oncohistones b) single-cell CRISPR screen c) bispecific antibodies d) PROTAC

Van den Steen:
# Give two examples of therapeutics of type 1 interferon. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
# What is the link between sequestration and evading the immune system regarding malaria? Could the molecules used for sequestration be a good vaccin target? Explain in detail why (not).

Lambrechts:
# What is measured with CITEseq, ATACseq and scTCRseq? Explain briefly
# How is zygote injection done to generate a transgenic mice? Give briefly 5 examples.

===19 januari 2023===
Cools:
# a) PROTAC b) Problems when using in cancer treatment
# ChIP-sequencing
# ShRNA screen against 100 genes of which 1 causing drug resistance
# a) What is clonal hematopoiesis? b) 100 people, how do you find out who has CH? Describe step by step: what do you need/what technology do you use/how do you perform data analysis?

Eelen:
# What is meant by 'Gene transfer in somatic cells'? Give an example. - max. 5 lines
# How can the Cre/LoxP system be made inducible? Can it be made tissue specific? - max. 5 lines
# Explain the Tet-on/Tet-off system schematically. Can it be made tissue specific? - max. 1 page

Lambrechts:
# PRS? How did it originate? How can it be used for breast cancer?
# Methylation as chemical marker? Chemical reaction? Use?

Van Den Steen:
# Passive immunisation therapy against cerebral malaria
# Difluoro-methylornithine

Applied Medical Biotechnology

2026-01-16T08:29:36Z

R0895938: /* 15 January 2026 */

[[Categorie: Mabb]]
==Vakinformatie==
Given by Philippe Van den Steen, Diether Lambrechts and Jan Cools. Each professor gave 4 classes. Each part has the same weight on the exam and one part is oral with written preparation. At the end of each chapter of the classes of professor Lambrechts are possible exam questions (questions are guaranteed to be from that list). This is a subject from the faculty of bioscience engineering. (2024-2025)

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/I0I27AE.htm#activetab=doelstellingen_idp1519328

==Exam questions==

===15 January 2026===
Oral parts were with Cools or Van der Steen

Cools:
# In a whole genome study on 100 patients they found the following mutations: What can you conclude from this? Wat advise would you give these patients? What risks do these patients have?
#* 3 patients with DNMT3A mutants: VAF=0.02, VAF = 0.01, VAF = 0.05
#* 1 patient with a TET2 mutant: VAF = 0.01
#* 1 patient with mutation is DNMT3A (VAF = 0.49), TET2 (VAF = 0.38) and P53 (VAF = 0.26)
# 4 Concepts to explain
#* PROTAC
#* CAR-T cell therapy
#* Irreversible vs reversible kinase inhibitor
#* How can you know lung cancer is caused by smoking?

Van der steen:
# Type one interferons. How are they used to treat disease? We saw two examples. Explain them both. On what mechanism do they work? In case of INF-beta, does it work better glycosylated or non-glycosylated and why?
# A group of researchers want to make a small biological against sequestration of malaria. Why could such a drug be useful? We saw to types of drug screens. Describe the differences and (dis)advantages. When developping the anti-sequestration drug, would you go for an intracellular or extracellular target?

Lambrechts:
# Give 2 examples of an inducible gene expression system. Describe them schematically.
# Somatic copy number alterations are frequent in solid tumors. We discussed 2 examples of how these copy number alterations can be used as biomarkers: 1/ to tailor PARP inhibitors to ovarian cancer patients or 2/ to aid in the pre-symptomatic detection of cancer in pregnant women. Give the name of both genetic tests and briefly describe how they work (give their underlying principle).

===09 January 2026===
Lambrechts was present for the oral exam

Cools:
# Explain PROTAC and molecular glues. Compare. Give an example in cancer-context. Which technique do you use for measuring if your PROTAC worked?
# Explain 4 definitions/concepts
#* Bispecific antibodies
#* Effect deamination on mutations
#* Why does clonal hematopoiesis increase with aging
#* How can we change a transcriptional repressor into an activator

Lambrechts:
# Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
# Describe schematicaly how i) chemical and ii) transposon insertional mutagenesis screens work in zebrafish and explain. How would you use a CRISPR screen in the zebrafish (discuss the example highlighted) and would this result in comparable data as in i) and ii). Finally, describe which system you use to induce gene expression in the zebrafish.

Van den Steen:
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

===09 January 2026 AM===
Cools and Lambrechts were present for the oral exam

Cools:
# Explain Clonal hematopoeisis (what it is). Why it is different from Leukemia. To what other disease/complications it is linked. Something about the expected VAF of CH.
# Explain 4 definitions/concepts
#* PROTAC
#* mutation signature
#* CAR T-cell
#* How can we change a transcriptional repressor into an activator

Lambrechts:
# Describe the Cre-recombinase system. Cre recombinase is used to generate 5 types of transgenic mice. Describe each type briefly.
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types

Van den Steen:
# What vaccination strategy should you use against leishamania polysaccharides, why do you think this would (not) be effective?
# Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?

===17 Januari 2025 AM===
Van Den Steen and Lambrechts were present for the oral exam

Cools:
# What is CAR T cell therapy? How can there be resistance against CAR T cell therapy? How can we improve the CAR T cell therapy to prevent resistance?
# Explain 4 definitions/concepts
#* H3K4me3
#* Effect deamination on mutations
#* siRNAs
#* Irreversible kinase inhibitors

Lambrechts:
# We discussed the usage of three model organisms. Can you describe their advantages and disadvantages that you would take into account when designing your laboratory experiments?
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.

Van den Steen:
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# monoclonal antibody (called malarimab) with high affinity for circum-sporozoite protein was designed: explain how this can be used in the fight against malaria - effector mechanisms, compare with vaccination and with antimalarial drugs chloroquine and artemisinine, how can there be optimisation of the monoclonal antibody and should the monoclonal antibody be sialylated to have good anti-malarial activity?

===16 Januari 2025 PM===
Cools and Lambrechts were present for the oral exam

Cools:
# What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
# Four questions:
#* What is the difference between bulk CRISPR screens and single cell CRISPR screens?
#* What is PROTAC?
#* What are CAR-T cells?
#* H3K27me3

Lambrechts:
#Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
#After quality control , scRNAseq can be analyzed in different ways. Please describe some of the methods typically used to assess differences between 2 conditions by scRNAseq.

Van den Steen:
#Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?
#Develop a vaccine against specific saccharide of T. Cruzi. Which vaccine do you use, how to adapt it, what process is used and how can T. cruzi acquire resistance?

===16 Januari 2025 AM===
Oral exam by one of the professors (we had the oral exam from Lambrechts)

Cools:
# Give the 3 ways to do immunotherapy on cancer cells, describe them, give their advantages and dis-
# Explain 4 definitions/concepts
#* PROTAC
#* H3K4me3
#* ChIP seq
#* Clonal hematopoeisis

Lambrechts:
# Question about somatic number mutations (PARP inhibitors etc)
# Question about Cre recombinase and the 5 applications (transgenic mice)

Van den Steen
# mRNA vaccin: explain design, mechanism and immunology of this concept
# explain malaria sequestration, if you would use small molecule inhibitors and explain difference between phenotype and targetting screening and explain how you could use targetting screens.

===10 Januari 2025 PM===
You had an oral exam by one of the professors (post-it note on exam paper which one)

Cools (oral: he read your answer and asked extra questions, do not need to explain again what you wrote down):
# What is CAR T cell therapy? How to detect if it worked (answer: PCR of TCR DNA)? What are some problems (at least 3) and how to solve these?
# Four questions:
#* genome instability
#* PROTAC
#* ChIPseq
#* bivalent antibodies (bijvraag: advantages and disadvantages compared to CAR T)

Lambrechts:
# scRNAseq can be complemented by CITEseq, scTCRseq and ATACseq. Can you explain how and what these 3 methods measure?
# How is zygote injection used to generate transgenic mice ? Which are the 5 potential applications in brief ?

Van den Steen (oral):
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# vaccination strategy against leishamania polysaccharides, why do you think this would (not) be effective?

===10 Januari 2025 AM===
Cools and Van den Steen were present for the oral exam
Cools:
# What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
# Four questions:
#* What is the difference between bulk CRISPR screens and single cell CRISPR screens?
#* What is PROTAC?
#* What are CAR-T cells?
#* H3K27me3

Lambrechts:
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
# Can you (schematically) describe the technology used by the scientist Jiankee He. Can you describe what Jiankee He did to upset the international scientic community. And why is there less controversy around the authorised use of Casegevy in humans - describe ?

Van den Steen:
# Give two examples of therapeutics of type 1 interferon. Also describe the underlying mechanism. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
# A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

===6 september 2024===
Cools:
# Whole-exome sequencing data of white blood cells of individuals given including the VAF of the mutations. The mutations that were found were DNMT3A, JAK2, TET2 and ASXL1: what is going on in these individuals, what can you conclude from the data, what would you recommend these individuals?
# Describe 3 different types of immunotherapy for cancer treatment in detail, compare these different types and give their advantages and disadvantages, also explain the main problems with these types of immunotherapy

Van Den Steen:
# What are the biological therapeutics for TNF-alfa. Compare, give advantages and disadvantages. What is the main therapeutic that is used? What is the main problem with it? Would you sialylate this biological therapeutic?
# Design a vaccination strategy against Trypanosoma cruzi

Lambrechts:
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
# Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?

===18 januari 2024===
Cools:
# what is clonal hematopoiesis? How to detect? Consequences/implications?
# a) CAR-T cell b) single-cell CRISPR screen c) ATAC sequencing d) PROTAC

Van den Steen:
# IFN-alfa: give the different types + their (dis)advantages, their application, should they be sialylated?
# Explain placental malaria + which type of vaccine would you make + would it be effective?

Lambrechts:
# PARP inhibitors and pre-symptomatic tumor detection; name of the two tests and how they work.
# Cre recombinase system + 4 types of mouse models

===12 januari 2024===
Cools:
# Ik heb 10 kankercellijnen waarvan er 4 een puntmutatie hebben op een non-coded region. De puntmutatie bevindt zich voor de promotor van een gekend oncogen. Hoe controleer ik of de puntmutatie invloed heeft op de expressie van dit oncogen? Beschrijf de methodes die je zou toepassen (ChIP sequencing + ATAC)
# a) oncohistones b) single-cell CRISPR screen c) bispecific antibodies d) PROTAC

Van den Steen:
# Give two examples of therapeutics of type 1 interferon. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
# What is the link between sequestration and evading the immune system regarding malaria? Could the molecules used for sequestration be a good vaccin target? Explain in detail why (not).

Lambrechts:
# What is measured with CITEseq, ATACseq and scTCRseq? Explain briefly
# How is zygote injection done to generate a transgenic mice? Give briefly 5 examples.

===19 januari 2023===
Cools:
# a) PROTAC b) Problems when using in cancer treatment
# ChIP-sequencing
# ShRNA screen against 100 genes of which 1 causing drug resistance
# a) What is clonal hematopoiesis? b) 100 people, how do you find out who has CH? Describe step by step: what do you need/what technology do you use/how do you perform data analysis?

Eelen:
# What is meant by 'Gene transfer in somatic cells'? Give an example. - max. 5 lines
# How can the Cre/LoxP system be made inducible? Can it be made tissue specific? - max. 5 lines
# Explain the Tet-on/Tet-off system schematically. Can it be made tissue specific? - max. 1 page

Lambrechts:
# PRS? How did it originate? How can it be used for breast cancer?
# Methylation as chemical marker? Chemical reaction? Use?

Van Den Steen:
# Passive immunisation therapy against cerebral malaria
# Difluoro-methylornithine

Applied Medical Biotechnology

2026-01-16T08:26:26Z

R0895938: /* 15 January 2026 */

[[Categorie: Mabb]]
==Vakinformatie==
Given by Philippe Van den Steen, Diether Lambrechts and Jan Cools. Each professor gave 4 classes. Each part has the same weight on the exam and one part is oral with written preparation. At the end of each chapter of the classes of professor Lambrechts are possible exam questions (questions are guaranteed to be from that list). This is a subject from the faculty of bioscience engineering. (2024-2025)

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/I0I27AE.htm#activetab=doelstellingen_idp1519328

==Exam questions==

===15 January 2026===
Oral parts were with Cools or Van der Steen

Cools:
# In a whole genome study on 100 patients they found the following mutations: What can you conclude from this? Wat advise would you give these patients? What risks do these patients have?
#* 3 patients with DNMT3A mutants: VAF=0.02, VAF = 0.01, VAF = 0.05
#* 1 patient with a TET2 mutant: VAF = 0.01
#* 1 patient with mutation is DNMT3A (VAF = 0.49), TET2 (VAF = 0.38) and P53 (VAF = 0.26)
# 4 Concepts to explain
#* PROTAC
#* CART
#* Irreversible vs reversible kinase inhibitor
#* How can you know lung cancer is caused by smoking?

Van der steen:
# Type one interferons. How are they used to treat disease? We saw two examples. Explain them both. On what mechanism do they work? In case of INF-beta, does it work better glycosylated or non-glycosylated and why?
# A group of researchers want to make a small biological against sequestration of malaria. Why could such a drug be useful? We saw to types of drug screens. Describe the differences and (dis)advantages. When developping the anti-sequestration drug, would you go for an intracellular or extracellular target?

Lambrechts:
# Give 2 examples of an inducible gene expression system. Describe them schematically.
# Somatic copy number alterations are frequent in solid tumors. We discussed 2 examples of how these copy number alterations can be used as biomarkers: 1/ to tailor PARP inhibitors to ovarian cancer patients or 2/ to aid in the pre-symptomatic detection of cancer in pregnant women. Give the name of both genetic tests and briefly describe how they work (give their underlying principle).

===09 January 2026===
Lambrechts was present for the oral exam

Cools:
# Explain PROTAC and molecular glues. Compare. Give an example in cancer-context. Which technique do you use for measuring if your PROTAC worked?
# Explain 4 definitions/concepts
#* Bispecific antibodies
#* Effect deamination on mutations
#* Why does clonal hematopoiesis increase with aging
#* How can we change a transcriptional repressor into an activator

Lambrechts:
# Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
# Describe schematicaly how i) chemical and ii) transposon insertional mutagenesis screens work in zebrafish and explain. How would you use a CRISPR screen in the zebrafish (discuss the example highlighted) and would this result in comparable data as in i) and ii). Finally, describe which system you use to induce gene expression in the zebrafish.

Van den Steen:
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

===09 January 2026 AM===
Cools and Lambrechts were present for the oral exam

Cools:
# Explain Clonal hematopoeisis (what it is). Why it is different from Leukemia. To what other disease/complications it is linked. Something about the expected VAF of CH.
# Explain 4 definitions/concepts
#* PROTAC
#* mutation signature
#* CAR T-cell
#* How can we change a transcriptional repressor into an activator

Lambrechts:
# Describe the Cre-recombinase system. Cre recombinase is used to generate 5 types of transgenic mice. Describe each type briefly.
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types

Van den Steen:
# What vaccination strategy should you use against leishamania polysaccharides, why do you think this would (not) be effective?
# Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?

===17 Januari 2025 AM===
Van Den Steen and Lambrechts were present for the oral exam

Cools:
# What is CAR T cell therapy? How can there be resistance against CAR T cell therapy? How can we improve the CAR T cell therapy to prevent resistance?
# Explain 4 definitions/concepts
#* H3K4me3
#* Effect deamination on mutations
#* siRNAs
#* Irreversible kinase inhibitors

Lambrechts:
# We discussed the usage of three model organisms. Can you describe their advantages and disadvantages that you would take into account when designing your laboratory experiments?
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.

Van den Steen:
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# monoclonal antibody (called malarimab) with high affinity for circum-sporozoite protein was designed: explain how this can be used in the fight against malaria - effector mechanisms, compare with vaccination and with antimalarial drugs chloroquine and artemisinine, how can there be optimisation of the monoclonal antibody and should the monoclonal antibody be sialylated to have good anti-malarial activity?

===16 Januari 2025 PM===
Cools and Lambrechts were present for the oral exam

Cools:
# What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
# Four questions:
#* What is the difference between bulk CRISPR screens and single cell CRISPR screens?
#* What is PROTAC?
#* What are CAR-T cells?
#* H3K27me3

Lambrechts:
#Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
#After quality control , scRNAseq can be analyzed in different ways. Please describe some of the methods typically used to assess differences between 2 conditions by scRNAseq.

Van den Steen:
#Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?
#Develop a vaccine against specific saccharide of T. Cruzi. Which vaccine do you use, how to adapt it, what process is used and how can T. cruzi acquire resistance?

===16 Januari 2025 AM===
Oral exam by one of the professors (we had the oral exam from Lambrechts)

Cools:
# Give the 3 ways to do immunotherapy on cancer cells, describe them, give their advantages and dis-
# Explain 4 definitions/concepts
#* PROTAC
#* H3K4me3
#* ChIP seq
#* Clonal hematopoeisis

Lambrechts:
# Question about somatic number mutations (PARP inhibitors etc)
# Question about Cre recombinase and the 5 applications (transgenic mice)

Van den Steen
# mRNA vaccin: explain design, mechanism and immunology of this concept
# explain malaria sequestration, if you would use small molecule inhibitors and explain difference between phenotype and targetting screening and explain how you could use targetting screens.

===10 Januari 2025 PM===
You had an oral exam by one of the professors (post-it note on exam paper which one)

Cools (oral: he read your answer and asked extra questions, do not need to explain again what you wrote down):
# What is CAR T cell therapy? How to detect if it worked (answer: PCR of TCR DNA)? What are some problems (at least 3) and how to solve these?
# Four questions:
#* genome instability
#* PROTAC
#* ChIPseq
#* bivalent antibodies (bijvraag: advantages and disadvantages compared to CAR T)

Lambrechts:
# scRNAseq can be complemented by CITEseq, scTCRseq and ATACseq. Can you explain how and what these 3 methods measure?
# How is zygote injection used to generate transgenic mice ? Which are the 5 potential applications in brief ?

Van den Steen (oral):
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# vaccination strategy against leishamania polysaccharides, why do you think this would (not) be effective?

===10 Januari 2025 AM===
Cools and Van den Steen were present for the oral exam
Cools:
# What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
# Four questions:
#* What is the difference between bulk CRISPR screens and single cell CRISPR screens?
#* What is PROTAC?
#* What are CAR-T cells?
#* H3K27me3

Lambrechts:
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
# Can you (schematically) describe the technology used by the scientist Jiankee He. Can you describe what Jiankee He did to upset the international scientic community. And why is there less controversy around the authorised use of Casegevy in humans - describe ?

Van den Steen:
# Give two examples of therapeutics of type 1 interferon. Also describe the underlying mechanism. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
# A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

===6 september 2024===
Cools:
# Whole-exome sequencing data of white blood cells of individuals given including the VAF of the mutations. The mutations that were found were DNMT3A, JAK2, TET2 and ASXL1: what is going on in these individuals, what can you conclude from the data, what would you recommend these individuals?
# Describe 3 different types of immunotherapy for cancer treatment in detail, compare these different types and give their advantages and disadvantages, also explain the main problems with these types of immunotherapy

Van Den Steen:
# What are the biological therapeutics for TNF-alfa. Compare, give advantages and disadvantages. What is the main therapeutic that is used? What is the main problem with it? Would you sialylate this biological therapeutic?
# Design a vaccination strategy against Trypanosoma cruzi

Lambrechts:
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
# Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?

===18 januari 2024===
Cools:
# what is clonal hematopoiesis? How to detect? Consequences/implications?
# a) CAR-T cell b) single-cell CRISPR screen c) ATAC sequencing d) PROTAC

Van den Steen:
# IFN-alfa: give the different types + their (dis)advantages, their application, should they be sialylated?
# Explain placental malaria + which type of vaccine would you make + would it be effective?

Lambrechts:
# PARP inhibitors and pre-symptomatic tumor detection; name of the two tests and how they work.
# Cre recombinase system + 4 types of mouse models

===12 januari 2024===
Cools:
# Ik heb 10 kankercellijnen waarvan er 4 een puntmutatie hebben op een non-coded region. De puntmutatie bevindt zich voor de promotor van een gekend oncogen. Hoe controleer ik of de puntmutatie invloed heeft op de expressie van dit oncogen? Beschrijf de methodes die je zou toepassen (ChIP sequencing + ATAC)
# a) oncohistones b) single-cell CRISPR screen c) bispecific antibodies d) PROTAC

Van den Steen:
# Give two examples of therapeutics of type 1 interferon. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
# What is the link between sequestration and evading the immune system regarding malaria? Could the molecules used for sequestration be a good vaccin target? Explain in detail why (not).

Lambrechts:
# What is measured with CITEseq, ATACseq and scTCRseq? Explain briefly
# How is zygote injection done to generate a transgenic mice? Give briefly 5 examples.

===19 januari 2023===
Cools:
# a) PROTAC b) Problems when using in cancer treatment
# ChIP-sequencing
# ShRNA screen against 100 genes of which 1 causing drug resistance
# a) What is clonal hematopoiesis? b) 100 people, how do you find out who has CH? Describe step by step: what do you need/what technology do you use/how do you perform data analysis?

Eelen:
# What is meant by 'Gene transfer in somatic cells'? Give an example. - max. 5 lines
# How can the Cre/LoxP system be made inducible? Can it be made tissue specific? - max. 5 lines
# Explain the Tet-on/Tet-off system schematically. Can it be made tissue specific? - max. 1 page

Lambrechts:
# PRS? How did it originate? How can it be used for breast cancer?
# Methylation as chemical marker? Chemical reaction? Use?

Van Den Steen:
# Passive immunisation therapy against cerebral malaria
# Difluoro-methylornithine

Applied Medical Biotechnology

2026-01-16T08:25:39Z

R0895938: /* 15 January 2026 */

[[Categorie: Mabb]]
==Vakinformatie==
Given by Philippe Van den Steen, Diether Lambrechts and Jan Cools. Each professor gave 4 classes. Each part has the same weight on the exam and one part is oral with written preparation. At the end of each chapter of the classes of professor Lambrechts are possible exam questions (questions are guaranteed to be from that list). This is a subject from the faculty of bioscience engineering. (2024-2025)

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/I0I27AE.htm#activetab=doelstellingen_idp1519328

==Exam questions==

===15 January 2026===
Oral parts were with Cools or Van der Steen

Cools:
# In a whole genome study on 100 patients they found the following mutations: What can you conclude from this? Wat advise would you give these patients? What risks do these patients have?
#* 3 patients with DNMT3A mutants: VAF=0.02, VAF = 0.01, VAF = 0.05
#* 1 patient with a TET2 mutant: VAF = 0.01
#* 1 patient with mutation is DNMT3A (VAF = 0.49), TET2 (VAF = 0.38) and P53 (VAF = 0.26)
# 4 Concepts to explain
#* PROTAC
#* CART
#* Irreversible vs reversible kinase inhibitor
#* Another I don't remember

Van der steen:
# Type one interferons. How are they used to treat disease? We saw two examples. Explain them both. On what mechanism do they work? In case of INF-beta, does it work better glycosylated or non-glycosylated and why?
# A group of researchers want to make a small biological against sequestration of malaria. Why could such a drug be useful? We saw to types of drug screens. Describe the differences and (dis)advantages. When developping the anti-sequestration drug, would you go for an intracellular or extracellular target?

Lambrechts:
# Give 2 examples of an inducible gene expression system. Describe them schematically.
# Somatic copy number alterations are frequent in solid tumors. We discussed 2 examples of how these copy number alterations can be used as biomarkers: 1/ to tailor PARP inhibitors to ovarian cancer patients or 2/ to aid in the pre-symptomatic detection of cancer in pregnant women. Give the name of both genetic tests and briefly describe how they work (give their underlying principle).

===09 January 2026===
Lambrechts was present for the oral exam

Cools:
# Explain PROTAC and molecular glues. Compare. Give an example in cancer-context. Which technique do you use for measuring if your PROTAC worked?
# Explain 4 definitions/concepts
#* Bispecific antibodies
#* Effect deamination on mutations
#* Why does clonal hematopoiesis increase with aging
#* How can we change a transcriptional repressor into an activator

Lambrechts:
# Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
# Describe schematicaly how i) chemical and ii) transposon insertional mutagenesis screens work in zebrafish and explain. How would you use a CRISPR screen in the zebrafish (discuss the example highlighted) and would this result in comparable data as in i) and ii). Finally, describe which system you use to induce gene expression in the zebrafish.

Van den Steen:
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

===09 January 2026 AM===
Cools and Lambrechts were present for the oral exam

Cools:
# Explain Clonal hematopoeisis (what it is). Why it is different from Leukemia. To what other disease/complications it is linked. Something about the expected VAF of CH.
# Explain 4 definitions/concepts
#* PROTAC
#* mutation signature
#* CAR T-cell
#* How can we change a transcriptional repressor into an activator

Lambrechts:
# Describe the Cre-recombinase system. Cre recombinase is used to generate 5 types of transgenic mice. Describe each type briefly.
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types

Van den Steen:
# What vaccination strategy should you use against leishamania polysaccharides, why do you think this would (not) be effective?
# Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?

===17 Januari 2025 AM===
Van Den Steen and Lambrechts were present for the oral exam

Cools:
# What is CAR T cell therapy? How can there be resistance against CAR T cell therapy? How can we improve the CAR T cell therapy to prevent resistance?
# Explain 4 definitions/concepts
#* H3K4me3
#* Effect deamination on mutations
#* siRNAs
#* Irreversible kinase inhibitors

Lambrechts:
# We discussed the usage of three model organisms. Can you describe their advantages and disadvantages that you would take into account when designing your laboratory experiments?
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.

Van den Steen:
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# monoclonal antibody (called malarimab) with high affinity for circum-sporozoite protein was designed: explain how this can be used in the fight against malaria - effector mechanisms, compare with vaccination and with antimalarial drugs chloroquine and artemisinine, how can there be optimisation of the monoclonal antibody and should the monoclonal antibody be sialylated to have good anti-malarial activity?

===16 Januari 2025 PM===
Cools and Lambrechts were present for the oral exam

Cools:
# What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
# Four questions:
#* What is the difference between bulk CRISPR screens and single cell CRISPR screens?
#* What is PROTAC?
#* What are CAR-T cells?
#* H3K27me3

Lambrechts:
#Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
#After quality control , scRNAseq can be analyzed in different ways. Please describe some of the methods typically used to assess differences between 2 conditions by scRNAseq.

Van den Steen:
#Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?
#Develop a vaccine against specific saccharide of T. Cruzi. Which vaccine do you use, how to adapt it, what process is used and how can T. cruzi acquire resistance?

===16 Januari 2025 AM===
Oral exam by one of the professors (we had the oral exam from Lambrechts)

Cools:
# Give the 3 ways to do immunotherapy on cancer cells, describe them, give their advantages and dis-
# Explain 4 definitions/concepts
#* PROTAC
#* H3K4me3
#* ChIP seq
#* Clonal hematopoeisis

Lambrechts:
# Question about somatic number mutations (PARP inhibitors etc)
# Question about Cre recombinase and the 5 applications (transgenic mice)

Van den Steen
# mRNA vaccin: explain design, mechanism and immunology of this concept
# explain malaria sequestration, if you would use small molecule inhibitors and explain difference between phenotype and targetting screening and explain how you could use targetting screens.

===10 Januari 2025 PM===
You had an oral exam by one of the professors (post-it note on exam paper which one)

Cools (oral: he read your answer and asked extra questions, do not need to explain again what you wrote down):
# What is CAR T cell therapy? How to detect if it worked (answer: PCR of TCR DNA)? What are some problems (at least 3) and how to solve these?
# Four questions:
#* genome instability
#* PROTAC
#* ChIPseq
#* bivalent antibodies (bijvraag: advantages and disadvantages compared to CAR T)

Lambrechts:
# scRNAseq can be complemented by CITEseq, scTCRseq and ATACseq. Can you explain how and what these 3 methods measure?
# How is zygote injection used to generate transgenic mice ? Which are the 5 potential applications in brief ?

Van den Steen (oral):
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# vaccination strategy against leishamania polysaccharides, why do you think this would (not) be effective?

===10 Januari 2025 AM===
Cools and Van den Steen were present for the oral exam
Cools:
# What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
# Four questions:
#* What is the difference between bulk CRISPR screens and single cell CRISPR screens?
#* What is PROTAC?
#* What are CAR-T cells?
#* H3K27me3

Lambrechts:
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
# Can you (schematically) describe the technology used by the scientist Jiankee He. Can you describe what Jiankee He did to upset the international scientic community. And why is there less controversy around the authorised use of Casegevy in humans - describe ?

Van den Steen:
# Give two examples of therapeutics of type 1 interferon. Also describe the underlying mechanism. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
# A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

===6 september 2024===
Cools:
# Whole-exome sequencing data of white blood cells of individuals given including the VAF of the mutations. The mutations that were found were DNMT3A, JAK2, TET2 and ASXL1: what is going on in these individuals, what can you conclude from the data, what would you recommend these individuals?
# Describe 3 different types of immunotherapy for cancer treatment in detail, compare these different types and give their advantages and disadvantages, also explain the main problems with these types of immunotherapy

Van Den Steen:
# What are the biological therapeutics for TNF-alfa. Compare, give advantages and disadvantages. What is the main therapeutic that is used? What is the main problem with it? Would you sialylate this biological therapeutic?
# Design a vaccination strategy against Trypanosoma cruzi

Lambrechts:
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
# Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?

===18 januari 2024===
Cools:
# what is clonal hematopoiesis? How to detect? Consequences/implications?
# a) CAR-T cell b) single-cell CRISPR screen c) ATAC sequencing d) PROTAC

Van den Steen:
# IFN-alfa: give the different types + their (dis)advantages, their application, should they be sialylated?
# Explain placental malaria + which type of vaccine would you make + would it be effective?

Lambrechts:
# PARP inhibitors and pre-symptomatic tumor detection; name of the two tests and how they work.
# Cre recombinase system + 4 types of mouse models

===12 januari 2024===
Cools:
# Ik heb 10 kankercellijnen waarvan er 4 een puntmutatie hebben op een non-coded region. De puntmutatie bevindt zich voor de promotor van een gekend oncogen. Hoe controleer ik of de puntmutatie invloed heeft op de expressie van dit oncogen? Beschrijf de methodes die je zou toepassen (ChIP sequencing + ATAC)
# a) oncohistones b) single-cell CRISPR screen c) bispecific antibodies d) PROTAC

Van den Steen:
# Give two examples of therapeutics of type 1 interferon. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
# What is the link between sequestration and evading the immune system regarding malaria? Could the molecules used for sequestration be a good vaccin target? Explain in detail why (not).

Lambrechts:
# What is measured with CITEseq, ATACseq and scTCRseq? Explain briefly
# How is zygote injection done to generate a transgenic mice? Give briefly 5 examples.

===19 januari 2023===
Cools:
# a) PROTAC b) Problems when using in cancer treatment
# ChIP-sequencing
# ShRNA screen against 100 genes of which 1 causing drug resistance
# a) What is clonal hematopoiesis? b) 100 people, how do you find out who has CH? Describe step by step: what do you need/what technology do you use/how do you perform data analysis?

Eelen:
# What is meant by 'Gene transfer in somatic cells'? Give an example. - max. 5 lines
# How can the Cre/LoxP system be made inducible? Can it be made tissue specific? - max. 5 lines
# Explain the Tet-on/Tet-off system schematically. Can it be made tissue specific? - max. 1 page

Lambrechts:
# PRS? How did it originate? How can it be used for breast cancer?
# Methylation as chemical marker? Chemical reaction? Use?

Van Den Steen:
# Passive immunisation therapy against cerebral malaria
# Difluoro-methylornithine

Applied Medical Biotechnology

2026-01-16T08:24:28Z

R0895938: /* 15 January 2026 */

[[Categorie: Mabb]]
==Vakinformatie==
Given by Philippe Van den Steen, Diether Lambrechts and Jan Cools. Each professor gave 4 classes. Each part has the same weight on the exam and one part is oral with written preparation. At the end of each chapter of the classes of professor Lambrechts are possible exam questions (questions are guaranteed to be from that list). This is a subject from the faculty of bioscience engineering. (2024-2025)

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/I0I27AE.htm#activetab=doelstellingen_idp1519328

==Exam questions==

===15 January 2026===
Oral parts were with Cools or Van der Steen

Cools:
# In a whole genome study on 100 patients they found the following mutations: What can you conclude from this? Wat advise would you give these patients? What risks do these patients have?
#* 3 patients with DNMT3A mutants: VAF=0.02, VAF = 0.01, VAF = 0.05
#* 1 patient with a TET2 mutant: VAF = 0.01
#* 1 patient with mutation is DNMT3A (VAF = 0.49), TET2 (VAF = 0.38) and P53 (VAF = 0.26)
# 4 Concepts to explain
#* PROTAC
#* CART
#* Irreversible vs reversible kinase inhibitor
#* Another I don't remember

Van der steen:
# Type one interferons. How are they used to treat disease? We saw two examples. Explain them both. On what mechanism do they work? In case of INF-beta, does it work better glycosylated or non-glycosylated and why?
# A group of researchers want to make a small biological against sequestration of malaria. Why could such a drug be useful? We saw to types of drug screens. Describe the differences and (dis)advantages. When developping the anti-sequestration drug, would you go for an intracellular or extracellular target?

Lambrechts:
# Give 2 examples of an inducible gene expression system. Describe them schematically.
# Somatic copy number alterations are frequent in solid tumors. We discussed 2 examples of how these copy number alterations can be used as biomarkers:
1/ to tailor PARP inhibitors to ovarian cancer patients or 2/ to aid in the pre-symptomatic detection of cancer in pregnant women. Give the name of both genetic tests and briefly describe how they work (give their underlying principle).

===09 January 2026===
Lambrechts was present for the oral exam

Cools:
# Explain PROTAC and molecular glues. Compare. Give an example in cancer-context. Which technique do you use for measuring if your PROTAC worked?
# Explain 4 definitions/concepts
#* Bispecific antibodies
#* Effect deamination on mutations
#* Why does clonal hematopoiesis increase with aging
#* How can we change a transcriptional repressor into an activator

Lambrechts:
# Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
# Describe schematicaly how i) chemical and ii) transposon insertional mutagenesis screens work in zebrafish and explain. How would you use a CRISPR screen in the zebrafish (discuss the example highlighted) and would this result in comparable data as in i) and ii). Finally, describe which system you use to induce gene expression in the zebrafish.

Van den Steen:
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

===09 January 2026 AM===
Cools and Lambrechts were present for the oral exam

Cools:
# Explain Clonal hematopoeisis (what it is). Why it is different from Leukemia. To what other disease/complications it is linked. Something about the expected VAF of CH.
# Explain 4 definitions/concepts
#* PROTAC
#* mutation signature
#* CAR T-cell
#* How can we change a transcriptional repressor into an activator

Lambrechts:
# Describe the Cre-recombinase system. Cre recombinase is used to generate 5 types of transgenic mice. Describe each type briefly.
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types

Van den Steen:
# What vaccination strategy should you use against leishamania polysaccharides, why do you think this would (not) be effective?
# Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?

===17 Januari 2025 AM===
Van Den Steen and Lambrechts were present for the oral exam

Cools:
# What is CAR T cell therapy? How can there be resistance against CAR T cell therapy? How can we improve the CAR T cell therapy to prevent resistance?
# Explain 4 definitions/concepts
#* H3K4me3
#* Effect deamination on mutations
#* siRNAs
#* Irreversible kinase inhibitors

Lambrechts:
# We discussed the usage of three model organisms. Can you describe their advantages and disadvantages that you would take into account when designing your laboratory experiments?
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.

Van den Steen:
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# monoclonal antibody (called malarimab) with high affinity for circum-sporozoite protein was designed: explain how this can be used in the fight against malaria - effector mechanisms, compare with vaccination and with antimalarial drugs chloroquine and artemisinine, how can there be optimisation of the monoclonal antibody and should the monoclonal antibody be sialylated to have good anti-malarial activity?

===16 Januari 2025 PM===
Cools and Lambrechts were present for the oral exam

Cools:
# What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
# Four questions:
#* What is the difference between bulk CRISPR screens and single cell CRISPR screens?
#* What is PROTAC?
#* What are CAR-T cells?
#* H3K27me3

Lambrechts:
#Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
#After quality control , scRNAseq can be analyzed in different ways. Please describe some of the methods typically used to assess differences between 2 conditions by scRNAseq.

Van den Steen:
#Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?
#Develop a vaccine against specific saccharide of T. Cruzi. Which vaccine do you use, how to adapt it, what process is used and how can T. cruzi acquire resistance?

===16 Januari 2025 AM===
Oral exam by one of the professors (we had the oral exam from Lambrechts)

Cools:
# Give the 3 ways to do immunotherapy on cancer cells, describe them, give their advantages and dis-
# Explain 4 definitions/concepts
#* PROTAC
#* H3K4me3
#* ChIP seq
#* Clonal hematopoeisis

Lambrechts:
# Question about somatic number mutations (PARP inhibitors etc)
# Question about Cre recombinase and the 5 applications (transgenic mice)

Van den Steen
# mRNA vaccin: explain design, mechanism and immunology of this concept
# explain malaria sequestration, if you would use small molecule inhibitors and explain difference between phenotype and targetting screening and explain how you could use targetting screens.

===10 Januari 2025 PM===
You had an oral exam by one of the professors (post-it note on exam paper which one)

Cools (oral: he read your answer and asked extra questions, do not need to explain again what you wrote down):
# What is CAR T cell therapy? How to detect if it worked (answer: PCR of TCR DNA)? What are some problems (at least 3) and how to solve these?
# Four questions:
#* genome instability
#* PROTAC
#* ChIPseq
#* bivalent antibodies (bijvraag: advantages and disadvantages compared to CAR T)

Lambrechts:
# scRNAseq can be complemented by CITEseq, scTCRseq and ATACseq. Can you explain how and what these 3 methods measure?
# How is zygote injection used to generate transgenic mice ? Which are the 5 potential applications in brief ?

Van den Steen (oral):
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# vaccination strategy against leishamania polysaccharides, why do you think this would (not) be effective?

===10 Januari 2025 AM===
Cools and Van den Steen were present for the oral exam
Cools:
# What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
# Four questions:
#* What is the difference between bulk CRISPR screens and single cell CRISPR screens?
#* What is PROTAC?
#* What are CAR-T cells?
#* H3K27me3

Lambrechts:
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
# Can you (schematically) describe the technology used by the scientist Jiankee He. Can you describe what Jiankee He did to upset the international scientic community. And why is there less controversy around the authorised use of Casegevy in humans - describe ?

Van den Steen:
# Give two examples of therapeutics of type 1 interferon. Also describe the underlying mechanism. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
# A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

===6 september 2024===
Cools:
# Whole-exome sequencing data of white blood cells of individuals given including the VAF of the mutations. The mutations that were found were DNMT3A, JAK2, TET2 and ASXL1: what is going on in these individuals, what can you conclude from the data, what would you recommend these individuals?
# Describe 3 different types of immunotherapy for cancer treatment in detail, compare these different types and give their advantages and disadvantages, also explain the main problems with these types of immunotherapy

Van Den Steen:
# What are the biological therapeutics for TNF-alfa. Compare, give advantages and disadvantages. What is the main therapeutic that is used? What is the main problem with it? Would you sialylate this biological therapeutic?
# Design a vaccination strategy against Trypanosoma cruzi

Lambrechts:
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
# Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?

===18 januari 2024===
Cools:
# what is clonal hematopoiesis? How to detect? Consequences/implications?
# a) CAR-T cell b) single-cell CRISPR screen c) ATAC sequencing d) PROTAC

Van den Steen:
# IFN-alfa: give the different types + their (dis)advantages, their application, should they be sialylated?
# Explain placental malaria + which type of vaccine would you make + would it be effective?

Lambrechts:
# PARP inhibitors and pre-symptomatic tumor detection; name of the two tests and how they work.
# Cre recombinase system + 4 types of mouse models

===12 januari 2024===
Cools:
# Ik heb 10 kankercellijnen waarvan er 4 een puntmutatie hebben op een non-coded region. De puntmutatie bevindt zich voor de promotor van een gekend oncogen. Hoe controleer ik of de puntmutatie invloed heeft op de expressie van dit oncogen? Beschrijf de methodes die je zou toepassen (ChIP sequencing + ATAC)
# a) oncohistones b) single-cell CRISPR screen c) bispecific antibodies d) PROTAC

Van den Steen:
# Give two examples of therapeutics of type 1 interferon. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
# What is the link between sequestration and evading the immune system regarding malaria? Could the molecules used for sequestration be a good vaccin target? Explain in detail why (not).

Lambrechts:
# What is measured with CITEseq, ATACseq and scTCRseq? Explain briefly
# How is zygote injection done to generate a transgenic mice? Give briefly 5 examples.

===19 januari 2023===
Cools:
# a) PROTAC b) Problems when using in cancer treatment
# ChIP-sequencing
# ShRNA screen against 100 genes of which 1 causing drug resistance
# a) What is clonal hematopoiesis? b) 100 people, how do you find out who has CH? Describe step by step: what do you need/what technology do you use/how do you perform data analysis?

Eelen:
# What is meant by 'Gene transfer in somatic cells'? Give an example. - max. 5 lines
# How can the Cre/LoxP system be made inducible? Can it be made tissue specific? - max. 5 lines
# Explain the Tet-on/Tet-off system schematically. Can it be made tissue specific? - max. 1 page

Lambrechts:
# PRS? How did it originate? How can it be used for breast cancer?
# Methylation as chemical marker? Chemical reaction? Use?

Van Den Steen:
# Passive immunisation therapy against cerebral malaria
# Difluoro-methylornithine

Applied Medical Biotechnology

2026-01-16T08:23:52Z

R0895938: /* Exam questions */

[[Categorie: Mabb]]
==Vakinformatie==
Given by Philippe Van den Steen, Diether Lambrechts and Jan Cools. Each professor gave 4 classes. Each part has the same weight on the exam and one part is oral with written preparation. At the end of each chapter of the classes of professor Lambrechts are possible exam questions (questions are guaranteed to be from that list). This is a subject from the faculty of bioscience engineering. (2024-2025)

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/I0I27AE.htm#activetab=doelstellingen_idp1519328

==Exam questions==

===15 January 2026===
Oral parts were with Cools or Van der Steen

Cools:
# In a whole genome study on 100 patients they found the following mutations:
#* 3 patients with DNMT3A mutants: VAF=0.02, VAF = 0.01, VAF = 0.05
#* 1 patient with a TET2 mutant: VAF = 0.01
#* 1 patient with mutation is DNMT3A (VAF = 0.49), TET2 (VAF = 0.38) and P53 (VAF = 0.26)
What can you conclude from this? Wat advise would you give these patients? What risks do these patients have?
# 4 Concepts to explain
#* PROTAC
#* CART
#* Irreversible vs reversible kinase inhibitor
#* Another I don't remember

Van der steen:
# Type one interferons. How are they used to treat disease? We saw two examples. Explain them both. On what mechanism do they work? In case of INF-beta, does it work better glycosylated or non-glycosylated and why?
# A group of researchers want to make a small biological against sequestration of malaria. Why could such a drug be useful? We saw to types of drug screens. Describe the differences and (dis)advantages. When developping the anti-sequestration drug, would you go for an intracellular or extracellular target?

Lambrechts:
# Give 2 examples of an inducible gene expression system. Describe them schematically.
# Somatic copy number alterations are frequent in solid tumors. We discussed 2 examples of how these copy number alterations can be used as biomarkers:
1/ to tailor PARP inhibitors to ovarian cancer patients or 2/ to aid in the pre-symptomatic detection of cancer in pregnant women. Give the name of both genetic tests and briefly describe how they work (give their underlying principle).

===09 January 2026===
Lambrechts was present for the oral exam

Cools:
# Explain PROTAC and molecular glues. Compare. Give an example in cancer-context. Which technique do you use for measuring if your PROTAC worked?
# Explain 4 definitions/concepts
#* Bispecific antibodies
#* Effect deamination on mutations
#* Why does clonal hematopoiesis increase with aging
#* How can we change a transcriptional repressor into an activator

Lambrechts:
# Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
# Describe schematicaly how i) chemical and ii) transposon insertional mutagenesis screens work in zebrafish and explain. How would you use a CRISPR screen in the zebrafish (discuss the example highlighted) and would this result in comparable data as in i) and ii). Finally, describe which system you use to induce gene expression in the zebrafish.

Van den Steen:
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

===09 January 2026 AM===
Cools and Lambrechts were present for the oral exam

Cools:
# Explain Clonal hematopoeisis (what it is). Why it is different from Leukemia. To what other disease/complications it is linked. Something about the expected VAF of CH.
# Explain 4 definitions/concepts
#* PROTAC
#* mutation signature
#* CAR T-cell
#* How can we change a transcriptional repressor into an activator

Lambrechts:
# Describe the Cre-recombinase system. Cre recombinase is used to generate 5 types of transgenic mice. Describe each type briefly.
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types

Van den Steen:
# What vaccination strategy should you use against leishamania polysaccharides, why do you think this would (not) be effective?
# Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?

===17 Januari 2025 AM===
Van Den Steen and Lambrechts were present for the oral exam

Cools:
# What is CAR T cell therapy? How can there be resistance against CAR T cell therapy? How can we improve the CAR T cell therapy to prevent resistance?
# Explain 4 definitions/concepts
#* H3K4me3
#* Effect deamination on mutations
#* siRNAs
#* Irreversible kinase inhibitors

Lambrechts:
# We discussed the usage of three model organisms. Can you describe their advantages and disadvantages that you would take into account when designing your laboratory experiments?
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.

Van den Steen:
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# monoclonal antibody (called malarimab) with high affinity for circum-sporozoite protein was designed: explain how this can be used in the fight against malaria - effector mechanisms, compare with vaccination and with antimalarial drugs chloroquine and artemisinine, how can there be optimisation of the monoclonal antibody and should the monoclonal antibody be sialylated to have good anti-malarial activity?

===16 Januari 2025 PM===
Cools and Lambrechts were present for the oral exam

Cools:
# What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
# Four questions:
#* What is the difference between bulk CRISPR screens and single cell CRISPR screens?
#* What is PROTAC?
#* What are CAR-T cells?
#* H3K27me3

Lambrechts:
#Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
#After quality control , scRNAseq can be analyzed in different ways. Please describe some of the methods typically used to assess differences between 2 conditions by scRNAseq.

Van den Steen:
#Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?
#Develop a vaccine against specific saccharide of T. Cruzi. Which vaccine do you use, how to adapt it, what process is used and how can T. cruzi acquire resistance?

===16 Januari 2025 AM===
Oral exam by one of the professors (we had the oral exam from Lambrechts)

Cools:
# Give the 3 ways to do immunotherapy on cancer cells, describe them, give their advantages and dis-
# Explain 4 definitions/concepts
#* PROTAC
#* H3K4me3
#* ChIP seq
#* Clonal hematopoeisis

Lambrechts:
# Question about somatic number mutations (PARP inhibitors etc)
# Question about Cre recombinase and the 5 applications (transgenic mice)

Van den Steen
# mRNA vaccin: explain design, mechanism and immunology of this concept
# explain malaria sequestration, if you would use small molecule inhibitors and explain difference between phenotype and targetting screening and explain how you could use targetting screens.

===10 Januari 2025 PM===
You had an oral exam by one of the professors (post-it note on exam paper which one)

Cools (oral: he read your answer and asked extra questions, do not need to explain again what you wrote down):
# What is CAR T cell therapy? How to detect if it worked (answer: PCR of TCR DNA)? What are some problems (at least 3) and how to solve these?
# Four questions:
#* genome instability
#* PROTAC
#* ChIPseq
#* bivalent antibodies (bijvraag: advantages and disadvantages compared to CAR T)

Lambrechts:
# scRNAseq can be complemented by CITEseq, scTCRseq and ATACseq. Can you explain how and what these 3 methods measure?
# How is zygote injection used to generate transgenic mice ? Which are the 5 potential applications in brief ?

Van den Steen (oral):
# difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
# vaccination strategy against leishamania polysaccharides, why do you think this would (not) be effective?

===10 Januari 2025 AM===
Cools and Van den Steen were present for the oral exam
Cools:
# What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
# Four questions:
#* What is the difference between bulk CRISPR screens and single cell CRISPR screens?
#* What is PROTAC?
#* What are CAR-T cells?
#* H3K27me3

Lambrechts:
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
# Can you (schematically) describe the technology used by the scientist Jiankee He. Can you describe what Jiankee He did to upset the international scientic community. And why is there less controversy around the authorised use of Casegevy in humans - describe ?

Van den Steen:
# Give two examples of therapeutics of type 1 interferon. Also describe the underlying mechanism. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
# A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

===6 september 2024===
Cools:
# Whole-exome sequencing data of white blood cells of individuals given including the VAF of the mutations. The mutations that were found were DNMT3A, JAK2, TET2 and ASXL1: what is going on in these individuals, what can you conclude from the data, what would you recommend these individuals?
# Describe 3 different types of immunotherapy for cancer treatment in detail, compare these different types and give their advantages and disadvantages, also explain the main problems with these types of immunotherapy

Van Den Steen:
# What are the biological therapeutics for TNF-alfa. Compare, give advantages and disadvantages. What is the main therapeutic that is used? What is the main problem with it? Would you sialylate this biological therapeutic?
# Design a vaccination strategy against Trypanosoma cruzi

Lambrechts:
# Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
# Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?

===18 januari 2024===
Cools:
# what is clonal hematopoiesis? How to detect? Consequences/implications?
# a) CAR-T cell b) single-cell CRISPR screen c) ATAC sequencing d) PROTAC

Van den Steen:
# IFN-alfa: give the different types + their (dis)advantages, their application, should they be sialylated?
# Explain placental malaria + which type of vaccine would you make + would it be effective?

Lambrechts:
# PARP inhibitors and pre-symptomatic tumor detection; name of the two tests and how they work.
# Cre recombinase system + 4 types of mouse models

===12 januari 2024===
Cools:
# Ik heb 10 kankercellijnen waarvan er 4 een puntmutatie hebben op een non-coded region. De puntmutatie bevindt zich voor de promotor van een gekend oncogen. Hoe controleer ik of de puntmutatie invloed heeft op de expressie van dit oncogen? Beschrijf de methodes die je zou toepassen (ChIP sequencing + ATAC)
# a) oncohistones b) single-cell CRISPR screen c) bispecific antibodies d) PROTAC

Van den Steen:
# Give two examples of therapeutics of type 1 interferon. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
# What is the link between sequestration and evading the immune system regarding malaria? Could the molecules used for sequestration be a good vaccin target? Explain in detail why (not).

Lambrechts:
# What is measured with CITEseq, ATACseq and scTCRseq? Explain briefly
# How is zygote injection done to generate a transgenic mice? Give briefly 5 examples.

===19 januari 2023===
Cools:
# a) PROTAC b) Problems when using in cancer treatment
# ChIP-sequencing
# ShRNA screen against 100 genes of which 1 causing drug resistance
# a) What is clonal hematopoiesis? b) 100 people, how do you find out who has CH? Describe step by step: what do you need/what technology do you use/how do you perform data analysis?

Eelen:
# What is meant by 'Gene transfer in somatic cells'? Give an example. - max. 5 lines
# How can the Cre/LoxP system be made inducible? Can it be made tissue specific? - max. 5 lines
# Explain the Tet-on/Tet-off system schematically. Can it be made tissue specific? - max. 1 page

Lambrechts:
# PRS? How did it originate? How can it be used for breast cancer?
# Methylation as chemical marker? Chemical reaction? Use?

Van Den Steen:
# Passive immunisation therapy against cerebral malaria
# Difluoro-methylornithine

Genoom-, proteoom- en metaboloomanalyse

2025-01-22T15:45:18Z

R0895938: /* 21/01/2025 */

[[Categorie:Mabb]]

==Vakinformatie==
Genoom-, proteoom- en metaboloomanalyse
Het vak wordt gegeven door prof. Landuyt en prof. Robben. Robben zijn deel is mondeling en gesloten boek. Robben maakt elk examen nieuwe vragen

2022-2023: het vak wordt gegeven door Landuyt (metabolomics), Robben (genomics), en Schoofs (proteomics). Alles is gesloten boek.

2023-2024: het vak wordt gegeven door Van Belleghem (genomics) en Schoofs (proteomics). Voor het metabolomics gedeelte van Landuyt moest je oude lesopnames kijken. Alles is gesloten boek, geschreven examen

2024-2025: Het vak wordt gegeven door Van Belleghem (genomics) en Temmerman (proteomics en metabolomics). Voor het deel van Temmerman waren er opnames van prof Schoofs en Landuyt, vanwege Temmerman haar zwangerschap. Ze was er wel voor vragen te beantwoorden. Alles is gesloten boek, geschreven examen.

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/n/G0G57AN.htm

==Examenvragen==
===21/01/2025===
SVB
* PAM-genome. What is it and how sequence? And some small questions.
* Terms
*# ATAC-seq
*# AP-MS
*# LINE

Temmerman
* Labels in proteomics: why used? Which labels are there? Give example for each type and explain differences.
* MS spectrum: Label the axes. Which peptides in spectrum? Identify which peaks belong to which peptides.
* Are the following statements true or false. Explain briefly
*# peptide mass fingerprint ?
*# peptide mass fingerprint requires MS/MS

===01/02/2024===
SVB
*Open question: 233 genomes of primates to be sequenced, focus on repetitive content in the genome. What sequencing technologies and equipment to use? Why?
*Explain how the chosen technologies work.
*Give two examples of how can be used

*Terms
*#Retrovirus-like elements
*#GWAS
*#ChIP-Seq

Schoofs
NO CALCULATOR ALLOWED

*Explain how to identify proteins with explorative (shotgun) proteomics
*Explain the differences between MALDI and ESI

*Multiple choice with explanation

*#No two identical compounds will ionise and fragment in exactly the same manner, true or false
*#Enriched proteins of cultured cells, appropriate method (DiGE, SILAC, SRM, Label-free methods)
*#What is SRM used for?
*#Which conclusion can be drawn from a 2D gel electrophoresis experiment?
*#m/z of 120, 121, 122, 123, which isotopes are responsible for signal at m/z 122 (12C, 35Cl, 1H; 12C, 35Cl, 2H; 12C, 37Cl, 1H; 12C, 37Cl, 2H)

*Exercises
*#Question about a fragmented peptide MS2 spectra
*#*Why do the y ions have different intensities?
*#*Explain how the peptide sequence (given) is derived from the spectrum.
*#Figure with mass spectrum, what is the mass of the peak? (2 peaks, second peak is isotopes with distance of +1)
*Definitions
*#Delayed extraction
*#Reflectron mode
*#Targeted proteomics
*#Mascot
*#DDA

===23/01/2024===
SVB
*Open question: 4000 genomes of Darwin's finches underwent resequencing encompassing individuals of 4 species
*#Explain the methodology in conducting resequencing. what are the key steps and technologies?
*#Evaluate the challenges of fragmentation of the reference genome, knowing that the genome existed of about 20.000 scaffolds of large size:
*#*What genomic properties caused it to be fragmented? (repeats)
*#*What is the significance of this issue?
*#*Propose a method to enhance the coherency of the reference genome.
*#Give two illustrative examples of insights that can be derived from experiments like these.
*Terms
*#Phylogenetic footprinting
*#AP-MS
*#Gene regulatory network

Schoofs
*Explain how proteins of a biological sample can be identified with peptide masss fingerprinting using a MALDI-TOF mass spectrometer.
*Multiple choice with explanation
*#Two compounds fragment in exactly the same manner, true or false
*#Enriched proteins of cultured cells, appropriate method (DiGE, SILAC, SRM, Label-free methods)
*#What is a proteotypic peptide?
*#Which conclusion can be drawn from a 2D gel electrophoresis experiment?
*#m/z of 120, 121, 122, 123, which isotopes are responsible for signal at m/z 122 (12C, 35Cl, 1H; 12C, 35Cl, 2H; 12C, 37Cl, 1H; 12C, 37Cl, 2H)
*Exercises
*#Question about the ICAT image from the slides
*#*Are the peptides (A to F) coming from the same protein?
*#*What is the distance between the green and the blue peaks?
*#*Explain how the peptide sequence is derived from the spectrum
*#Figure with mass spectrum, what is the mass of the peak? (2 peaks, second peak is isotopes with distance of 0,5)
*Definitions
*#SRM
*#Isobaric tag
*#Mass spectrometric resolution
*#Mascot
*#E-value

===5/09/2023===
Robben:
# Jarenlang geduurd om genoom van een specifieke boonsoort te sequencen (genoomgrootte = 4x menselijk genoom).
## Speculeer waarom het zo lang geduurd heeft.
## Geef schematisch weer welke strategie jij zou gebruiken om het genoom vandaag sneller te sequencen.
## Leg de principes van jouw gekozen technieken uit.
# Terms
## ribosome profiling
## scale free networks
## endogenous retrovirus

===24/01/2023===
Robben:
# Illumina, pacbio and oxford nanopore all have their own transcriptomics approach.
## Give the working principle
## critically discuss strengths and weaknesses of the platforms
## Which platform would you choose to study the transcriptome of a cancer tissue? argue.
# Terms
## paired end sequencing
## haplotype association analysis
## protein-protein interaction networks are scale free

Schoofs:
# Open vraag: membraanproteïnen van gezonde muizen en muizen met pituitary tumor onderzoeken. Hoe ga je de identificatie en kwanitificatie doen? aanpak volledig uitleggen.
# kleine vraagjes
## 2 meerkeuze
## 2 begrippen (razor peptide en delayed extraction tof)
## vraag met grafiek (intensiteit vs m/z), hoe massa van ongeladen peptide bepalen adh van deze grafiek?
## iets met de score-value voor peptide mass fingerprint verhogen
# oefening op computer
## frataxin mature peptide spot in een gel picken; welke pI en welke MW?
## Zijn er modificaties, waarom (niet)?
## Geef een lijst met 10 pieken die het hele spectrum weergeven.

===18/01/2021===
Robben:
# SMRT and nanopore can be used to finish the human X chromosome.
## Give the working principle and details of SMRT and nanopore.
## Why are these methods better than Illumina?
## Give the strategy to finish the other chromosomes.
# Terms
## Affymetrix chip
## Gene acquisition (by gene evolution)
## Genomic interactions

Landuyt:
# You get a safe denatured protein mixture from the Sars-Cov-2 virus.
## Describe a method how this mixture is made. (2p)
## If you would be pick the spike protein in a gel-based proteomics experiment, at which MW and PI would you look. Do you expect modifications and why (not)? (3p)
## Give a peak list of 10 peaks that cover the whole spectrum if you use trypsin to digest the spike protein. (4p)
## How can you see the difference between the UK and the standard viariant? Give the principle and calculations. (3)
# Hydroxychloroquine (HCQ) was developed for malaria treatment and seems to be working against corona in patients with less severe symptomes. We need to know the blood concentrations of HCQ in treated patients. Therefore, you are offered a mass spectrometer with a mass accuracy of 5 ppm.
## How would you prepare the blood samples for this analysis. (3p)
## What is the mass you are going to look after? (...,... Da +- ...,... Da) (4p)
## BONUS question: can you give the mechanism of action of HCQ? (1p)

===28/01/2020===
Robben:
#SMRT sequencing recently had update, something with circularization.
##Discuss the technical aspects etc
##Why is it important?
#Terms
##Polyploidy and genome variation
##NanoString nCounter expression system
##Rosetta Stone Method

Landuyt:
Same as 14/01/2020, 15/01/2020 and 21/01/2020

===21/01/2020===
Robben:
#The genome of cotton was already sequenced in 2012 via Sanger. Which NGS will you use to redo the sequencing?
## Give the working principle and details of the chosen platform.
#Terms
##Gene ontology
##Affimix chip
##Gene interaction mapping

Landuyt (exact same questions as yesterday):
# Placental Growth Factor is an interesting protein.
## Describe briefly what makes this protein so interesting (1p)
## If PlGF would be picked up in a gel-based proteomics experiment, how would the spectrum then look like (provide the exact masses of at least 5 peaks). (4p)
## Describe the workflow of this proteomics strategy starting from a tissue sample (4p)
## What are the shortcoming and advantages of the gel-based approach (3p)
# Curcumin, one of the bioactive metabolites from plants of the ginger family, has many potential medical uses. However, bioavailibility of curcumin is low, and therefore, many research is conducted to find better formulations to reach optimal blood concentrations. In order to support this research, you need to build an assay to asses blood plasma concentrations of curcumin. Therefore, you are offered a mass spectrometer with a mass accuracy of 30 ppm.
## How would you prepare the blood samples for this analysis. (3p)
## What is the mass you are going to look after? (...,... Da +- ...,... Da) (4p)
## BONUS question: can you give one possible strategy to formulate an oral curcumin preparation with better bioavailability. (1p)

===15/01/2020 (afternoon)===
Robben:
# Infection of a certain type of phage in a bacterial cell. You would like to execute a transcriptomal analysis at the moment of encounter of the phage and 15 minutes later.
## Defend which platform/technique you would use.
## Explain the working principles and technical details of the chosen platform/technique.
# Terms
## Optical mapping
## Sequence scaffold
## Interaction network

Landuyt (exact same questions as yesterday):
# Placental Growth Factor is an interesting protein.
## Describe briefly what makes this protein so interesting (1p)
## If PlGF would be picked up in a gel-based proteomics experiment, how would the spectrum then look like (provide the exact masses of at least 5 peaks). (4p)
## Describe the workflow of this proteomics strategy starting from a tissue sample (4p)
## What are the shortcoming and advantages of the gel-based approach (3p)
# Curcumin, one of the bioactive metabolites from plants of the ginger family, has many potential medical uses. However, bioavailibility of curcumin is low, and therefore, many research is conducted to find better formulations to reach optimal blood concentrations. In order to support this research, you need to build an assay to asses blood plasma concentrations of curcumin. Therefore, you are offered a mass spectrometer with a mass accuracy of 30 ppm.
## How would you prepare the blood samples for this analysis. (3p)
## What is the mass you are going to look after? (...,... Da +- ...,... Da) (4p)
## BONUS question: can you give one possible strategy to formulate an oral curcumin preparation with better bioavailability. (1p)

===14/01/2020 (morning)===
Robben:
# Phenotypic differences between closely related almond and peach might largely be attributed to transposable elements. Your lab received funding for comparative genomic sequencing to elucidate the differences.
## Explain schematically the sequencing strategy you would propose.
## Which commerically available next-gen sequencing platform(s) would you propose to use. '''Argue your choice.'''
## Explain the working principles of the chosen platform(s)
# Terms
## Ribosome profiling
## (Transcriptomics) microarray target labeling
## Protein-protein interaction maps are scale free

Landuyt:
# Placental Growth Factor is an interesting protein.
## Describe briefly what makes this protein so interesting (1p)
## If PlGF would be picked up in a gel-based proteomics experiment, how would the spectrum then look like (provide the exact masses of at least 5 peaks). (4p)
## Describe the workflow of this proteomics strategy starting from a tissue sample (4p)
## What are the shortcoming and advantages of the gel-based approach (3p)
# Curcumin, one of the bioactive metabolites from plants of the ginger family, has many potential medical uses. However, bioavailibility of curcumin is low, and therefore, many research is conducted to find better formulations to reach optimal blood concentrations. In order to support this research, you need to build an assay to asses blood plasma concentrations of curcumin. Therefore, you are offered a mass spectrometer with a mass accuracy of 30 ppm.
## How would you prepare the blood samples for this analysis. (3p)
## What is the mass you are going to look after? (...,... Da +- ...,... Da) (4p)
## BONUS question: can you give one possible strategy to formulate an oral curcumin preparation with better bioavailability. (1p)

===29/01/2019===
Robben:
#je hebt een genoom van een axolotl dat je wil analyseren. Het heeft een genoom meer dan dubbel zo groot als dat van de mens. Welke next generation sequencing techniek ga je gebruiken + verdedig waarom
#woordjes:
##Ribsome profiling
##Array protein targetting
##protein-protein interaction map is scale free

Landuyt:
# you receive a peak list: 148.07574, 175.11900, 219.11285, 322.18741, 334.13979, 423.23509, 447.22386, 480.25655, 504.24532, 593.34062, 605.29300, 708.36756, 752.36141, 779.40467, 908.46252, 926.47309
##Which type of proteomic analysis has been used? (explain thoroughly)
##What is the identity of the protein (explain your strategy for interpretation and the certainty regarding your identification)
##How would the spectrum look like if the other proteomics method would have been used?
##Search for a recent article concerning the protein of interest and give a brief discussion (if you are not sure about your identification (question 2), please use human epidermal growth factor as a substitute (not both! or you pick your identified protein, or the substitute)
#Verhaaltje rond onderzoekers die de bioavailability willen onderzoeken van de stof curcumin, deze stof bevindt zich in het bloed. via MS zul je curcumin kunnen analyseren.
##How would you prepare the patient blood plasma samples to extract the drug? 3p
##Which mass will you be looking for? 4p
##bonus punt: describe a innovative preparation of curcumin for improved oral bioavailability. 1p

===22/01/2019===
Robben:
#verhaal rond een proteïne dat kan instaan voor vele zaken via interacties met een bepaald domein. Hoe kan je deze interacties best bestuderen?
##bespreek welke methode je het best kan gebruiken en vergelijk met andere technieken.
##bespreek kort de manier van werking van de methode die je gekozen hebt.
#begrippen
##paired end sequencing
##nanopore sequencing
##affimetrix chip

Landuyt:
#A proteomics researcher working on a major human disease discovers a significantly expressed protein in a set of biopsies taken from patients, compared with a set of biopsies from healthy individuals. Below you can find the peak list that can be used to identify this protein. peak list :920.48 902.47 791.43 774.37 720.40 661.29 607.31 532.24 476.27 445.21 389.24 314.17 260.20 201.09 147.11 130.05
##Which type of proteomics approach has been used? Explain briefly 3p
##What is the identity of the protein? 4p
##What would the spectrum look like if the other proteomics approach would have been used? Give 5 examples masses that could appear in this spectrum. If you do not feel confident about your protein ID, use human epidermal growth factor (EGF) as an alternative for this assignment. 4p
##Briefly explain the biological role of this protein. What type of disease is being studied? 1p
#Some patients are selected for treatment with imatinib mesylate. In order to check the pharmacology of the drug, you are offered an old single quadrupole MS with a mass accuracy of 100ppm.
##How would you prepare the patient blood plasma samples to extract the drug? 3p
##Which mass will you be looking for? 4p
##Bonus question: Can you explain the mode of action of this drug in relation to the drug target (= the protein from question 1)? 1p

===16/01/2019===

Deel Robben:
# je stuurt een bacterie naar de ruimte en laat deze daar groeien, je laat dezelfde bacterie op aarde groeien. Hoe zou jij het transcriptoom onderzoeken? welke techniek gebruik je + verdedig waarom deze en niet de andere. Leg deze techniek uit.
# woordjes:
##SMRT,
##gene altering,
##genetic interactomics
#
Deel Landuyt
#Je hebt een pieklijst, welke methode van proteomics is hier gebruikt om het proteïnen te onderzoeken. er was een verhaaltje bij dat het ging over een meneer met plotse diarree en je neemt een stoelsample om te onderzoeken. Pieklijst: 997.49 979.49 868.46 851.31 754.34 705.39 640.30 592.31 505.28 493.23 406.20 358.21 293.11 244.17 147.11 130.05
Het is volgens de prof : EYI/LSFNPK
# welk protein is het?
# wat zou een 2e mogelijkheid zijn om dit proteïnen te onderzoeken en wat zou je verkrijgen?
# geef meer info over de werking van het proteïnen

Deel 2: Je wilt het actief component van motilium onderzoeken, wat is je strategie?
# De accuraatheid van je ms machine is 10 ppm, waar ga je de piek zien van het actief component?
# Geef meer info over dit component

===15 januari 2019===
Robben
#Solexa sequencing en SMRT vergelijken.
#Begrippen:
##Polyploidie en genomic evolution,
##Nanostring nCounter technologie
##Rosetta stone method

Landuyt
#Proteomics
#* Piekenlijst : 1425.63 1407.62 1297.57 1279.53 1168.53 1165.48 1078.48 1069.46 981.4 968.41 853.39 818.34 722.35 704.29 608.3 573.25 458.23 445.24 357.18 348.19 261.16 258.11 147.11 129.07
#* Welk proteïne is dit?
#* Wat zou het resultaat zijn als er een andere proteomics techniek wordt gebruikt?
#* Geef meer info over de werking van het proteïne

#Metabolomics
#* Je hebt een metaboliet resveratrol dat in rode wijn voorkomt en efficiënt hieruit geëxtraheerd kan worden.
#* Hoe zou je resveratrol opzuiveren? (HPLC-MS)
#* Wat is de monoisotopische massa bij 2ppm
#* Kan je uit deze opgaven een link tussen proteomics en metabolomics vinden?

===23/08/2018===

* proteomics :A clinician working on a major disease discovers a significantly up-regulated protein in a large number of patient samples. The conclusion is simple: this protein could be a major breakthrough! However, the medical doctor leading the study learned how to use a mass spectrometer, but was not yet trained in the interpretation of the data. Can you help our desperate clinician in identifying the protein based on the peak list below?
148.07574
175.11900
219.11285
322.18741
334.13979
423.23509
447.22386
480.25655
504.24532
593.34062
605.29300
708.36756
752.36141
779.40467
908.46252
926.47309
#Questions:
#* Which type of proteomic analysis has been used? (explain thoroughly) …/2
#* What is the identity of the protein (explain your strategy for interpretation and the certainty regarding your identification) …/3
#* Which disease is studied? …/1
#* How would the spectrum look like if the other proteomics method would have been used? (if you are not sure about your identification (question 2), please use human epidermal growth factor as a substitute (not both! or you pick your identified protein, or the substitute) …/3
#*Search for a recent article concerning the protein of interest and give a brief discussion (again, same principle as for question 4)

Metabolomics
accuraatheid berekenen, je krijgt de M/Z van het toestel. De exacte massa moet je opzoeken
is dit een goede accuraatheid, leg uit?

===23/01/2018 NM===
Robben:
# Ze willen het genoom van een rendier achterhalen. de dichtst verwante soort waarvan ze het genoom kennen is een rund.
#* Hoe ga je te werk? welk next generation sequencing platform kies je (je kan er maar 1 kopen) en waarom?
#* Leg de sample prep en voornaamste principes uit.
#* Woordjes
## Scaffold sequentie
## Genetic interactomics
## PMAGE
Landuyt:
# PROTEOMICS
#* Na 2D gel kiest researcher een spot en behandelt die met trypsine en krijgt bij MS een lijst pieken (die je dus krijgt). De researcher herkent 'familiar' masses en kiest 1 peptide om te fragmenteren omdat het het enige 'non-suspicious' fragment is. (je weet welke massa dat is). Na fragmentatie krijg je een volgende piekenlijst.
## Wat ging er verkeerd in het experiment?
## Welke MS methoden of componenten werden er gebruikt?
## Welk proteine analyseert hij en wat is de functie ervan.
# METABOLOMICS
#* Een researcher in colombia krijgt een ms toestel ter beschikking, analyseert koffiebonen (denk ik) en krijgt een dominante piek op 195,xx m/z.
## Wat is da accuraatheid van het machien op ca 200 Da? Is dit oke voor metabolomics?
## BONUS er was nog een tweede dominante piek xxx m/z, welk molecule is dit?

===23/01/2018 VM===
Robben:
#Je wilt met behulp van next generation sequencing mutaties en rearrangments onderzoeken in kanker.
#* Wat is je sequencing strategy?
#* Welk platform zou je gebruiken? (Je mag er maar 1 geven).
#* Geef uitgebreid de sample prep en de werking van het platform.
#Woordjes:
#* Endogenous Retrovirus
#* Affrimex Genechip
#*nCounter technology

Landuyt:
#PROTEOMICS
#* A lab technician in a proteomics core facility receives samples for identification, one from a lab working with human cancer tissues and one from a lab working on neuro degenerating deseases. One of the proteins was cut from a 2D gel and the other protein was found to be up-regulated in a gel-free proteomics experiment. Both analysis yielded nice mass spectra, the respective peak lists can be found below. However, due to some solvent spilling, the ink on the tubes was ruined and the origin of the samples got lost. The lab technician is very concerned with this issue because he is afraid to lose his job.
#** Peak list 1: 1743,83; 1716,82; 1605,79; 1560,72; 1474,75; 1473,69; 1417,73; 1360,61; 1303,69; 1259,56; 1174,64; 1172,53; 1073,46; 1060,6; 972,41; 947,52; 885,38; 850,46; 788,32; 763,43; 675,24; 662,38; 563,32; 561,2; 476,28; 432,16; 375,24; 318,11; 262,15; 261,09; 175,12; 130,05
#** Peak list 2: 4356,00; 4435,97; 3243,61; 3563,47; 2709,32; 2622,32; 2391,03; 2550,96; 2356,24; 2270,15; 2165,90; 2245,87; 2053,89; 2133,86; 1980,09; 2064,11; 2008,12; 2060,06; 1954,96; 2114,89; 1916,98; 1958,99; 1996,94; 1697,83; 1681,90; 1578,82; 1620,83; 1658,79; 1522,77; 1487,65; 1393,63; 1596,71; 1873,43; 1387,60; 1326,64; 1309,72; 1292,60; 1132,56; 1212,53; 1114,53; 1101,55; 1304,63; 1421,42; 1066,59; 1306,49; 1003,54; 1045,55; 1163,48;
## Which peak list was generated from the gel-based and which was generated with gel-free proteomic analysis. Please comment on how you come to you conclusion.
## What is the identity of the two proteins? Give a brief summary of the biological significance of both proteins. (= eerste lijst De novo en BLASTEN & tweede lijst in MASCOT steken --> neem taxonomy homo sapience!)
## By now, you should be able to transferrin the identity of proteins to the correct lab. Which comes from the cancer lab and which from neuro degeneration lab?
#METABOLOMICS
#* The popular cocktail mojito was initially created as a medicine to treat various conditions such as bad digestion. Therefore, it is nowadays consumed to stimulate appetite before a meal or to stimulate digestion after a heavy meal. The core ingredient is mint, which undergoes a successful extraction with rum an lime juice.
## If you would like to purify the metabolites from mint in a lab setting, how would you do this knowing the above.
## In case the extraction is successful and you have a mass spectrometer with a mass accuracy of 2 ppm, then what would be the mono-isotopic mass would you record for the most dominant metabolite from the mint?
## BONUS: If mint would be an illegal substance and you were asked to make a test to detect it in blood of suspected users, which metabolite would you go afer? (multi answers possible).

===16/01/2018 (NM)===
Robben
#Sequencing platform (welk en waarom) + uitleggen hoe. voor een transcriptomics studie van de gifklier van een schorpioen, hoe ge u staalvoorbereiding zou doen.
#woordjes: Massive parallel signature sequencing, proteome array en genetic interactomics.

Landuyt,
# Proteomics. Onderzoek(st)er vind interresant proteine bij een zieke persoon gegeven onderstaand massa spectrum (piekenlijst van een peptide).
#* Welke proteomics aanpak is er gebruikt en leg deze kort uit
#* Van welk proteine is dit peptiede
#* Als je de andere proteomics aanpak gebruikt wat voor pieken bekom je dan bij je massaspectrum, geef 5 voorbeelden van massa's die hierbij voorkomen
#*wat is de biologische relevantie van dit proteine aka in welke ziekte speelt dit proteine een rol

# Metabolomics gegeven een drug-metaboliet met een piekhalfwaardebreedte 0.0001en een monoisotopische massa 480.2531
#* Wat is de resolutie van dit spectrum en is dit nodig?
#* Waarom zien we typisch 2 pieken of meer van hetzelfde ion op een massa spectrum
#* Over welke drug gaat het hier in dit geval
#* Bonus vraag: Wat is de exacte mode of action van deze drug met betrekking tot het proteïne uit vraag 1

===16/01/2018 (VM)===

Robben
# RNA-seq uitleggen + 1 sequencing platform + voor en nadelen van RNAseq en andere analyse platvormen (kader met PCR, microarrays, SAGE en RNAseq
# woordjes: polyploidie en genoom evolutie, gene ontology, Rosetta stone method
Landuyt
# MS pieken gegeven: welk proteïne, welk proteomics methode, wat als ze de andere methode gebruikte (geef 5 massa's), mode of action van dat proteine
# massa en half height gegeven: wat is de resolutie en is het een goede resolutie, over welk metaboliet zijn we bezig, soms zijn er meerdere pieken voor hetzelfde metaboliet en waarom
#Bonus vraag: wat is de link tussen het proteïne en het metaboliet volgens recente studies

===10/06/2014===
====prof. Robben (gesloten boek)====
#Wat doet RNA-seq?
#Geef 1 van de ontwikkelde technieken vrij te kiezen (454/solid/...) (commercieel platform)
#Vergelijk RNA-seq met andere technieken (voordelen/nadelen) (concurrerende methoden)
====prof. Landuyt (open boek/open pc)====
#Krijgt waarden van MS moet eiwit geven
#Waarom kan je een vertekend beeld krijgen en geef de statistische realiteit
#Welke ziekte zou er hier onderzocht zijn?
#Als er een fout is opgetreden bij de MS kan je een andere methode gebruiken?
#Moest ge zelf onderzoek willen doen op dit eiwit met welke dingen zou je dan rekening willen houden en hoe los je dit op?

====Johan Robben====
#In het kader van een onderzoeksproject krijg je de opdracht om bij een industriële giststam de transcriptoom verschillen bij het brouwen van Westmalle en Duvel in kaart te brengen. Stel een methode voor en bespreek een concreet analyseplatform voor waarvoor je zou kiezen. Beargumenteer je keuze.
#Bespreek bondig de belangrijkste 'second generation' sequencing methoden. Vergelijk en evalueer kritisch.
#Bespreek drie experimentele methoden om interacties te ontdekken. Geef voor- en nadelen.
#Sequencing. Bespreek de Solexa-methode (Illumina) vanaf de bereiding van het DNA tot het sequeneren zelf. Welke toepassingen heeft Solexa? Wanneer is de Sanger-methode te verkiezen?
#Interactomics. Bespreek kort drie methoden om te onderzoeken. Geef sterktes/zwaktes van elke techniek. Hoe ga je met gegevens uit deze technieken (in essentie) interactienetwerken opbouwen.
#Bespreek de Affymetrix GeneChip en de Illumina random BeadArrays. En maak een kwalitatieve vergelijking.
#Bespreek Illumina Sequencing van DNA-preparatie tot uitlezing. Vergelijk kwalitatief met Sanger sequencing.
#Bespreek 454 sequencing (van DNA library construction tot sequentie analyse). Vergelijk kwantitatief 454 met Sanger.
#De hoge druk sequencers van de nieuwe generatie vormen een bedreiging voor de traditionele micro-arrays. Leg uit.
#Bespreek oligonucleotide arrays en random beads in transcriptoomanalyse en vergelijk. Bespreek targetlabelling en uitlezing.
#Leg volgende begrippen kort uit:
#*whole shotgun sequencing
#*paired end ditags
#*gene ontology
#*scale free network

====Bart Landuyt====
#Hoe zijn massaspectrometers over het algemeen opgebouwd? Geef enkele vb van veel gebruikte opstellingen.
#Waarin verschilt peptidomics fundamenteel van proteomics?
#Bespreek de uitdagingen van het metaboloom en de gevolgen ervan op de analyse

====Baggerman====
#Hoe bepaal je de sequentie van een peptide met MS?
#Bespreek ESI-Q-TOF massa spectrometrie
#Vergelijk MALDI en ESI. Geef voor- en nadelen.
#Bespreek resolutie in MS, geef relevantie bij analyse.
#Leg het principe van een time-of-flight analysator uit

====Filip Roland====
#chemische uitdagingen van het metaboloom + relevantie voor staalname en staalbereiding
#Bespreek de belangrijkste verschillen tussen metaboloom - gen/transcr/proteoom. Hoe uit zich dat in de analyse.
#Bespreek de klassieke workflow van een metabolomics-analyse. Welke keuzes moeten gemaakt worden en wat zijn de mogelijke technieken die gebruikt kunnen worden

Genoom-, proteoom- en metaboloomanalyse

2025-01-22T15:43:02Z

R0895938: /* Examenvragen */

[[Categorie:Mabb]]

==Vakinformatie==
Genoom-, proteoom- en metaboloomanalyse
Het vak wordt gegeven door prof. Landuyt en prof. Robben. Robben zijn deel is mondeling en gesloten boek. Robben maakt elk examen nieuwe vragen

2022-2023: het vak wordt gegeven door Landuyt (metabolomics), Robben (genomics), en Schoofs (proteomics). Alles is gesloten boek.

2023-2024: het vak wordt gegeven door Van Belleghem (genomics) en Schoofs (proteomics). Voor het metabolomics gedeelte van Landuyt moest je oude lesopnames kijken. Alles is gesloten boek, geschreven examen

2024-2025: Het vak wordt gegeven door Van Belleghem (genomics) en Temmerman (proteomics en metabolomics). Voor het deel van Temmerman waren er opnames van prof Schoofs en Landuyt, vanwege Temmerman haar zwangerschap. Ze was er wel voor vragen te beantwoorden. Alles is gesloten boek, geschreven examen.

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/n/G0G57AN.htm

==Examenvragen==
===21/01/2025===
SVB
* PAM-genome. What is it and how sequence? And some small questions.
* Terms
*# ATAC-seq
*# AP-MS
*# LINE

Temmerman
* Labels in proteomics: why used? Which labels are there? Give example for each type and explain differences.
* MS spectrum: Label the axes. Which peptides in spectrum? Idententify which peaks belong to which peptides.
* Are the following statements true or false. Explain briefly

===01/02/2024===
SVB
*Open question: 233 genomes of primates to be sequenced, focus on repetitive content in the genome. What sequencing technologies and equipment to use? Why?
*Explain how the chosen technologies work.
*Give two examples of how can be used

*Terms
*#Retrovirus-like elements
*#GWAS
*#ChIP-Seq

Schoofs
NO CALCULATOR ALLOWED

*Explain how to identify proteins with explorative (shotgun) proteomics
*Explain the differences between MALDI and ESI

*Multiple choice with explanation

*#No two identical compounds will ionise and fragment in exactly the same manner, true or false
*#Enriched proteins of cultured cells, appropriate method (DiGE, SILAC, SRM, Label-free methods)
*#What is SRM used for?
*#Which conclusion can be drawn from a 2D gel electrophoresis experiment?
*#m/z of 120, 121, 122, 123, which isotopes are responsible for signal at m/z 122 (12C, 35Cl, 1H; 12C, 35Cl, 2H; 12C, 37Cl, 1H; 12C, 37Cl, 2H)

*Exercises
*#Question about a fragmented peptide MS2 spectra
*#*Why do the y ions have different intensities?
*#*Explain how the peptide sequence (given) is derived from the spectrum.
*#Figure with mass spectrum, what is the mass of the peak? (2 peaks, second peak is isotopes with distance of +1)
*Definitions
*#Delayed extraction
*#Reflectron mode
*#Targeted proteomics
*#Mascot
*#DDA

===23/01/2024===
SVB
*Open question: 4000 genomes of Darwin's finches underwent resequencing encompassing individuals of 4 species
*#Explain the methodology in conducting resequencing. what are the key steps and technologies?
*#Evaluate the challenges of fragmentation of the reference genome, knowing that the genome existed of about 20.000 scaffolds of large size:
*#*What genomic properties caused it to be fragmented? (repeats)
*#*What is the significance of this issue?
*#*Propose a method to enhance the coherency of the reference genome.
*#Give two illustrative examples of insights that can be derived from experiments like these.
*Terms
*#Phylogenetic footprinting
*#AP-MS
*#Gene regulatory network

Schoofs
*Explain how proteins of a biological sample can be identified with peptide masss fingerprinting using a MALDI-TOF mass spectrometer.
*Multiple choice with explanation
*#Two compounds fragment in exactly the same manner, true or false
*#Enriched proteins of cultured cells, appropriate method (DiGE, SILAC, SRM, Label-free methods)
*#What is a proteotypic peptide?
*#Which conclusion can be drawn from a 2D gel electrophoresis experiment?
*#m/z of 120, 121, 122, 123, which isotopes are responsible for signal at m/z 122 (12C, 35Cl, 1H; 12C, 35Cl, 2H; 12C, 37Cl, 1H; 12C, 37Cl, 2H)
*Exercises
*#Question about the ICAT image from the slides
*#*Are the peptides (A to F) coming from the same protein?
*#*What is the distance between the green and the blue peaks?
*#*Explain how the peptide sequence is derived from the spectrum
*#Figure with mass spectrum, what is the mass of the peak? (2 peaks, second peak is isotopes with distance of 0,5)
*Definitions
*#SRM
*#Isobaric tag
*#Mass spectrometric resolution
*#Mascot
*#E-value

===5/09/2023===
Robben:
# Jarenlang geduurd om genoom van een specifieke boonsoort te sequencen (genoomgrootte = 4x menselijk genoom).
## Speculeer waarom het zo lang geduurd heeft.
## Geef schematisch weer welke strategie jij zou gebruiken om het genoom vandaag sneller te sequencen.
## Leg de principes van jouw gekozen technieken uit.
# Terms
## ribosome profiling
## scale free networks
## endogenous retrovirus

===24/01/2023===
Robben:
# Illumina, pacbio and oxford nanopore all have their own transcriptomics approach.
## Give the working principle
## critically discuss strengths and weaknesses of the platforms
## Which platform would you choose to study the transcriptome of a cancer tissue? argue.
# Terms
## paired end sequencing
## haplotype association analysis
## protein-protein interaction networks are scale free

Schoofs:
# Open vraag: membraanproteïnen van gezonde muizen en muizen met pituitary tumor onderzoeken. Hoe ga je de identificatie en kwanitificatie doen? aanpak volledig uitleggen.
# kleine vraagjes
## 2 meerkeuze
## 2 begrippen (razor peptide en delayed extraction tof)
## vraag met grafiek (intensiteit vs m/z), hoe massa van ongeladen peptide bepalen adh van deze grafiek?
## iets met de score-value voor peptide mass fingerprint verhogen
# oefening op computer
## frataxin mature peptide spot in een gel picken; welke pI en welke MW?
## Zijn er modificaties, waarom (niet)?
## Geef een lijst met 10 pieken die het hele spectrum weergeven.

===18/01/2021===
Robben:
# SMRT and nanopore can be used to finish the human X chromosome.
## Give the working principle and details of SMRT and nanopore.
## Why are these methods better than Illumina?
## Give the strategy to finish the other chromosomes.
# Terms
## Affymetrix chip
## Gene acquisition (by gene evolution)
## Genomic interactions

Landuyt:
# You get a safe denatured protein mixture from the Sars-Cov-2 virus.
## Describe a method how this mixture is made. (2p)
## If you would be pick the spike protein in a gel-based proteomics experiment, at which MW and PI would you look. Do you expect modifications and why (not)? (3p)
## Give a peak list of 10 peaks that cover the whole spectrum if you use trypsin to digest the spike protein. (4p)
## How can you see the difference between the UK and the standard viariant? Give the principle and calculations. (3)
# Hydroxychloroquine (HCQ) was developed for malaria treatment and seems to be working against corona in patients with less severe symptomes. We need to know the blood concentrations of HCQ in treated patients. Therefore, you are offered a mass spectrometer with a mass accuracy of 5 ppm.
## How would you prepare the blood samples for this analysis. (3p)
## What is the mass you are going to look after? (...,... Da +- ...,... Da) (4p)
## BONUS question: can you give the mechanism of action of HCQ? (1p)

===28/01/2020===
Robben:
#SMRT sequencing recently had update, something with circularization.
##Discuss the technical aspects etc
##Why is it important?
#Terms
##Polyploidy and genome variation
##NanoString nCounter expression system
##Rosetta Stone Method

Landuyt:
Same as 14/01/2020, 15/01/2020 and 21/01/2020

===21/01/2020===
Robben:
#The genome of cotton was already sequenced in 2012 via Sanger. Which NGS will you use to redo the sequencing?
## Give the working principle and details of the chosen platform.
#Terms
##Gene ontology
##Affimix chip
##Gene interaction mapping

Landuyt (exact same questions as yesterday):
# Placental Growth Factor is an interesting protein.
## Describe briefly what makes this protein so interesting (1p)
## If PlGF would be picked up in a gel-based proteomics experiment, how would the spectrum then look like (provide the exact masses of at least 5 peaks). (4p)
## Describe the workflow of this proteomics strategy starting from a tissue sample (4p)
## What are the shortcoming and advantages of the gel-based approach (3p)
# Curcumin, one of the bioactive metabolites from plants of the ginger family, has many potential medical uses. However, bioavailibility of curcumin is low, and therefore, many research is conducted to find better formulations to reach optimal blood concentrations. In order to support this research, you need to build an assay to asses blood plasma concentrations of curcumin. Therefore, you are offered a mass spectrometer with a mass accuracy of 30 ppm.
## How would you prepare the blood samples for this analysis. (3p)
## What is the mass you are going to look after? (...,... Da +- ...,... Da) (4p)
## BONUS question: can you give one possible strategy to formulate an oral curcumin preparation with better bioavailability. (1p)

===15/01/2020 (afternoon)===
Robben:
# Infection of a certain type of phage in a bacterial cell. You would like to execute a transcriptomal analysis at the moment of encounter of the phage and 15 minutes later.
## Defend which platform/technique you would use.
## Explain the working principles and technical details of the chosen platform/technique.
# Terms
## Optical mapping
## Sequence scaffold
## Interaction network

Landuyt (exact same questions as yesterday):
# Placental Growth Factor is an interesting protein.
## Describe briefly what makes this protein so interesting (1p)
## If PlGF would be picked up in a gel-based proteomics experiment, how would the spectrum then look like (provide the exact masses of at least 5 peaks). (4p)
## Describe the workflow of this proteomics strategy starting from a tissue sample (4p)
## What are the shortcoming and advantages of the gel-based approach (3p)
# Curcumin, one of the bioactive metabolites from plants of the ginger family, has many potential medical uses. However, bioavailibility of curcumin is low, and therefore, many research is conducted to find better formulations to reach optimal blood concentrations. In order to support this research, you need to build an assay to asses blood plasma concentrations of curcumin. Therefore, you are offered a mass spectrometer with a mass accuracy of 30 ppm.
## How would you prepare the blood samples for this analysis. (3p)
## What is the mass you are going to look after? (...,... Da +- ...,... Da) (4p)
## BONUS question: can you give one possible strategy to formulate an oral curcumin preparation with better bioavailability. (1p)

===14/01/2020 (morning)===
Robben:
# Phenotypic differences between closely related almond and peach might largely be attributed to transposable elements. Your lab received funding for comparative genomic sequencing to elucidate the differences.
## Explain schematically the sequencing strategy you would propose.
## Which commerically available next-gen sequencing platform(s) would you propose to use. '''Argue your choice.'''
## Explain the working principles of the chosen platform(s)
# Terms
## Ribosome profiling
## (Transcriptomics) microarray target labeling
## Protein-protein interaction maps are scale free

Landuyt:
# Placental Growth Factor is an interesting protein.
## Describe briefly what makes this protein so interesting (1p)
## If PlGF would be picked up in a gel-based proteomics experiment, how would the spectrum then look like (provide the exact masses of at least 5 peaks). (4p)
## Describe the workflow of this proteomics strategy starting from a tissue sample (4p)
## What are the shortcoming and advantages of the gel-based approach (3p)
# Curcumin, one of the bioactive metabolites from plants of the ginger family, has many potential medical uses. However, bioavailibility of curcumin is low, and therefore, many research is conducted to find better formulations to reach optimal blood concentrations. In order to support this research, you need to build an assay to asses blood plasma concentrations of curcumin. Therefore, you are offered a mass spectrometer with a mass accuracy of 30 ppm.
## How would you prepare the blood samples for this analysis. (3p)
## What is the mass you are going to look after? (...,... Da +- ...,... Da) (4p)
## BONUS question: can you give one possible strategy to formulate an oral curcumin preparation with better bioavailability. (1p)

===29/01/2019===
Robben:
#je hebt een genoom van een axolotl dat je wil analyseren. Het heeft een genoom meer dan dubbel zo groot als dat van de mens. Welke next generation sequencing techniek ga je gebruiken + verdedig waarom
#woordjes:
##Ribsome profiling
##Array protein targetting
##protein-protein interaction map is scale free

Landuyt:
# you receive a peak list: 148.07574, 175.11900, 219.11285, 322.18741, 334.13979, 423.23509, 447.22386, 480.25655, 504.24532, 593.34062, 605.29300, 708.36756, 752.36141, 779.40467, 908.46252, 926.47309
##Which type of proteomic analysis has been used? (explain thoroughly)
##What is the identity of the protein (explain your strategy for interpretation and the certainty regarding your identification)
##How would the spectrum look like if the other proteomics method would have been used?
##Search for a recent article concerning the protein of interest and give a brief discussion (if you are not sure about your identification (question 2), please use human epidermal growth factor as a substitute (not both! or you pick your identified protein, or the substitute)
#Verhaaltje rond onderzoekers die de bioavailability willen onderzoeken van de stof curcumin, deze stof bevindt zich in het bloed. via MS zul je curcumin kunnen analyseren.
##How would you prepare the patient blood plasma samples to extract the drug? 3p
##Which mass will you be looking for? 4p
##bonus punt: describe a innovative preparation of curcumin for improved oral bioavailability. 1p

===22/01/2019===
Robben:
#verhaal rond een proteïne dat kan instaan voor vele zaken via interacties met een bepaald domein. Hoe kan je deze interacties best bestuderen?
##bespreek welke methode je het best kan gebruiken en vergelijk met andere technieken.
##bespreek kort de manier van werking van de methode die je gekozen hebt.
#begrippen
##paired end sequencing
##nanopore sequencing
##affimetrix chip

Landuyt:
#A proteomics researcher working on a major human disease discovers a significantly expressed protein in a set of biopsies taken from patients, compared with a set of biopsies from healthy individuals. Below you can find the peak list that can be used to identify this protein. peak list :920.48 902.47 791.43 774.37 720.40 661.29 607.31 532.24 476.27 445.21 389.24 314.17 260.20 201.09 147.11 130.05
##Which type of proteomics approach has been used? Explain briefly 3p
##What is the identity of the protein? 4p
##What would the spectrum look like if the other proteomics approach would have been used? Give 5 examples masses that could appear in this spectrum. If you do not feel confident about your protein ID, use human epidermal growth factor (EGF) as an alternative for this assignment. 4p
##Briefly explain the biological role of this protein. What type of disease is being studied? 1p
#Some patients are selected for treatment with imatinib mesylate. In order to check the pharmacology of the drug, you are offered an old single quadrupole MS with a mass accuracy of 100ppm.
##How would you prepare the patient blood plasma samples to extract the drug? 3p
##Which mass will you be looking for? 4p
##Bonus question: Can you explain the mode of action of this drug in relation to the drug target (= the protein from question 1)? 1p

===16/01/2019===

Deel Robben:
# je stuurt een bacterie naar de ruimte en laat deze daar groeien, je laat dezelfde bacterie op aarde groeien. Hoe zou jij het transcriptoom onderzoeken? welke techniek gebruik je + verdedig waarom deze en niet de andere. Leg deze techniek uit.
# woordjes:
##SMRT,
##gene altering,
##genetic interactomics
#
Deel Landuyt
#Je hebt een pieklijst, welke methode van proteomics is hier gebruikt om het proteïnen te onderzoeken. er was een verhaaltje bij dat het ging over een meneer met plotse diarree en je neemt een stoelsample om te onderzoeken. Pieklijst: 997.49 979.49 868.46 851.31 754.34 705.39 640.30 592.31 505.28 493.23 406.20 358.21 293.11 244.17 147.11 130.05
Het is volgens de prof : EYI/LSFNPK
# welk protein is het?
# wat zou een 2e mogelijkheid zijn om dit proteïnen te onderzoeken en wat zou je verkrijgen?
# geef meer info over de werking van het proteïnen

Deel 2: Je wilt het actief component van motilium onderzoeken, wat is je strategie?
# De accuraatheid van je ms machine is 10 ppm, waar ga je de piek zien van het actief component?
# Geef meer info over dit component

===15 januari 2019===
Robben
#Solexa sequencing en SMRT vergelijken.
#Begrippen:
##Polyploidie en genomic evolution,
##Nanostring nCounter technologie
##Rosetta stone method

Landuyt
#Proteomics
#* Piekenlijst : 1425.63 1407.62 1297.57 1279.53 1168.53 1165.48 1078.48 1069.46 981.4 968.41 853.39 818.34 722.35 704.29 608.3 573.25 458.23 445.24 357.18 348.19 261.16 258.11 147.11 129.07
#* Welk proteïne is dit?
#* Wat zou het resultaat zijn als er een andere proteomics techniek wordt gebruikt?
#* Geef meer info over de werking van het proteïne

#Metabolomics
#* Je hebt een metaboliet resveratrol dat in rode wijn voorkomt en efficiënt hieruit geëxtraheerd kan worden.
#* Hoe zou je resveratrol opzuiveren? (HPLC-MS)
#* Wat is de monoisotopische massa bij 2ppm
#* Kan je uit deze opgaven een link tussen proteomics en metabolomics vinden?

===23/08/2018===

* proteomics :A clinician working on a major disease discovers a significantly up-regulated protein in a large number of patient samples. The conclusion is simple: this protein could be a major breakthrough! However, the medical doctor leading the study learned how to use a mass spectrometer, but was not yet trained in the interpretation of the data. Can you help our desperate clinician in identifying the protein based on the peak list below?
148.07574
175.11900
219.11285
322.18741
334.13979
423.23509
447.22386
480.25655
504.24532
593.34062
605.29300
708.36756
752.36141
779.40467
908.46252
926.47309
#Questions:
#* Which type of proteomic analysis has been used? (explain thoroughly) …/2
#* What is the identity of the protein (explain your strategy for interpretation and the certainty regarding your identification) …/3
#* Which disease is studied? …/1
#* How would the spectrum look like if the other proteomics method would have been used? (if you are not sure about your identification (question 2), please use human epidermal growth factor as a substitute (not both! or you pick your identified protein, or the substitute) …/3
#*Search for a recent article concerning the protein of interest and give a brief discussion (again, same principle as for question 4)

Metabolomics
accuraatheid berekenen, je krijgt de M/Z van het toestel. De exacte massa moet je opzoeken
is dit een goede accuraatheid, leg uit?

===23/01/2018 NM===
Robben:
# Ze willen het genoom van een rendier achterhalen. de dichtst verwante soort waarvan ze het genoom kennen is een rund.
#* Hoe ga je te werk? welk next generation sequencing platform kies je (je kan er maar 1 kopen) en waarom?
#* Leg de sample prep en voornaamste principes uit.
#* Woordjes
## Scaffold sequentie
## Genetic interactomics
## PMAGE
Landuyt:
# PROTEOMICS
#* Na 2D gel kiest researcher een spot en behandelt die met trypsine en krijgt bij MS een lijst pieken (die je dus krijgt). De researcher herkent 'familiar' masses en kiest 1 peptide om te fragmenteren omdat het het enige 'non-suspicious' fragment is. (je weet welke massa dat is). Na fragmentatie krijg je een volgende piekenlijst.
## Wat ging er verkeerd in het experiment?
## Welke MS methoden of componenten werden er gebruikt?
## Welk proteine analyseert hij en wat is de functie ervan.
# METABOLOMICS
#* Een researcher in colombia krijgt een ms toestel ter beschikking, analyseert koffiebonen (denk ik) en krijgt een dominante piek op 195,xx m/z.
## Wat is da accuraatheid van het machien op ca 200 Da? Is dit oke voor metabolomics?
## BONUS er was nog een tweede dominante piek xxx m/z, welk molecule is dit?

===23/01/2018 VM===
Robben:
#Je wilt met behulp van next generation sequencing mutaties en rearrangments onderzoeken in kanker.
#* Wat is je sequencing strategy?
#* Welk platform zou je gebruiken? (Je mag er maar 1 geven).
#* Geef uitgebreid de sample prep en de werking van het platform.
#Woordjes:
#* Endogenous Retrovirus
#* Affrimex Genechip
#*nCounter technology

Landuyt:
#PROTEOMICS
#* A lab technician in a proteomics core facility receives samples for identification, one from a lab working with human cancer tissues and one from a lab working on neuro degenerating deseases. One of the proteins was cut from a 2D gel and the other protein was found to be up-regulated in a gel-free proteomics experiment. Both analysis yielded nice mass spectra, the respective peak lists can be found below. However, due to some solvent spilling, the ink on the tubes was ruined and the origin of the samples got lost. The lab technician is very concerned with this issue because he is afraid to lose his job.
#** Peak list 1: 1743,83; 1716,82; 1605,79; 1560,72; 1474,75; 1473,69; 1417,73; 1360,61; 1303,69; 1259,56; 1174,64; 1172,53; 1073,46; 1060,6; 972,41; 947,52; 885,38; 850,46; 788,32; 763,43; 675,24; 662,38; 563,32; 561,2; 476,28; 432,16; 375,24; 318,11; 262,15; 261,09; 175,12; 130,05
#** Peak list 2: 4356,00; 4435,97; 3243,61; 3563,47; 2709,32; 2622,32; 2391,03; 2550,96; 2356,24; 2270,15; 2165,90; 2245,87; 2053,89; 2133,86; 1980,09; 2064,11; 2008,12; 2060,06; 1954,96; 2114,89; 1916,98; 1958,99; 1996,94; 1697,83; 1681,90; 1578,82; 1620,83; 1658,79; 1522,77; 1487,65; 1393,63; 1596,71; 1873,43; 1387,60; 1326,64; 1309,72; 1292,60; 1132,56; 1212,53; 1114,53; 1101,55; 1304,63; 1421,42; 1066,59; 1306,49; 1003,54; 1045,55; 1163,48;
## Which peak list was generated from the gel-based and which was generated with gel-free proteomic analysis. Please comment on how you come to you conclusion.
## What is the identity of the two proteins? Give a brief summary of the biological significance of both proteins. (= eerste lijst De novo en BLASTEN & tweede lijst in MASCOT steken --> neem taxonomy homo sapience!)
## By now, you should be able to transferrin the identity of proteins to the correct lab. Which comes from the cancer lab and which from neuro degeneration lab?
#METABOLOMICS
#* The popular cocktail mojito was initially created as a medicine to treat various conditions such as bad digestion. Therefore, it is nowadays consumed to stimulate appetite before a meal or to stimulate digestion after a heavy meal. The core ingredient is mint, which undergoes a successful extraction with rum an lime juice.
## If you would like to purify the metabolites from mint in a lab setting, how would you do this knowing the above.
## In case the extraction is successful and you have a mass spectrometer with a mass accuracy of 2 ppm, then what would be the mono-isotopic mass would you record for the most dominant metabolite from the mint?
## BONUS: If mint would be an illegal substance and you were asked to make a test to detect it in blood of suspected users, which metabolite would you go afer? (multi answers possible).

===16/01/2018 (NM)===
Robben
#Sequencing platform (welk en waarom) + uitleggen hoe. voor een transcriptomics studie van de gifklier van een schorpioen, hoe ge u staalvoorbereiding zou doen.
#woordjes: Massive parallel signature sequencing, proteome array en genetic interactomics.

Landuyt,
# Proteomics. Onderzoek(st)er vind interresant proteine bij een zieke persoon gegeven onderstaand massa spectrum (piekenlijst van een peptide).
#* Welke proteomics aanpak is er gebruikt en leg deze kort uit
#* Van welk proteine is dit peptiede
#* Als je de andere proteomics aanpak gebruikt wat voor pieken bekom je dan bij je massaspectrum, geef 5 voorbeelden van massa's die hierbij voorkomen
#*wat is de biologische relevantie van dit proteine aka in welke ziekte speelt dit proteine een rol

# Metabolomics gegeven een drug-metaboliet met een piekhalfwaardebreedte 0.0001en een monoisotopische massa 480.2531
#* Wat is de resolutie van dit spectrum en is dit nodig?
#* Waarom zien we typisch 2 pieken of meer van hetzelfde ion op een massa spectrum
#* Over welke drug gaat het hier in dit geval
#* Bonus vraag: Wat is de exacte mode of action van deze drug met betrekking tot het proteïne uit vraag 1

===16/01/2018 (VM)===

Robben
# RNA-seq uitleggen + 1 sequencing platform + voor en nadelen van RNAseq en andere analyse platvormen (kader met PCR, microarrays, SAGE en RNAseq
# woordjes: polyploidie en genoom evolutie, gene ontology, Rosetta stone method
Landuyt
# MS pieken gegeven: welk proteïne, welk proteomics methode, wat als ze de andere methode gebruikte (geef 5 massa's), mode of action van dat proteine
# massa en half height gegeven: wat is de resolutie en is het een goede resolutie, over welk metaboliet zijn we bezig, soms zijn er meerdere pieken voor hetzelfde metaboliet en waarom
#Bonus vraag: wat is de link tussen het proteïne en het metaboliet volgens recente studies

===10/06/2014===
====prof. Robben (gesloten boek)====
#Wat doet RNA-seq?
#Geef 1 van de ontwikkelde technieken vrij te kiezen (454/solid/...) (commercieel platform)
#Vergelijk RNA-seq met andere technieken (voordelen/nadelen) (concurrerende methoden)
====prof. Landuyt (open boek/open pc)====
#Krijgt waarden van MS moet eiwit geven
#Waarom kan je een vertekend beeld krijgen en geef de statistische realiteit
#Welke ziekte zou er hier onderzocht zijn?
#Als er een fout is opgetreden bij de MS kan je een andere methode gebruiken?
#Moest ge zelf onderzoek willen doen op dit eiwit met welke dingen zou je dan rekening willen houden en hoe los je dit op?

====Johan Robben====
#In het kader van een onderzoeksproject krijg je de opdracht om bij een industriële giststam de transcriptoom verschillen bij het brouwen van Westmalle en Duvel in kaart te brengen. Stel een methode voor en bespreek een concreet analyseplatform voor waarvoor je zou kiezen. Beargumenteer je keuze.
#Bespreek bondig de belangrijkste 'second generation' sequencing methoden. Vergelijk en evalueer kritisch.
#Bespreek drie experimentele methoden om interacties te ontdekken. Geef voor- en nadelen.
#Sequencing. Bespreek de Solexa-methode (Illumina) vanaf de bereiding van het DNA tot het sequeneren zelf. Welke toepassingen heeft Solexa? Wanneer is de Sanger-methode te verkiezen?
#Interactomics. Bespreek kort drie methoden om te onderzoeken. Geef sterktes/zwaktes van elke techniek. Hoe ga je met gegevens uit deze technieken (in essentie) interactienetwerken opbouwen.
#Bespreek de Affymetrix GeneChip en de Illumina random BeadArrays. En maak een kwalitatieve vergelijking.
#Bespreek Illumina Sequencing van DNA-preparatie tot uitlezing. Vergelijk kwalitatief met Sanger sequencing.
#Bespreek 454 sequencing (van DNA library construction tot sequentie analyse). Vergelijk kwantitatief 454 met Sanger.
#De hoge druk sequencers van de nieuwe generatie vormen een bedreiging voor de traditionele micro-arrays. Leg uit.
#Bespreek oligonucleotide arrays en random beads in transcriptoomanalyse en vergelijk. Bespreek targetlabelling en uitlezing.
#Leg volgende begrippen kort uit:
#*whole shotgun sequencing
#*paired end ditags
#*gene ontology
#*scale free network

====Bart Landuyt====
#Hoe zijn massaspectrometers over het algemeen opgebouwd? Geef enkele vb van veel gebruikte opstellingen.
#Waarin verschilt peptidomics fundamenteel van proteomics?
#Bespreek de uitdagingen van het metaboloom en de gevolgen ervan op de analyse

====Baggerman====
#Hoe bepaal je de sequentie van een peptide met MS?
#Bespreek ESI-Q-TOF massa spectrometrie
#Vergelijk MALDI en ESI. Geef voor- en nadelen.
#Bespreek resolutie in MS, geef relevantie bij analyse.
#Leg het principe van een time-of-flight analysator uit

====Filip Roland====
#chemische uitdagingen van het metaboloom + relevantie voor staalname en staalbereiding
#Bespreek de belangrijkste verschillen tussen metaboloom - gen/transcr/proteoom. Hoe uit zich dat in de analyse.
#Bespreek de klassieke workflow van een metabolomics-analyse. Welke keuzes moeten gemaakt worden en wat zijn de mogelijke technieken die gebruikt kunnen worden

Advanced biochemistry and biotechnology

2025-01-17T08:31:25Z

R0895938: /* 16 januari 2025 */

[[Categorie: Mabb]]
==Vakinformatie==
Verdiepend vervolg op Moleculaire Biologie en Dynamische Biochemie van de 2e bachelor.
In 2021 - 2022 gedoceerd door Prof Johan Robben en Shehab Ismail. Voor 2009-2010 door Prof M. De Ley en J. Robben. Van 2010 - 2021 gedoceerd door J. Robben. Vanaf 2019-2020 is dit vak van naam veranderd, het heet nu Advanced Biochemistry and biotechnology.
Vanaf 2023-2024 wordt het vak volledig gedoceerd door Shehab Ismail.

Het examen is opgebouwd uit 2 grote, open vragen en 4 begrippen. De eerste vraag en de begrippen zijn schriftelijk met mondelinge toelichting: hij leest je antwoorden en stelt bijvragen indien nodig. De tweede open vraag is schriftelijk af te geven.

"De studenten hebben mij iets heel handig gegeven om na te gaan welke examenvragen ik de laatste jaren gesteld heb, ze houden het beter bij als ik zelf."
-- Quote Johan Robben, 2014

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/n/G0G74AN.htm

==Examenvragen==
===16 januari 2025===
Research paper:
Question about Hif-1α and VHL and their roles in hypoxia.
* Gel with VHL and Hif-1α in hypoxia and normoxia. What can you conclude?
* Gel with VHL, Hif-1α and compound X. What is the role of compound X?
* Another gel which I forgot.
* Gel with mutated Hif-1α. What conclusions can you draw here?
* Can you give a summary of / total conclusion from this experiment?
Answer the following questions:
* Exercise with half-life of protein, total protein at steady state is 10,2 femtogram, kdeg is given, in a steady state. Calculate how many time is needed to degrade 5,1 and synthesize new 5,1. And calculate synthesis rate constant. There is 10 mRNA in the cell.
* CRISPR can overlook a few not-correct bonded nucleotides so can cause off-target mutagenesis. How can you increase specificity of CRISPR?
* Nonsense mediated decay
* Why do some protein have longer lifetime than others?
Answere these questions
* Mechanisms of prokaryotic transcription activation
* miRNA target mRNA. How do they do this? Give different target sites on mRNA? (or something like this)
* maybe some other questions which i forgot :(

===20 augustus 2024===
Research paper: SAR genes mad2 and mad3 were examined because little is known about them. (12/40)
* Determine the half lifetime of mad2 and mad3 (read from graph).
* Why did the researchers not use temperature-sensitive methods?
* Why did they add cycloheximide (CHX)?
* Why did they also use Dhhp1 mutants? What can you conclude from this experiment?
Small questions (15/40)
* Translational coupling
* PROTAC + give the advantages compared to small molecule inhibitors
* Nonsense-mediated decay
* Chaperone mediated autophagy
* Attenuation of trp operon transcription in E.coli
Answer these questions (13/40)
* CRISPR can overlook a few not-correct bonded nucleotides so can cause off-target mutagenesis. How can you increase specificity of CRISPR?
* Describe how histone mutations, that are not post translational modification mutations, can cause cancer.
* Ago (=argonaute) is shown to increase the specificity of miRNA to its target RNA up to a fold of 300. How does the argonaute increase the specificity between its miRNA and the target mRNA?
* One more question which i forgot :/

===26 januari 2024===
Research paper: A proteasome without USP14 was found, do study with ubiquitinated cyclinB and non-ubi cyclinB showed different bands when in mixture with proteasome, proteasome+USP14, proteasome+USP14+IU1. (12/40)
*In lanes 5 and 6 (Proteasome+USP14) we can see a lower molecular weight compared to lanes 2 and 3 (Proteasome without USP14), explain why.
*In lane 3 we see no more band compared to lane 6, explain why.
*In the lane with non-ubi cyclinB we always see a band, why?
*What function do you think that IU1 has?

Small questions (15/40)
*Attenuation of trp operon transcription in E.coli
*How can you discover aptamers when binding to a molecule of interest?
*Issues with using siRNA
*Chaperone mediated autophagy
*Genetic code flexibility

Answer these questions (13/40)
*Exercise with half-life of protein, total protein is 4,2, kdeg is given, in a steady state. Calculate how many time is needed to degrade 2,1 and synthesize new 2,1.
*CRISPR can overlook a few not-correct bonded nucleotides so can cause off-target mutagenesis. How can you increase specificity of CRISPR?
*What is the influence of codon-dependent translational elongation on the half-life of mRNA?
*1 more question

===18 januari 2024===
Research paper: SAR genes mad2 and mad3 were examined because little is known about them. (12/40)
* Determine the half lifetime of mad2 and mad3 (read from graph).
* Why did the researchers not use temperature-sensitive methods?
* Why did they add cycloheximide (CHX)?
* Why did they also use Dhhp1 mutants? What can you conclude from this experiment?
Small questions (15/40)
* Translational coupling
* Mechanisms of prokaryotic transcription activation
* PROTAC + give the advantages compared to small molecule inhibitors
* Nonsense-mediated decay
* Types of miRNA targets
Answer these questions (13/40)
* CRISPR allows for gene editing, but sometimes mutations are allowed that cause non-specific targeting. Describe a way in which you can enhance the specificity of CRISPR-Cas9.
* Describe how histone mutations, that are not post translational modification mutations, can cause cancer.
* What are the properties of proteins that affect their lifetime?
* eIF2-GDP is recycled back to reproduce the ternary complex to start translation initiation. eIF2B can be inhibited by phosphorylation of eIF2 by eIF2alpha. Phosphorylation increases affinity of eIF2 to eIF2B. How does this inhibit translation initiation?
===19 januari 2023===
J. Robben's deel
#mRNA cap van expressieregulatie. (5)
#Begrippen: Translational coupling, Genomic imprinting, Nonsense suppression, RNA turnover analysis (5)

S. Ismail's deel
#Grote vraag (6)
#* Vraagstuk over deletion Ups14 uit proteasome en dan een SDS-PAGE gedaan en visualisatie met een Western blot. 3 verschillende toestanden (Ups14 weg, + WT, + catalytic inactive Usp14) op 3 verschillende tijdspunten.
#*Verklaar de resultaten van het experiment
#Kleinere vraag
#* RNA interference: 2 ssRNA (sense & antisense) and 1 dsRNA --> he changed conclusion and you had to find the mistake & in C.elegans also effect seen in offspring, how possible? (4)
#Kleine vraagjes
#* PROTAC uitleggen (3)
#* 3 fasen CRISPR-interference in bacteria (3)
#* different endocytosis (2)
#* 2 names for miRNA expression analysis (2)

===30 augustus 2022===
J. Robben's deel
#5’ UTR en cap van expressieregulatie bij eukaryoten. (5)
#Begrippen: Translational coupling, RNA editing, Rip: regulated intramembrane proteolysis & exosome (5)

S. Ismail's deel
#Grote vraag (6)
#* Vraagstuk waarin er 6 verschillende tubes waren die een andere inhoud hadden. Hierop werd een northern blot gedaan en je kreeg een foto van de bekomen gel hiervan. Elke 1ste tube bevatte een pri-miRNA, elke tweede tube een pri-miRNA + microprocessor complex. De eerste pri-miRNA had een stemloop van 35 bp, een tweede met een 35 bp +1 en een derde met 35 bp + 3. Van elke tube werden de bandjes op de gel weergegeven.
#*Verklaar de resultaten van het experiment
#*Uit wat bestaat het microprocessor complex?
#*Geef een andere naam voor het microprocessor complex.
#Kleinere vraagjes
#* The two-signal membrane binding model bij meristoylation - uitleggen wat dit inhoudt (4)
#* Geef de factoren die de stabiliteit van proteïnen kunnen beïnvloeden - leg 1 uit. (4)
#Kleine vraagjes
#* 3 fasen tot komen van CRISPR-Cas systeem in bacteria (2)
#* Verschillende manieren van lysosomale degradatie (2)
#* Verschil in mechanisme van HECT en RING - E3 (2)

===28 januari 2022===
J. Robben's deel
#5’ UTR van expressieregulatie bij prokaryoten. (5)
#Begrippen: DNA acetylation, RNA editing, eIF4-binding proteïne & NMD (5)

S. Ismail's deel
#Kleine vragen (6)
#* Geef 2 voorbeelden van small interfering RNA.
#* Geef een detectietechniek voor je miRNA of interest.
#* Foto van goed opgevouwen proteïne en minder goed opgevouwen proteïne. Welke heeft de langste half-time?
#* Functie E3.
#* Geef 3 soorten lipid modifications.
#* Geef 1 functie van CRISPR in bacteriën
#Uitleggen hoe je van pri-miRNA tot mature miRNA geraakt. (4)

===20 januari 2022===
J. Robben's deel
#Bespreek op welke wijze(n) de poly(A)-staart van mRNA fungeert in eukaryote expressie regulatie. (5)
#Begrippen: Selenocysteine, Translational coupling, Genomic imprinting & toxin-antitoxin (5)

S. Ismail's deel
#Kleine vragen (6)
#* Welke van de RNA duplexen (2 fotos) zal door AGO2 worden geknipt voor het maken van guide strand
#* Welke is beter voor stabiele cellijn te maken: synthetische siRNA of vectorbased siRNA.
#* Noem de stappen/ fasen op om tot het CRISPR-Cas system te komen.
#* Noem 3 verschillende autophagie types op.
#* E1, E2 en E3 zijn enzymen in de ubiquitinylatie pathway. Wat doet E1?
#* Wat is het 2e aminozuur waaraan de myristoyltie plaats vindt en waarom kan het enkel deze aminozuur zijn?
#Bespreek hoe dat topologie, disorderd protein en protein-protein interacties de stabiliteit beïnvloeden. (4)

===22 januari 2021===
#Welk mechanisme voor controleren van nieuw geproduceerde membraaneiwitten en eiwitten voor export, en wat gebeurt er bij stress? (= ERAD en UPR)
#Experimenteel knockdown van genen adhv RNAi, geef de experimentele wijze, welke moeilijkheden kunnen optreden en hoe kan je dit voorkomen?
#Begrippen
#*Translationele koppeling
#*Prime edditing (met Crispr)
#*foto-entrainment
#*selenocysteïne

===14 januari 2021 NM===
#Bespreek overzichtelijk de werking en rol van lysosomen in eiwit-turnover. Vermeld een voorbeeld van een biotechnologische toepassing die gebruikt maakt van deze kennis.
#Cas9 is recentelijk aangepast voor andere toepassingen dan deze van genomische "schaar". Verduidelijk en concretiseer.
#Begrippen
#*Genomische imprinting
#*RNA-editing
#*RNA-induced silencing complex (RISC)
#*Periodosoom

===24 januari 2020 NM===
#Globale translatiemechanismen bij eukaryoten. Wanneer is dit van toepassing? Hoe kunnen genen dit ontwijken?
#Op welke wijze(n) kan je RNAi experimenteel uitvoeren?
#Begrippen
#*Translationele koppeling
#*CMA
#*PAM
#*Selenocysteïne

=== 20 januari 2020 NM===
#Bespreek hoe prokaryoten genexpressie reguleren via anti-sense mechanismen.
#Bespreek de N-endrule en eiwitafbraak. Vergelijk tussen eukaryoten en prokaryoten.
#Begrippen
#*Hfq
#*RNA editing
#*shRNA
#*prime editing

=== 17 januari 2020 VM===

#5’ UTR van expressieregulatie bij eukaryoten
#cas9 systeem waar CRISPR is op gebaseerd en vergelijk met Argonaut
#Begrippen
#*attenuatie
#*nonsense-mediated decay
#*looped primer RT-PCR
#*proteasome stress response (Rpn4 + PACE)

=== 25 januari 2019 NM===

#Leg de regulatie van het trp-operon uit
#Geef een schematisch overzicht van unfolded protein respons
#Begrippen
#* RITS
#* Shutdown decay
#* BMAL
#* uORF

=== 18 januari 2019 NM===

#3’ UTR bij eukaryoten
#Experimenteel knockdown van genen adhv RNAi
#Begrippen
#* RNA switch
#* Periodosoom
#* RNA editing
#* CMA

=== 18 januari 2019 VM===
#Bespreek de structuur en werking van riboschakelaars (riboswitches). Wat weet je over hun functie? Illustreer je antwoord met voorbeelden.
#Bespreek de moleculair-dynamische mechanismen die aan de basis liggen van het metabolische dag-nacht ritme bij zoogdieren.
#Begrippen
#* Selenocysteine
#* Nonsense-mediated decay
#* shRNA
#* Proximity-induced autoactivation

===22 januari 2018, VM===
#Geef overzicht van de regelmechanismen waarmee eukaryoten de translatie globaal (=niet eiwit specifiek) kan worden geregeld. In welke situatie is een dergelijke regeling van toepassing? Hoe ontsnappen sommige genen aan deze regeling?
#Bespreek op welke wijze(n) de poly(a)-staart van mRNA fungeert in expressie regulatie. (ook iets over de lengte ervan)
#Begrippen:
#* Retroreulatie
#* Genomische imprinting (+voorbeeld)
#* Nonsense-mediated decay
#*Nocturnine

===19 januari 2018, VM===
#Geef de gelijkenissen en verschillen voor de expressie regulatie aan de 5'-UTR en 5'-uiteinde regio bij prokaryoten en eukaryoten.
#Welk mechanisme voor controleren van nieuw geproduceerde membraaneiwitten en eiwitten voor export, en wat gebeurt er bij stress? (= ERAD en UPR)
#Begrippen:
#* Tac promotor (= is die gefuseerde promotor van lac operon en tac operon vanuit de werkzitting)
#* Rip: regulated intramembrane proteolysis
#* RITS
#* foto-entrainment

===21 augustus 2017===
#Controlemechanismen van mRNA bij eukaryoten.
#De rol van ubiquitine ligasen in proteïne turnover
#Begrippen:
#*Transcriptional gene silencing
#*Peptide mediated protein knockdownn
#*Familial fast sleep syndrome
#*Een vierde begrip

===3 februari 2017===
#Verduidelijk de structuur en werking van riboswitches . Leg hun functie uit
#Rol van Poly-A-staart bij regulatie van expressie
#Woordjes:
#*Nocturnine
#*uORF
#*Genetic imprinting
#*Chaperone-gemedieerde autofagie

===23 januari 2017===
#Globale translatie regulatie mechanisme uitleggen, wanneer is dit van toepassing en hoe ontsnappen genen eraan
#Op welke wijze(n) kan je de functie en voorkomen RNAi experimenteel uitvoeren?
#Bespreek kort
#*Retroregulation
#*Rip: regulated intramembrane proteolyse
#*nonsense mediated decay
#*Periodosoom

===20 januari 2017===
#Welke elementen in 3'-UTR voor expressieregulatie?
#Welk mechanisme voor controleren van nieuw geproduceerde membraaneiwitten en eiwitten voor export, en wat gebeurt er bij stress?
#Bespreek kort:
#*Attenuatie
#*Hairpin silencing
#*Translational recoding
#*Photo-entrainment

===29 januari 2016===
#UPR
#Circadische clock in zoogdieren
#Bespreek kort:
#*hairpin silencing
#*argonaut
#*genomic imprinting
#*riboswitch

===27 januari 2016===
#Geef overzichtelijk de technieken die kunnen gebruikt worden om het voorkomen en functies van kleine RNA's te bestuderen. (Hij was precies niet geÃ¯nteresseerd in RAKE, looped primer en al die dingen... Hij zei iets over sRNA sponzen en stabiele nucleïnezuuranalogen)
#Geef de werking en functie(s) van macroautophagie.
#Bespreek kort:
#*real-time RT-PCR
#*selenocysteÃ¯ne
#*caspasen
#*RIP.

===18 januari 2016===
#Hoe knockdown van genen bekomen via experimenten met RNA interferentie? wat zijn de aandachtpunten? bijvraag: wat zou je eerder gebruiken siRNA of via vector shRNA? en wat bij de mens?
#Translationele recoding wat is het en op welke manieren wordt het bereikt?
#Bespreek kort:
#*histonehermodellering
#*shut down decay
#*RNA editing
#*BMAL-CLOCK

===15 januari 2016===
#Globale translatie regulatie mechanisme uitleggen, wanneer is dit van toepassing (Stress enz), en hoe ontsnappen genen eraan (uORF)
#Rol van ubiquitinr ligases in proteïne turnover.
#Bespreek kort:
#*Chromatine remoddeling
#*Non stop decay
#*Periodosoom
#*Seed sequentie

===28 januari 2015===
#Bespreek het purine katabolisme + welke afwijkingen bij de mens?
#Wat weet je over Ubiquitine ligases in proteïne metabolisme?
#Bespreek kort:
#*RIP
#*Translationele hercodering
#*Exosoom
#*Looped-primer RT-PCR

===september 2014 ===
#Bespreek de N-endrule en eiwitafbraak. Vergelijk tussen eukaryoten en prokaryoten.
#Stel een dierenexperiment met RNAi; welke methoden voor knockdown van een gen stel je voor, welke verkies je voor het maximale resultaat?
#Bespreek kort:
#*RIP
#*Icterus
#*UPR
#*Nocturine

===31 januari 2014 ===
#Geef de diverse regulatiemechanismes van het (chole)sterolmetabolisme.
#Bespreek de invloed van ubiquitineligases op de proteïne turnover.
#Bespreek kort:
#*Geelzucht
#*genome imprinting
#*Initiator caspase
#*KiaC

===29 januari 2014 ===
# Bespreek overzichtelijk de mRNA kwaliteitscontrolemechanismen bij prokaryoten en eukaryoten
# Geef een overzicht van de verschillende mechanismen van cel-gecontroleerde eiwitafbraak die niet via proteasomen verloopt
#Bespreek kort:
#*Lesch-Nyhan-syndroom
#*Selenocysteine
#*Calnexin-calreticuline cyclus
#*Clock/BMAL1

===20 januari 2014===
#Bespreek schematische de biosynthese van heem. Hoe wordt het gereguleerd? En hoe werkt heem bij de algemene genexpressie?
#Bespreek "unfolded protein response" (UPR)?
#Leg kort uit
#* Trans-translatie
#*RNA editering
#*shRNA
#*Nocturnine

=== 21 januari 2013 ===
# Bespreek de mogelijke rol van de 5'-UTR in de posttranscriptionele expressieregultatie van prokaryoten.
# Bespreek het controlemechanisme van membraaneiwitten en eiwitten vÃ³Ã³r secretie. Welke mechanismen treden er op bij stress?
# Bespreek kort:
#* ALA-synthase
#* transtranslatie
#* Seed sequentie
#* nocturnine

=== 15 januari 2013 ===
# Bespreek de moleculaire mechanismen voor ijzerhomeostase.
# Bespreek het kloksysteem van Synechococcus (cyanobacterie). bijvraag: grote verschil met zoogdieren (= eiwitklok vs gen-gereguleerd)
# Bespreek kort:
#* thymidylaatsynthase
#* RNA editering
#* chaperone gemedieerde autofagie
#* argonaut

=== 3 februari 2012 ===
# Bespreek de moleculaire mechanismen voor de overerving van expressiepatronen tijdens de celcyclus. Wat is het belang hiervan?
# Bespreek de globale regulatiemechanismen bij proteasoom-afhankelijke proteolysis.
# Bespreek kort:
#* 5-FOA
#* RNA editering
#* seed sequence
#* nocturnine

=== 17 januari 2012 ===
# Bespreek de mogelijke rol van de 5'-UTR in de posttranscriptionele expressieregultatie van prokaryoten.
# Bespreek de globale regulatiemechanismen bij proteasoom-afhankelijke proteolysis.
# Bespreek kort:
#* Thymidilaatsynthetase
#* Geelzucht
#* CpG eiland
#* RITS

=== 1 september 2011 ===
# Schematische beschrijving heem biosynthese + hoe wordt cellulaire homeostase van heem bereikt?
# Geef overzicht van regelmechanismen waarmee bij eukaryoten de translatie globaal kan worden geregeld. In welke situaties is dergelijke regeling van toepassing? Hoe ontsnappen sommige genen aan de regeling?
# Bespreek kort:
#* histonmethyltransferase
#* nonsense mediated decay
#* photo entrainment
#* shRNA

=== 4 februari 2011 ===
# N-end rule
# Moleculaire dag en nacht ritme van het metabolisme van zoogdiercellen
# Bespreek kort:
#* geelzucht
#* selenocysteïne
#* Shutdown decay (SSD)
#* eIF2

=== 24 januari 2011 ===
# Geef het belang van de 3' Untranslated region bij expressie in eukaryoten.
# Leg het klok systeem van cyanobacteriÃ«n uit
# Bespreek kort:
#* OMP
#* RNA editing
#* toxine-antitoxine
#* ubiquitineligase E3

=== 18 januari 2011 ===
# Bespreek riboswitches.
# Op welke wijze(n) kan je RNAi experimenteel uitvoeren?
# Bespreek kort:
#* allopurinol
#* uORFs
#* ERAD
#* photo-entrainment

=== 29 januari 2010 ===
# Geef het belang van de 3' Untranslated region bij expressie in eukaryoten.
# Leg het klok systeem van cyanobacteriÃ«n uit, en de invloed op transcriptie.
# Bespreek kort:
#* OMP
#* ERAD
#* initiator caspases
#* myristoylisatie
=== 18 januari 2010 ===
# N-end rule
# Moleculaire dag en nacht ritme van het metabolisme van zoogdiercellen
# Bespreek kort:
#* geelzucht
#* selenocysteïne
#* RISC
#* endosomale lokalisatiesignaal

===12 januari 2010===
# Bespreek de purineafbraak en de verschillende metabole stoornissen bij de mens die hiermee verband houden.
# Bespreek de globale regulatie van eukaryote translatie. Hoe kunnen sommige genen aan deze regulatie ontsnappen?
# Bespreek kort:
#* Nocturnine
#* uORFs (valt weg, want bij vraag twee zitten ook al uORFs)
#* shRNA
#* nuclear localisation signal

===29 januari 2009===
MDL:
# purinebiosynthese en regulatie
# kaartjes:
#* Adaptor
#* Cascades, waarom?

JR:
# Controlemechanismen mRNA in eukaryoten
# kaartjes:
#* histonmethyltransferase
#* RITS

===29 januari 2009===
MDL: Calcium
JR: N end rule

===20 januari 2009===
Deley:
# Afbraak van vetzuren
# Kaartjes:
#* GPCR
#* werking van groeifactoren
Robben: manieren van doorgeven van expressie patronen bij celdeling. Waarom deze regeling? (epigenetic inheritance)

Nog Kaartjes:
# calnexine/calreticuline cycle
# Argonaut
# SH2 en SH3
# stimulatie van proteïnesynthese door hemine
# Ubiquitine als sorteringssignaal
# Thio-etherankers en thio-esterankers
# shRNA
# riboswitch
# RITS
# ARE (AU-rich element)
# transition state analog (daar moest hij n-PALA hebben)
# cascade, waarom?

===31 januari 2008===
MDL:
# Bespreek purineafbraak + storingen
# kaartjes: GPCR en de tabel heel in't begin van 't eerste hoofdstuk met E.Coli, S. Cerevisiae, ...

JRB:
# Bespreek lysosomale afbraak
# kaartjes: mRNA localizatie en non-sense mediated decay

===31 januari 2008===
MDL:
# Bespreek de vorming van deoxyribonucleotiden + regulatie
# kaartjes: oncogenen en amidelinked ankers

JRB:
# Bespreek methylering van histonen en DNA en hoe deze expressie kunnen reguleren
# kaartjes: eIF4E-bindend proteine en sRNA switch

===30 januari 2008===
# MDL: Pyrimidinebiosynthese
# JRB: Welke rol speelt poly(A) bij de vorming van proteinen (of zoiets)

===16 januari 2008===

MDL:
# Heem oxygenase systeem
# Kaartjes:
#* Amide linked myristoyl anchors
#* Calcium oscillaties

JR:

# Bespreek de globale mechanismen van translatieregulatie.
# Kaartjes:
#* miRNA
#* Calnexin-Calreticulin cycling

===16 januari 2008===
Hoofdvragen:
# op welke wijzen knockdown door RNA interferentie experimenteel kan gebruikt worden?
# Deoxyribunucleotide synthese en regulatie

Korte vragen:
# lambda repressor
# mRNA turnover
# cascades
# proteïnesynthese en hemine

Advanced biochemistry and biotechnology

2025-01-17T08:29:53Z

R0895938: /* Examenvragen */

[[Categorie: Mabb]]
==Vakinformatie==
Verdiepend vervolg op Moleculaire Biologie en Dynamische Biochemie van de 2e bachelor.
In 2021 - 2022 gedoceerd door Prof Johan Robben en Shehab Ismail. Voor 2009-2010 door Prof M. De Ley en J. Robben. Van 2010 - 2021 gedoceerd door J. Robben. Vanaf 2019-2020 is dit vak van naam veranderd, het heet nu Advanced Biochemistry and biotechnology.
Vanaf 2023-2024 wordt het vak volledig gedoceerd door Shehab Ismail.

Het examen is opgebouwd uit 2 grote, open vragen en 4 begrippen. De eerste vraag en de begrippen zijn schriftelijk met mondelinge toelichting: hij leest je antwoorden en stelt bijvragen indien nodig. De tweede open vraag is schriftelijk af te geven.

"De studenten hebben mij iets heel handig gegeven om na te gaan welke examenvragen ik de laatste jaren gesteld heb, ze houden het beter bij als ik zelf."
-- Quote Johan Robben, 2014

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/n/G0G74AN.htm

==Examenvragen==
===16 januari 2025===
Research paper:
Question about Hif-1α and VHL and their roles in hypoxia.
* Gel with VHL and Hif-1α in hypoxia and normoxia. What can you conclude?
* Gel with VHL, Hif-1α and compound X. What is the role of compound X?
* Another gel which I forgot.
* Gel with mutated Hif-1α. What conclusions can you draw here?
* Can you give a summary of / total conclusion from this experiment?
Answer the following questions:
* Exercise with half-life of protein, total protein is 10,2, kdeg is given, in a steady state. Calculate how many time is needed to degrade 5,1 and synthesize new 5,1. And calculate synthesis rate constant. There is 10 mRNA in the cell.
* CRISPR can overlook a few not-correct bonded nucleotides so can cause off-target mutagenesis. How can you increase specificity of CRISPR?
* Nonsense mediated decay
* Why do some protein have longer lifetime than others?
Answere these questions
* Mechanisms of prokaryotic transcription activation
* miRNA target mRNA. How do they do this? Give different target sites on mRNA? (or something like this)
* maybe some other questions which i forgot :(

===20 augustus 2024===
Research paper: SAR genes mad2 and mad3 were examined because little is known about them. (12/40)
* Determine the half lifetime of mad2 and mad3 (read from graph).
* Why did the researchers not use temperature-sensitive methods?
* Why did they add cycloheximide (CHX)?
* Why did they also use Dhhp1 mutants? What can you conclude from this experiment?
Small questions (15/40)
* Translational coupling
* PROTAC + give the advantages compared to small molecule inhibitors
* Nonsense-mediated decay
* Chaperone mediated autophagy
* Attenuation of trp operon transcription in E.coli
Answer these questions (13/40)
* CRISPR can overlook a few not-correct bonded nucleotides so can cause off-target mutagenesis. How can you increase specificity of CRISPR?
* Describe how histone mutations, that are not post translational modification mutations, can cause cancer.
* Ago (=argonaute) is shown to increase the specificity of miRNA to its target RNA up to a fold of 300. How does the argonaute increase the specificity between its miRNA and the target mRNA?
* One more question which i forgot :/

===26 januari 2024===
Research paper: A proteasome without USP14 was found, do study with ubiquitinated cyclinB and non-ubi cyclinB showed different bands when in mixture with proteasome, proteasome+USP14, proteasome+USP14+IU1. (12/40)
*In lanes 5 and 6 (Proteasome+USP14) we can see a lower molecular weight compared to lanes 2 and 3 (Proteasome without USP14), explain why.
*In lane 3 we see no more band compared to lane 6, explain why.
*In the lane with non-ubi cyclinB we always see a band, why?
*What function do you think that IU1 has?

Small questions (15/40)
*Attenuation of trp operon transcription in E.coli
*How can you discover aptamers when binding to a molecule of interest?
*Issues with using siRNA
*Chaperone mediated autophagy
*Genetic code flexibility

Answer these questions (13/40)
*Exercise with half-life of protein, total protein is 4,2, kdeg is given, in a steady state. Calculate how many time is needed to degrade 2,1 and synthesize new 2,1.
*CRISPR can overlook a few not-correct bonded nucleotides so can cause off-target mutagenesis. How can you increase specificity of CRISPR?
*What is the influence of codon-dependent translational elongation on the half-life of mRNA?
*1 more question

===18 januari 2024===
Research paper: SAR genes mad2 and mad3 were examined because little is known about them. (12/40)
* Determine the half lifetime of mad2 and mad3 (read from graph).
* Why did the researchers not use temperature-sensitive methods?
* Why did they add cycloheximide (CHX)?
* Why did they also use Dhhp1 mutants? What can you conclude from this experiment?
Small questions (15/40)
* Translational coupling
* Mechanisms of prokaryotic transcription activation
* PROTAC + give the advantages compared to small molecule inhibitors
* Nonsense-mediated decay
* Types of miRNA targets
Answer these questions (13/40)
* CRISPR allows for gene editing, but sometimes mutations are allowed that cause non-specific targeting. Describe a way in which you can enhance the specificity of CRISPR-Cas9.
* Describe how histone mutations, that are not post translational modification mutations, can cause cancer.
* What are the properties of proteins that affect their lifetime?
* eIF2-GDP is recycled back to reproduce the ternary complex to start translation initiation. eIF2B can be inhibited by phosphorylation of eIF2 by eIF2alpha. Phosphorylation increases affinity of eIF2 to eIF2B. How does this inhibit translation initiation?
===19 januari 2023===
J. Robben's deel
#mRNA cap van expressieregulatie. (5)
#Begrippen: Translational coupling, Genomic imprinting, Nonsense suppression, RNA turnover analysis (5)

S. Ismail's deel
#Grote vraag (6)
#* Vraagstuk over deletion Ups14 uit proteasome en dan een SDS-PAGE gedaan en visualisatie met een Western blot. 3 verschillende toestanden (Ups14 weg, + WT, + catalytic inactive Usp14) op 3 verschillende tijdspunten.
#*Verklaar de resultaten van het experiment
#Kleinere vraag
#* RNA interference: 2 ssRNA (sense & antisense) and 1 dsRNA --> he changed conclusion and you had to find the mistake & in C.elegans also effect seen in offspring, how possible? (4)
#Kleine vraagjes
#* PROTAC uitleggen (3)
#* 3 fasen CRISPR-interference in bacteria (3)
#* different endocytosis (2)
#* 2 names for miRNA expression analysis (2)

===30 augustus 2022===
J. Robben's deel
#5’ UTR en cap van expressieregulatie bij eukaryoten. (5)
#Begrippen: Translational coupling, RNA editing, Rip: regulated intramembrane proteolysis & exosome (5)

S. Ismail's deel
#Grote vraag (6)
#* Vraagstuk waarin er 6 verschillende tubes waren die een andere inhoud hadden. Hierop werd een northern blot gedaan en je kreeg een foto van de bekomen gel hiervan. Elke 1ste tube bevatte een pri-miRNA, elke tweede tube een pri-miRNA + microprocessor complex. De eerste pri-miRNA had een stemloop van 35 bp, een tweede met een 35 bp +1 en een derde met 35 bp + 3. Van elke tube werden de bandjes op de gel weergegeven.
#*Verklaar de resultaten van het experiment
#*Uit wat bestaat het microprocessor complex?
#*Geef een andere naam voor het microprocessor complex.
#Kleinere vraagjes
#* The two-signal membrane binding model bij meristoylation - uitleggen wat dit inhoudt (4)
#* Geef de factoren die de stabiliteit van proteïnen kunnen beïnvloeden - leg 1 uit. (4)
#Kleine vraagjes
#* 3 fasen tot komen van CRISPR-Cas systeem in bacteria (2)
#* Verschillende manieren van lysosomale degradatie (2)
#* Verschil in mechanisme van HECT en RING - E3 (2)

===28 januari 2022===
J. Robben's deel
#5’ UTR van expressieregulatie bij prokaryoten. (5)
#Begrippen: DNA acetylation, RNA editing, eIF4-binding proteïne & NMD (5)

S. Ismail's deel
#Kleine vragen (6)
#* Geef 2 voorbeelden van small interfering RNA.
#* Geef een detectietechniek voor je miRNA of interest.
#* Foto van goed opgevouwen proteïne en minder goed opgevouwen proteïne. Welke heeft de langste half-time?
#* Functie E3.
#* Geef 3 soorten lipid modifications.
#* Geef 1 functie van CRISPR in bacteriën
#Uitleggen hoe je van pri-miRNA tot mature miRNA geraakt. (4)

===20 januari 2022===
J. Robben's deel
#Bespreek op welke wijze(n) de poly(A)-staart van mRNA fungeert in eukaryote expressie regulatie. (5)
#Begrippen: Selenocysteine, Translational coupling, Genomic imprinting & toxin-antitoxin (5)

S. Ismail's deel
#Kleine vragen (6)
#* Welke van de RNA duplexen (2 fotos) zal door AGO2 worden geknipt voor het maken van guide strand
#* Welke is beter voor stabiele cellijn te maken: synthetische siRNA of vectorbased siRNA.
#* Noem de stappen/ fasen op om tot het CRISPR-Cas system te komen.
#* Noem 3 verschillende autophagie types op.
#* E1, E2 en E3 zijn enzymen in de ubiquitinylatie pathway. Wat doet E1?
#* Wat is het 2e aminozuur waaraan de myristoyltie plaats vindt en waarom kan het enkel deze aminozuur zijn?
#Bespreek hoe dat topologie, disorderd protein en protein-protein interacties de stabiliteit beïnvloeden. (4)

===22 januari 2021===
#Welk mechanisme voor controleren van nieuw geproduceerde membraaneiwitten en eiwitten voor export, en wat gebeurt er bij stress? (= ERAD en UPR)
#Experimenteel knockdown van genen adhv RNAi, geef de experimentele wijze, welke moeilijkheden kunnen optreden en hoe kan je dit voorkomen?
#Begrippen
#*Translationele koppeling
#*Prime edditing (met Crispr)
#*foto-entrainment
#*selenocysteïne

===14 januari 2021 NM===
#Bespreek overzichtelijk de werking en rol van lysosomen in eiwit-turnover. Vermeld een voorbeeld van een biotechnologische toepassing die gebruikt maakt van deze kennis.
#Cas9 is recentelijk aangepast voor andere toepassingen dan deze van genomische "schaar". Verduidelijk en concretiseer.
#Begrippen
#*Genomische imprinting
#*RNA-editing
#*RNA-induced silencing complex (RISC)
#*Periodosoom

===24 januari 2020 NM===
#Globale translatiemechanismen bij eukaryoten. Wanneer is dit van toepassing? Hoe kunnen genen dit ontwijken?
#Op welke wijze(n) kan je RNAi experimenteel uitvoeren?
#Begrippen
#*Translationele koppeling
#*CMA
#*PAM
#*Selenocysteïne

=== 20 januari 2020 NM===
#Bespreek hoe prokaryoten genexpressie reguleren via anti-sense mechanismen.
#Bespreek de N-endrule en eiwitafbraak. Vergelijk tussen eukaryoten en prokaryoten.
#Begrippen
#*Hfq
#*RNA editing
#*shRNA
#*prime editing

=== 17 januari 2020 VM===

#5’ UTR van expressieregulatie bij eukaryoten
#cas9 systeem waar CRISPR is op gebaseerd en vergelijk met Argonaut
#Begrippen
#*attenuatie
#*nonsense-mediated decay
#*looped primer RT-PCR
#*proteasome stress response (Rpn4 + PACE)

=== 25 januari 2019 NM===

#Leg de regulatie van het trp-operon uit
#Geef een schematisch overzicht van unfolded protein respons
#Begrippen
#* RITS
#* Shutdown decay
#* BMAL
#* uORF

=== 18 januari 2019 NM===

#3’ UTR bij eukaryoten
#Experimenteel knockdown van genen adhv RNAi
#Begrippen
#* RNA switch
#* Periodosoom
#* RNA editing
#* CMA

=== 18 januari 2019 VM===
#Bespreek de structuur en werking van riboschakelaars (riboswitches). Wat weet je over hun functie? Illustreer je antwoord met voorbeelden.
#Bespreek de moleculair-dynamische mechanismen die aan de basis liggen van het metabolische dag-nacht ritme bij zoogdieren.
#Begrippen
#* Selenocysteine
#* Nonsense-mediated decay
#* shRNA
#* Proximity-induced autoactivation

===22 januari 2018, VM===
#Geef overzicht van de regelmechanismen waarmee eukaryoten de translatie globaal (=niet eiwit specifiek) kan worden geregeld. In welke situatie is een dergelijke regeling van toepassing? Hoe ontsnappen sommige genen aan deze regeling?
#Bespreek op welke wijze(n) de poly(a)-staart van mRNA fungeert in expressie regulatie. (ook iets over de lengte ervan)
#Begrippen:
#* Retroreulatie
#* Genomische imprinting (+voorbeeld)
#* Nonsense-mediated decay
#*Nocturnine

===19 januari 2018, VM===
#Geef de gelijkenissen en verschillen voor de expressie regulatie aan de 5'-UTR en 5'-uiteinde regio bij prokaryoten en eukaryoten.
#Welk mechanisme voor controleren van nieuw geproduceerde membraaneiwitten en eiwitten voor export, en wat gebeurt er bij stress? (= ERAD en UPR)
#Begrippen:
#* Tac promotor (= is die gefuseerde promotor van lac operon en tac operon vanuit de werkzitting)
#* Rip: regulated intramembrane proteolysis
#* RITS
#* foto-entrainment

===21 augustus 2017===
#Controlemechanismen van mRNA bij eukaryoten.
#De rol van ubiquitine ligasen in proteïne turnover
#Begrippen:
#*Transcriptional gene silencing
#*Peptide mediated protein knockdownn
#*Familial fast sleep syndrome
#*Een vierde begrip

===3 februari 2017===
#Verduidelijk de structuur en werking van riboswitches . Leg hun functie uit
#Rol van Poly-A-staart bij regulatie van expressie
#Woordjes:
#*Nocturnine
#*uORF
#*Genetic imprinting
#*Chaperone-gemedieerde autofagie

===23 januari 2017===
#Globale translatie regulatie mechanisme uitleggen, wanneer is dit van toepassing en hoe ontsnappen genen eraan
#Op welke wijze(n) kan je de functie en voorkomen RNAi experimenteel uitvoeren?
#Bespreek kort
#*Retroregulation
#*Rip: regulated intramembrane proteolyse
#*nonsense mediated decay
#*Periodosoom

===20 januari 2017===
#Welke elementen in 3'-UTR voor expressieregulatie?
#Welk mechanisme voor controleren van nieuw geproduceerde membraaneiwitten en eiwitten voor export, en wat gebeurt er bij stress?
#Bespreek kort:
#*Attenuatie
#*Hairpin silencing
#*Translational recoding
#*Photo-entrainment

===29 januari 2016===
#UPR
#Circadische clock in zoogdieren
#Bespreek kort:
#*hairpin silencing
#*argonaut
#*genomic imprinting
#*riboswitch

===27 januari 2016===
#Geef overzichtelijk de technieken die kunnen gebruikt worden om het voorkomen en functies van kleine RNA's te bestuderen. (Hij was precies niet geÃ¯nteresseerd in RAKE, looped primer en al die dingen... Hij zei iets over sRNA sponzen en stabiele nucleïnezuuranalogen)
#Geef de werking en functie(s) van macroautophagie.
#Bespreek kort:
#*real-time RT-PCR
#*selenocysteÃ¯ne
#*caspasen
#*RIP.

===18 januari 2016===
#Hoe knockdown van genen bekomen via experimenten met RNA interferentie? wat zijn de aandachtpunten? bijvraag: wat zou je eerder gebruiken siRNA of via vector shRNA? en wat bij de mens?
#Translationele recoding wat is het en op welke manieren wordt het bereikt?
#Bespreek kort:
#*histonehermodellering
#*shut down decay
#*RNA editing
#*BMAL-CLOCK

===15 januari 2016===
#Globale translatie regulatie mechanisme uitleggen, wanneer is dit van toepassing (Stress enz), en hoe ontsnappen genen eraan (uORF)
#Rol van ubiquitinr ligases in proteïne turnover.
#Bespreek kort:
#*Chromatine remoddeling
#*Non stop decay
#*Periodosoom
#*Seed sequentie

===28 januari 2015===
#Bespreek het purine katabolisme + welke afwijkingen bij de mens?
#Wat weet je over Ubiquitine ligases in proteïne metabolisme?
#Bespreek kort:
#*RIP
#*Translationele hercodering
#*Exosoom
#*Looped-primer RT-PCR

===september 2014 ===
#Bespreek de N-endrule en eiwitafbraak. Vergelijk tussen eukaryoten en prokaryoten.
#Stel een dierenexperiment met RNAi; welke methoden voor knockdown van een gen stel je voor, welke verkies je voor het maximale resultaat?
#Bespreek kort:
#*RIP
#*Icterus
#*UPR
#*Nocturine

===31 januari 2014 ===
#Geef de diverse regulatiemechanismes van het (chole)sterolmetabolisme.
#Bespreek de invloed van ubiquitineligases op de proteïne turnover.
#Bespreek kort:
#*Geelzucht
#*genome imprinting
#*Initiator caspase
#*KiaC

===29 januari 2014 ===
# Bespreek overzichtelijk de mRNA kwaliteitscontrolemechanismen bij prokaryoten en eukaryoten
# Geef een overzicht van de verschillende mechanismen van cel-gecontroleerde eiwitafbraak die niet via proteasomen verloopt
#Bespreek kort:
#*Lesch-Nyhan-syndroom
#*Selenocysteine
#*Calnexin-calreticuline cyclus
#*Clock/BMAL1

===20 januari 2014===
#Bespreek schematische de biosynthese van heem. Hoe wordt het gereguleerd? En hoe werkt heem bij de algemene genexpressie?
#Bespreek "unfolded protein response" (UPR)?
#Leg kort uit
#* Trans-translatie
#*RNA editering
#*shRNA
#*Nocturnine

=== 21 januari 2013 ===
# Bespreek de mogelijke rol van de 5'-UTR in de posttranscriptionele expressieregultatie van prokaryoten.
# Bespreek het controlemechanisme van membraaneiwitten en eiwitten vÃ³Ã³r secretie. Welke mechanismen treden er op bij stress?
# Bespreek kort:
#* ALA-synthase
#* transtranslatie
#* Seed sequentie
#* nocturnine

=== 15 januari 2013 ===
# Bespreek de moleculaire mechanismen voor ijzerhomeostase.
# Bespreek het kloksysteem van Synechococcus (cyanobacterie). bijvraag: grote verschil met zoogdieren (= eiwitklok vs gen-gereguleerd)
# Bespreek kort:
#* thymidylaatsynthase
#* RNA editering
#* chaperone gemedieerde autofagie
#* argonaut

=== 3 februari 2012 ===
# Bespreek de moleculaire mechanismen voor de overerving van expressiepatronen tijdens de celcyclus. Wat is het belang hiervan?
# Bespreek de globale regulatiemechanismen bij proteasoom-afhankelijke proteolysis.
# Bespreek kort:
#* 5-FOA
#* RNA editering
#* seed sequence
#* nocturnine

=== 17 januari 2012 ===
# Bespreek de mogelijke rol van de 5'-UTR in de posttranscriptionele expressieregultatie van prokaryoten.
# Bespreek de globale regulatiemechanismen bij proteasoom-afhankelijke proteolysis.
# Bespreek kort:
#* Thymidilaatsynthetase
#* Geelzucht
#* CpG eiland
#* RITS

=== 1 september 2011 ===
# Schematische beschrijving heem biosynthese + hoe wordt cellulaire homeostase van heem bereikt?
# Geef overzicht van regelmechanismen waarmee bij eukaryoten de translatie globaal kan worden geregeld. In welke situaties is dergelijke regeling van toepassing? Hoe ontsnappen sommige genen aan de regeling?
# Bespreek kort:
#* histonmethyltransferase
#* nonsense mediated decay
#* photo entrainment
#* shRNA

=== 4 februari 2011 ===
# N-end rule
# Moleculaire dag en nacht ritme van het metabolisme van zoogdiercellen
# Bespreek kort:
#* geelzucht
#* selenocysteïne
#* Shutdown decay (SSD)
#* eIF2

=== 24 januari 2011 ===
# Geef het belang van de 3' Untranslated region bij expressie in eukaryoten.
# Leg het klok systeem van cyanobacteriÃ«n uit
# Bespreek kort:
#* OMP
#* RNA editing
#* toxine-antitoxine
#* ubiquitineligase E3

=== 18 januari 2011 ===
# Bespreek riboswitches.
# Op welke wijze(n) kan je RNAi experimenteel uitvoeren?
# Bespreek kort:
#* allopurinol
#* uORFs
#* ERAD
#* photo-entrainment

=== 29 januari 2010 ===
# Geef het belang van de 3' Untranslated region bij expressie in eukaryoten.
# Leg het klok systeem van cyanobacteriÃ«n uit, en de invloed op transcriptie.
# Bespreek kort:
#* OMP
#* ERAD
#* initiator caspases
#* myristoylisatie
=== 18 januari 2010 ===
# N-end rule
# Moleculaire dag en nacht ritme van het metabolisme van zoogdiercellen
# Bespreek kort:
#* geelzucht
#* selenocysteïne
#* RISC
#* endosomale lokalisatiesignaal

===12 januari 2010===
# Bespreek de purineafbraak en de verschillende metabole stoornissen bij de mens die hiermee verband houden.
# Bespreek de globale regulatie van eukaryote translatie. Hoe kunnen sommige genen aan deze regulatie ontsnappen?
# Bespreek kort:
#* Nocturnine
#* uORFs (valt weg, want bij vraag twee zitten ook al uORFs)
#* shRNA
#* nuclear localisation signal

===29 januari 2009===
MDL:
# purinebiosynthese en regulatie
# kaartjes:
#* Adaptor
#* Cascades, waarom?

JR:
# Controlemechanismen mRNA in eukaryoten
# kaartjes:
#* histonmethyltransferase
#* RITS

===29 januari 2009===
MDL: Calcium
JR: N end rule

===20 januari 2009===
Deley:
# Afbraak van vetzuren
# Kaartjes:
#* GPCR
#* werking van groeifactoren
Robben: manieren van doorgeven van expressie patronen bij celdeling. Waarom deze regeling? (epigenetic inheritance)

Nog Kaartjes:
# calnexine/calreticuline cycle
# Argonaut
# SH2 en SH3
# stimulatie van proteïnesynthese door hemine
# Ubiquitine als sorteringssignaal
# Thio-etherankers en thio-esterankers
# shRNA
# riboswitch
# RITS
# ARE (AU-rich element)
# transition state analog (daar moest hij n-PALA hebben)
# cascade, waarom?

===31 januari 2008===
MDL:
# Bespreek purineafbraak + storingen
# kaartjes: GPCR en de tabel heel in't begin van 't eerste hoofdstuk met E.Coli, S. Cerevisiae, ...

JRB:
# Bespreek lysosomale afbraak
# kaartjes: mRNA localizatie en non-sense mediated decay

===31 januari 2008===
MDL:
# Bespreek de vorming van deoxyribonucleotiden + regulatie
# kaartjes: oncogenen en amidelinked ankers

JRB:
# Bespreek methylering van histonen en DNA en hoe deze expressie kunnen reguleren
# kaartjes: eIF4E-bindend proteine en sRNA switch

===30 januari 2008===
# MDL: Pyrimidinebiosynthese
# JRB: Welke rol speelt poly(A) bij de vorming van proteinen (of zoiets)

===16 januari 2008===

MDL:
# Heem oxygenase systeem
# Kaartjes:
#* Amide linked myristoyl anchors
#* Calcium oscillaties

JR:

# Bespreek de globale mechanismen van translatieregulatie.
# Kaartjes:
#* miRNA
#* Calnexin-Calreticulin cycling

===16 januari 2008===
Hoofdvragen:
# op welke wijzen knockdown door RNA interferentie experimenteel kan gebruikt worden?
# Deoxyribunucleotide synthese en regulatie

Korte vragen:
# lambda repressor
# mRNA turnover
# cascades
# proteïnesynthese en hemine

Genoom-, proteoom- en metaboloomanalyse

2024-12-18T09:16:13Z

R0895938: /* Vakinformatie */

[[Categorie:Mabb]]

==Vakinformatie==
Genoom-, proteoom- en metaboloomanalyse
Het vak wordt gegeven door prof. Landuyt en prof. Robben. Robben zijn deel is mondeling en gesloten boek. Robben maakt elk examen nieuwe vragen

2022-2023: het vak wordt gegeven door Landuyt (metabolomics), Robben (genomics), en Schoofs (proteomics). Alles is gesloten boek.

2023-2024: het vak wordt gegeven door Van Belleghem (genomics) en Schoofs (proteomics). Voor het metabolomics gedeelte van Landuyt moest je oude lesopnames kijken. Alles is gesloten boek, geschreven examen

2024-2025: Het vak wordt gegeven door Van Belleghem (genomics) en Temmerman (proteomics en metabolomics). Voor het deel van Temmerman waren er opnames van prof Schoofs en Landuyt, vanwege Temmerman haar zwangerschap. Ze was er wel voor vragen te beantwoorden. Alles is gesloten boek, geschreven examen.

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/n/G0G57AN.htm

==Examenvragen==
===01/02/2024===
SVB
*Open question: 233 genomes of primates to be sequenced, focus on repetitive content in the genome. What sequencing technologies and equipment to use? Why?
*Explain how the chosen technologies work.
*Give two examples of how can be used

*Terms
*#Retrovirus-like elements
*#GWAS
*#ChIP-Seq

Schoofs
NO CALCULATOR ALLOWED

*Explain how to identify proteins with explorative (shotgun) proteomics
*Explain the differences between MALDI and ESI

*Multiple choice with explanation

*#No two identical compounds will ionise and fragment in exactly the same manner, true or false
*#Enriched proteins of cultured cells, appropriate method (DiGE, SILAC, SRM, Label-free methods)
*#What is SRM used for?
*#Which conclusion can be drawn from a 2D gel electrophoresis experiment?
*#m/z of 120, 121, 122, 123, which isotopes are responsible for signal at m/z 122 (12C, 35Cl, 1H; 12C, 35Cl, 2H; 12C, 37Cl, 1H; 12C, 37Cl, 2H)

*Exercises
*#Question about a fragmented peptide MS2 spectra
*#*Why do the y ions have different intensities?
*#*Explain how the peptide sequence (given) is derived from the spectrum.
*#Figure with mass spectrum, what is the mass of the peak? (2 peaks, second peak is isotopes with distance of +1)
*Definitions
*#Delayed extraction
*#Reflectron mode
*#Targeted proteomics
*#Mascot
*#DDA

===23/01/2024===
SVB
*Open question: 4000 genomes of Darwin's finches underwent resequencing encompassing individuals of 4 species
*#Explain the methodology in conducting resequencing. what are the key steps and technologies?
*#Evaluate the challenges of fragmentation of the reference genome, knowing that the genome existed of about 20.000 scaffolds of large size:
*#*What genomic properties caused it to be fragmented? (repeats)
*#*What is the significance of this issue?
*#*Propose a method to enhance the coherency of the reference genome.
*#Give two illustrative examples of insights that can be derived from experiments like these.
*Terms
*#Phylogenetic footprinting
*#AP-MS
*#Gene regulatory network

Schoofs
*Explain how proteins of a biological sample can be identified with peptide masss fingerprinting using a MALDI-TOF mass spectrometer.
*Multiple choice with explanation
*#Two compounds fragment in exactly the same manner, true or false
*#Enriched proteins of cultured cells, appropriate method (DiGE, SILAC, SRM, Label-free methods)
*#What is a proteotypic peptide?
*#Which conclusion can be drawn from a 2D gel electrophoresis experiment?
*#m/z of 120, 121, 122, 123, which isotopes are responsible for signal at m/z 122 (12C, 35Cl, 1H; 12C, 35Cl, 2H; 12C, 37Cl, 1H; 12C, 37Cl, 2H)
*Exercises
*#Question about the ICAT image from the slides
*#*Are the peptides (A to F) coming from the same protein?
*#*What is the distance between the green and the blue peaks?
*#*Explain how the peptide sequence is derived from the spectrum
*#Figure with mass spectrum, what is the mass of the peak? (2 peaks, second peak is isotopes with distance of 0,5)
*Definitions
*#SRM
*#Isobaric tag
*#Mass spectrometric resolution
*#Mascot
*#E-value

===5/09/2023===
Robben:
# Jarenlang geduurd om genoom van een specifieke boonsoort te sequencen (genoomgrootte = 4x menselijk genoom).
## Speculeer waarom het zo lang geduurd heeft.
## Geef schematisch weer welke strategie jij zou gebruiken om het genoom vandaag sneller te sequencen.
## Leg de principes van jouw gekozen technieken uit.
# Terms
## ribosome profiling
## scale free networks
## endogenous retrovirus

===24/01/2023===
Robben:
# Illumina, pacbio and oxford nanopore all have their own transcriptomics approach.
## Give the working principle
## critically discuss strengths and weaknesses of the platforms
## Which platform would you choose to study the transcriptome of a cancer tissue? argue.
# Terms
## paired end sequencing
## haplotype association analysis
## protein-protein interaction networks are scale free

Schoofs:
# Open vraag: membraanproteïnen van gezonde muizen en muizen met pituitary tumor onderzoeken. Hoe ga je de identificatie en kwanitificatie doen? aanpak volledig uitleggen.
# kleine vraagjes
## 2 meerkeuze
## 2 begrippen (razor peptide en delayed extraction tof)
## vraag met grafiek (intensiteit vs m/z), hoe massa van ongeladen peptide bepalen adh van deze grafiek?
## iets met de score-value voor peptide mass fingerprint verhogen
# oefening op computer
## frataxin mature peptide spot in een gel picken; welke pI en welke MW?
## Zijn er modificaties, waarom (niet)?
## Geef een lijst met 10 pieken die het hele spectrum weergeven.

===18/01/2021===
Robben:
# SMRT and nanopore can be used to finish the human X chromosome.
## Give the working principle and details of SMRT and nanopore.
## Why are these methods better than Illumina?
## Give the strategy to finish the other chromosomes.
# Terms
## Affymetrix chip
## Gene acquisition (by gene evolution)
## Genomic interactions

Landuyt:
# You get a safe denatured protein mixture from the Sars-Cov-2 virus.
## Describe a method how this mixture is made. (2p)
## If you would be pick the spike protein in a gel-based proteomics experiment, at which MW and PI would you look. Do you expect modifications and why (not)? (3p)
## Give a peak list of 10 peaks that cover the whole spectrum if you use trypsin to digest the spike protein. (4p)
## How can you see the difference between the UK and the standard viariant? Give the principle and calculations. (3)
# Hydroxychloroquine (HCQ) was developed for malaria treatment and seems to be working against corona in patients with less severe symptomes. We need to know the blood concentrations of HCQ in treated patients. Therefore, you are offered a mass spectrometer with a mass accuracy of 5 ppm.
## How would you prepare the blood samples for this analysis. (3p)
## What is the mass you are going to look after? (...,... Da +- ...,... Da) (4p)
## BONUS question: can you give the mechanism of action of HCQ? (1p)

===28/01/2020===
Robben:
#SMRT sequencing recently had update, something with circularization.
##Discuss the technical aspects etc
##Why is it important?
#Terms
##Polyploidy and genome variation
##NanoString nCounter expression system
##Rosetta Stone Method

Landuyt:
Same as 14/01/2020, 15/01/2020 and 21/01/2020

===21/01/2020===
Robben:
#The genome of cotton was already sequenced in 2012 via Sanger. Which NGS will you use to redo the sequencing?
## Give the working principle and details of the chosen platform.
#Terms
##Gene ontology
##Affimix chip
##Gene interaction mapping

Landuyt (exact same questions as yesterday):
# Placental Growth Factor is an interesting protein.
## Describe briefly what makes this protein so interesting (1p)
## If PlGF would be picked up in a gel-based proteomics experiment, how would the spectrum then look like (provide the exact masses of at least 5 peaks). (4p)
## Describe the workflow of this proteomics strategy starting from a tissue sample (4p)
## What are the shortcoming and advantages of the gel-based approach (3p)
# Curcumin, one of the bioactive metabolites from plants of the ginger family, has many potential medical uses. However, bioavailibility of curcumin is low, and therefore, many research is conducted to find better formulations to reach optimal blood concentrations. In order to support this research, you need to build an assay to asses blood plasma concentrations of curcumin. Therefore, you are offered a mass spectrometer with a mass accuracy of 30 ppm.
## How would you prepare the blood samples for this analysis. (3p)
## What is the mass you are going to look after? (...,... Da +- ...,... Da) (4p)
## BONUS question: can you give one possible strategy to formulate an oral curcumin preparation with better bioavailability. (1p)

===15/01/2020 (afternoon)===
Robben:
# Infection of a certain type of phage in a bacterial cell. You would like to execute a transcriptomal analysis at the moment of encounter of the phage and 15 minutes later.
## Defend which platform/technique you would use.
## Explain the working principles and technical details of the chosen platform/technique.
# Terms
## Optical mapping
## Sequence scaffold
## Interaction network

Landuyt (exact same questions as yesterday):
# Placental Growth Factor is an interesting protein.
## Describe briefly what makes this protein so interesting (1p)
## If PlGF would be picked up in a gel-based proteomics experiment, how would the spectrum then look like (provide the exact masses of at least 5 peaks). (4p)
## Describe the workflow of this proteomics strategy starting from a tissue sample (4p)
## What are the shortcoming and advantages of the gel-based approach (3p)
# Curcumin, one of the bioactive metabolites from plants of the ginger family, has many potential medical uses. However, bioavailibility of curcumin is low, and therefore, many research is conducted to find better formulations to reach optimal blood concentrations. In order to support this research, you need to build an assay to asses blood plasma concentrations of curcumin. Therefore, you are offered a mass spectrometer with a mass accuracy of 30 ppm.
## How would you prepare the blood samples for this analysis. (3p)
## What is the mass you are going to look after? (...,... Da +- ...,... Da) (4p)
## BONUS question: can you give one possible strategy to formulate an oral curcumin preparation with better bioavailability. (1p)

===14/01/2020 (morning)===
Robben:
# Phenotypic differences between closely related almond and peach might largely be attributed to transposable elements. Your lab received funding for comparative genomic sequencing to elucidate the differences.
## Explain schematically the sequencing strategy you would propose.
## Which commerically available next-gen sequencing platform(s) would you propose to use. '''Argue your choice.'''
## Explain the working principles of the chosen platform(s)
# Terms
## Ribosome profiling
## (Transcriptomics) microarray target labeling
## Protein-protein interaction maps are scale free

Landuyt:
# Placental Growth Factor is an interesting protein.
## Describe briefly what makes this protein so interesting (1p)
## If PlGF would be picked up in a gel-based proteomics experiment, how would the spectrum then look like (provide the exact masses of at least 5 peaks). (4p)
## Describe the workflow of this proteomics strategy starting from a tissue sample (4p)
## What are the shortcoming and advantages of the gel-based approach (3p)
# Curcumin, one of the bioactive metabolites from plants of the ginger family, has many potential medical uses. However, bioavailibility of curcumin is low, and therefore, many research is conducted to find better formulations to reach optimal blood concentrations. In order to support this research, you need to build an assay to asses blood plasma concentrations of curcumin. Therefore, you are offered a mass spectrometer with a mass accuracy of 30 ppm.
## How would you prepare the blood samples for this analysis. (3p)
## What is the mass you are going to look after? (...,... Da +- ...,... Da) (4p)
## BONUS question: can you give one possible strategy to formulate an oral curcumin preparation with better bioavailability. (1p)

===29/01/2019===
Robben:
#je hebt een genoom van een axolotl dat je wil analyseren. Het heeft een genoom meer dan dubbel zo groot als dat van de mens. Welke next generation sequencing techniek ga je gebruiken + verdedig waarom
#woordjes:
##Ribsome profiling
##Array protein targetting
##protein-protein interaction map is scale free

Landuyt:
# you receive a peak list: 148.07574, 175.11900, 219.11285, 322.18741, 334.13979, 423.23509, 447.22386, 480.25655, 504.24532, 593.34062, 605.29300, 708.36756, 752.36141, 779.40467, 908.46252, 926.47309
##Which type of proteomic analysis has been used? (explain thoroughly)
##What is the identity of the protein (explain your strategy for interpretation and the certainty regarding your identification)
##How would the spectrum look like if the other proteomics method would have been used?
##Search for a recent article concerning the protein of interest and give a brief discussion (if you are not sure about your identification (question 2), please use human epidermal growth factor as a substitute (not both! or you pick your identified protein, or the substitute)
#Verhaaltje rond onderzoekers die de bioavailability willen onderzoeken van de stof curcumin, deze stof bevindt zich in het bloed. via MS zul je curcumin kunnen analyseren.
##How would you prepare the patient blood plasma samples to extract the drug? 3p
##Which mass will you be looking for? 4p
##bonus punt: describe a innovative preparation of curcumin for improved oral bioavailability. 1p

===22/01/2019===
Robben:
#verhaal rond een proteïne dat kan instaan voor vele zaken via interacties met een bepaald domein. Hoe kan je deze interacties best bestuderen?
##bespreek welke methode je het best kan gebruiken en vergelijk met andere technieken.
##bespreek kort de manier van werking van de methode die je gekozen hebt.
#begrippen
##paired end sequencing
##nanopore sequencing
##affimetrix chip

Landuyt:
#A proteomics researcher working on a major human disease discovers a significantly expressed protein in a set of biopsies taken from patients, compared with a set of biopsies from healthy individuals. Below you can find the peak list that can be used to identify this protein. peak list :920.48 902.47 791.43 774.37 720.40 661.29 607.31 532.24 476.27 445.21 389.24 314.17 260.20 201.09 147.11 130.05
##Which type of proteomics approach has been used? Explain briefly 3p
##What is the identity of the protein? 4p
##What would the spectrum look like if the other proteomics approach would have been used? Give 5 examples masses that could appear in this spectrum. If you do not feel confident about your protein ID, use human epidermal growth factor (EGF) as an alternative for this assignment. 4p
##Briefly explain the biological role of this protein. What type of disease is being studied? 1p
#Some patients are selected for treatment with imatinib mesylate. In order to check the pharmacology of the drug, you are offered an old single quadrupole MS with a mass accuracy of 100ppm.
##How would you prepare the patient blood plasma samples to extract the drug? 3p
##Which mass will you be looking for? 4p
##Bonus question: Can you explain the mode of action of this drug in relation to the drug target (= the protein from question 1)? 1p

===16/01/2019===

Deel Robben:
# je stuurt een bacterie naar de ruimte en laat deze daar groeien, je laat dezelfde bacterie op aarde groeien. Hoe zou jij het transcriptoom onderzoeken? welke techniek gebruik je + verdedig waarom deze en niet de andere. Leg deze techniek uit.
# woordjes:
##SMRT,
##gene altering,
##genetic interactomics
#
Deel Landuyt
#Je hebt een pieklijst, welke methode van proteomics is hier gebruikt om het proteïnen te onderzoeken. er was een verhaaltje bij dat het ging over een meneer met plotse diarree en je neemt een stoelsample om te onderzoeken. Pieklijst: 997.49 979.49 868.46 851.31 754.34 705.39 640.30 592.31 505.28 493.23 406.20 358.21 293.11 244.17 147.11 130.05
Het is volgens de prof : EYI/LSFNPK
# welk protein is het?
# wat zou een 2e mogelijkheid zijn om dit proteïnen te onderzoeken en wat zou je verkrijgen?
# geef meer info over de werking van het proteïnen

Deel 2: Je wilt het actief component van motilium onderzoeken, wat is je strategie?
# De accuraatheid van je ms machine is 10 ppm, waar ga je de piek zien van het actief component?
# Geef meer info over dit component

===15 januari 2019===
Robben
#Solexa sequencing en SMRT vergelijken.
#Begrippen:
##Polyploidie en genomic evolution,
##Nanostring nCounter technologie
##Rosetta stone method

Landuyt
#Proteomics
#* Piekenlijst : 1425.63 1407.62 1297.57 1279.53 1168.53 1165.48 1078.48 1069.46 981.4 968.41 853.39 818.34 722.35 704.29 608.3 573.25 458.23 445.24 357.18 348.19 261.16 258.11 147.11 129.07
#* Welk proteïne is dit?
#* Wat zou het resultaat zijn als er een andere proteomics techniek wordt gebruikt?
#* Geef meer info over de werking van het proteïne

#Metabolomics
#* Je hebt een metaboliet resveratrol dat in rode wijn voorkomt en efficiënt hieruit geëxtraheerd kan worden.
#* Hoe zou je resveratrol opzuiveren? (HPLC-MS)
#* Wat is de monoisotopische massa bij 2ppm
#* Kan je uit deze opgaven een link tussen proteomics en metabolomics vinden?

===23/08/2018===

* proteomics :A clinician working on a major disease discovers a significantly up-regulated protein in a large number of patient samples. The conclusion is simple: this protein could be a major breakthrough! However, the medical doctor leading the study learned how to use a mass spectrometer, but was not yet trained in the interpretation of the data. Can you help our desperate clinician in identifying the protein based on the peak list below?
148.07574
175.11900
219.11285
322.18741
334.13979
423.23509
447.22386
480.25655
504.24532
593.34062
605.29300
708.36756
752.36141
779.40467
908.46252
926.47309
#Questions:
#* Which type of proteomic analysis has been used? (explain thoroughly) …/2
#* What is the identity of the protein (explain your strategy for interpretation and the certainty regarding your identification) …/3
#* Which disease is studied? …/1
#* How would the spectrum look like if the other proteomics method would have been used? (if you are not sure about your identification (question 2), please use human epidermal growth factor as a substitute (not both! or you pick your identified protein, or the substitute) …/3
#*Search for a recent article concerning the protein of interest and give a brief discussion (again, same principle as for question 4)

Metabolomics
accuraatheid berekenen, je krijgt de M/Z van het toestel. De exacte massa moet je opzoeken
is dit een goede accuraatheid, leg uit?

===23/01/2018 NM===
Robben:
# Ze willen het genoom van een rendier achterhalen. de dichtst verwante soort waarvan ze het genoom kennen is een rund.
#* Hoe ga je te werk? welk next generation sequencing platform kies je (je kan er maar 1 kopen) en waarom?
#* Leg de sample prep en voornaamste principes uit.
#* Woordjes
## Scaffold sequentie
## Genetic interactomics
## PMAGE
Landuyt:
# PROTEOMICS
#* Na 2D gel kiest researcher een spot en behandelt die met trypsine en krijgt bij MS een lijst pieken (die je dus krijgt). De researcher herkent 'familiar' masses en kiest 1 peptide om te fragmenteren omdat het het enige 'non-suspicious' fragment is. (je weet welke massa dat is). Na fragmentatie krijg je een volgende piekenlijst.
## Wat ging er verkeerd in het experiment?
## Welke MS methoden of componenten werden er gebruikt?
## Welk proteine analyseert hij en wat is de functie ervan.
# METABOLOMICS
#* Een researcher in colombia krijgt een ms toestel ter beschikking, analyseert koffiebonen (denk ik) en krijgt een dominante piek op 195,xx m/z.
## Wat is da accuraatheid van het machien op ca 200 Da? Is dit oke voor metabolomics?
## BONUS er was nog een tweede dominante piek xxx m/z, welk molecule is dit?

===23/01/2018 VM===
Robben:
#Je wilt met behulp van next generation sequencing mutaties en rearrangments onderzoeken in kanker.
#* Wat is je sequencing strategy?
#* Welk platform zou je gebruiken? (Je mag er maar 1 geven).
#* Geef uitgebreid de sample prep en de werking van het platform.
#Woordjes:
#* Endogenous Retrovirus
#* Affrimex Genechip
#*nCounter technology

Landuyt:
#PROTEOMICS
#* A lab technician in a proteomics core facility receives samples for identification, one from a lab working with human cancer tissues and one from a lab working on neuro degenerating deseases. One of the proteins was cut from a 2D gel and the other protein was found to be up-regulated in a gel-free proteomics experiment. Both analysis yielded nice mass spectra, the respective peak lists can be found below. However, due to some solvent spilling, the ink on the tubes was ruined and the origin of the samples got lost. The lab technician is very concerned with this issue because he is afraid to lose his job.
#** Peak list 1: 1743,83; 1716,82; 1605,79; 1560,72; 1474,75; 1473,69; 1417,73; 1360,61; 1303,69; 1259,56; 1174,64; 1172,53; 1073,46; 1060,6; 972,41; 947,52; 885,38; 850,46; 788,32; 763,43; 675,24; 662,38; 563,32; 561,2; 476,28; 432,16; 375,24; 318,11; 262,15; 261,09; 175,12; 130,05
#** Peak list 2: 4356,00; 4435,97; 3243,61; 3563,47; 2709,32; 2622,32; 2391,03; 2550,96; 2356,24; 2270,15; 2165,90; 2245,87; 2053,89; 2133,86; 1980,09; 2064,11; 2008,12; 2060,06; 1954,96; 2114,89; 1916,98; 1958,99; 1996,94; 1697,83; 1681,90; 1578,82; 1620,83; 1658,79; 1522,77; 1487,65; 1393,63; 1596,71; 1873,43; 1387,60; 1326,64; 1309,72; 1292,60; 1132,56; 1212,53; 1114,53; 1101,55; 1304,63; 1421,42; 1066,59; 1306,49; 1003,54; 1045,55; 1163,48;
## Which peak list was generated from the gel-based and which was generated with gel-free proteomic analysis. Please comment on how you come to you conclusion.
## What is the identity of the two proteins? Give a brief summary of the biological significance of both proteins. (= eerste lijst De novo en BLASTEN & tweede lijst in MASCOT steken --> neem taxonomy homo sapience!)
## By now, you should be able to transferrin the identity of proteins to the correct lab. Which comes from the cancer lab and which from neuro degeneration lab?
#METABOLOMICS
#* The popular cocktail mojito was initially created as a medicine to treat various conditions such as bad digestion. Therefore, it is nowadays consumed to stimulate appetite before a meal or to stimulate digestion after a heavy meal. The core ingredient is mint, which undergoes a successful extraction with rum an lime juice.
## If you would like to purify the metabolites from mint in a lab setting, how would you do this knowing the above.
## In case the extraction is successful and you have a mass spectrometer with a mass accuracy of 2 ppm, then what would be the mono-isotopic mass would you record for the most dominant metabolite from the mint?
## BONUS: If mint would be an illegal substance and you were asked to make a test to detect it in blood of suspected users, which metabolite would you go afer? (multi answers possible).

===16/01/2018 (NM)===
Robben
#Sequencing platform (welk en waarom) + uitleggen hoe. voor een transcriptomics studie van de gifklier van een schorpioen, hoe ge u staalvoorbereiding zou doen.
#woordjes: Massive parallel signature sequencing, proteome array en genetic interactomics.

Landuyt,
# Proteomics. Onderzoek(st)er vind interresant proteine bij een zieke persoon gegeven onderstaand massa spectrum (piekenlijst van een peptide).
#* Welke proteomics aanpak is er gebruikt en leg deze kort uit
#* Van welk proteine is dit peptiede
#* Als je de andere proteomics aanpak gebruikt wat voor pieken bekom je dan bij je massaspectrum, geef 5 voorbeelden van massa's die hierbij voorkomen
#*wat is de biologische relevantie van dit proteine aka in welke ziekte speelt dit proteine een rol

# Metabolomics gegeven een drug-metaboliet met een piekhalfwaardebreedte 0.0001en een monoisotopische massa 480.2531
#* Wat is de resolutie van dit spectrum en is dit nodig?
#* Waarom zien we typisch 2 pieken of meer van hetzelfde ion op een massa spectrum
#* Over welke drug gaat het hier in dit geval
#* Bonus vraag: Wat is de exacte mode of action van deze drug met betrekking tot het proteïne uit vraag 1

===16/01/2018 (VM)===

Robben
# RNA-seq uitleggen + 1 sequencing platform + voor en nadelen van RNAseq en andere analyse platvormen (kader met PCR, microarrays, SAGE en RNAseq
# woordjes: polyploidie en genoom evolutie, gene ontology, Rosetta stone method
Landuyt
# MS pieken gegeven: welk proteïne, welk proteomics methode, wat als ze de andere methode gebruikte (geef 5 massa's), mode of action van dat proteine
# massa en half height gegeven: wat is de resolutie en is het een goede resolutie, over welk metaboliet zijn we bezig, soms zijn er meerdere pieken voor hetzelfde metaboliet en waarom
#Bonus vraag: wat is de link tussen het proteïne en het metaboliet volgens recente studies

===10/06/2014===
====prof. Robben (gesloten boek)====
#Wat doet RNA-seq?
#Geef 1 van de ontwikkelde technieken vrij te kiezen (454/solid/...) (commercieel platform)
#Vergelijk RNA-seq met andere technieken (voordelen/nadelen) (concurrerende methoden)
====prof. Landuyt (open boek/open pc)====
#Krijgt waarden van MS moet eiwit geven
#Waarom kan je een vertekend beeld krijgen en geef de statistische realiteit
#Welke ziekte zou er hier onderzocht zijn?
#Als er een fout is opgetreden bij de MS kan je een andere methode gebruiken?
#Moest ge zelf onderzoek willen doen op dit eiwit met welke dingen zou je dan rekening willen houden en hoe los je dit op?

====Johan Robben====
#In het kader van een onderzoeksproject krijg je de opdracht om bij een industriële giststam de transcriptoom verschillen bij het brouwen van Westmalle en Duvel in kaart te brengen. Stel een methode voor en bespreek een concreet analyseplatform voor waarvoor je zou kiezen. Beargumenteer je keuze.
#Bespreek bondig de belangrijkste 'second generation' sequencing methoden. Vergelijk en evalueer kritisch.
#Bespreek drie experimentele methoden om interacties te ontdekken. Geef voor- en nadelen.
#Sequencing. Bespreek de Solexa-methode (Illumina) vanaf de bereiding van het DNA tot het sequeneren zelf. Welke toepassingen heeft Solexa? Wanneer is de Sanger-methode te verkiezen?
#Interactomics. Bespreek kort drie methoden om te onderzoeken. Geef sterktes/zwaktes van elke techniek. Hoe ga je met gegevens uit deze technieken (in essentie) interactienetwerken opbouwen.
#Bespreek de Affymetrix GeneChip en de Illumina random BeadArrays. En maak een kwalitatieve vergelijking.
#Bespreek Illumina Sequencing van DNA-preparatie tot uitlezing. Vergelijk kwalitatief met Sanger sequencing.
#Bespreek 454 sequencing (van DNA library construction tot sequentie analyse). Vergelijk kwantitatief 454 met Sanger.
#De hoge druk sequencers van de nieuwe generatie vormen een bedreiging voor de traditionele micro-arrays. Leg uit.
#Bespreek oligonucleotide arrays en random beads in transcriptoomanalyse en vergelijk. Bespreek targetlabelling en uitlezing.
#Leg volgende begrippen kort uit:
#*whole shotgun sequencing
#*paired end ditags
#*gene ontology
#*scale free network

====Bart Landuyt====
#Hoe zijn massaspectrometers over het algemeen opgebouwd? Geef enkele vb van veel gebruikte opstellingen.
#Waarin verschilt peptidomics fundamenteel van proteomics?
#Bespreek de uitdagingen van het metaboloom en de gevolgen ervan op de analyse

====Baggerman====
#Hoe bepaal je de sequentie van een peptide met MS?
#Bespreek ESI-Q-TOF massa spectrometrie
#Vergelijk MALDI en ESI. Geef voor- en nadelen.
#Bespreek resolutie in MS, geef relevantie bij analyse.
#Leg het principe van een time-of-flight analysator uit

====Filip Roland====
#chemische uitdagingen van het metaboloom + relevantie voor staalname en staalbereiding
#Bespreek de belangrijkste verschillen tussen metaboloom - gen/transcr/proteoom. Hoe uit zich dat in de analyse.
#Bespreek de klassieke workflow van een metabolomics-analyse. Welke keuzes moeten gemaakt worden en wat zijn de mogelijke technieken die gebruikt kunnen worden

Physical Chemistry of Biological Systems

2024-12-14T09:17:27Z

R0895938: /* Vakinformatie */

[[Categorie: Mabb]]
==Vakinformatie==
Sinds academiejaar 2014-2015 enkel nog door Hideaki Mizuno gedoceerd. Examen bestaat uit 2 vragen, beide schriftelijk.
In academiejaar 2011-2012 tot 2013-2014 werd het vak gedoceerd door Prof. Yves Engelborghs en Prof. Hideaki Mizuno. Daarvoor enkel Prof. Yves Engelborghs. Staat in de basisopleiding.

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0G71AE.htm

==Examenvragen==
===20 Augustus 2024===
# How can we determine rate constants for the situation: first and second step equally fast. Suppose you have measured λ1 and λ2 of the exponential decay, how can we determine the rate constants? S = k'1+k-1+k2+k-2 and P = k'1k2+k'1k-2+k-1k-2 is given.
# Discuss Fluorescence Correlation Spectroscopy, what information can we deduce with this technique. What adapation can we use to study the interactions of molecules?

===29 Januari 2024===
# How can we determine rate constants for the situation: first and second step equally fast. Suppose you have measured λ1 and λ2 of the exponential decay, how can we determine the rate constants? S = k'1+k-1+k2+k-2 and P = k'1k2+k'1k-2+k-1k-2 is given.
# Discuss how DNA binding proteins specifically bind to DNA. Use the structures of the base pairs shown below.

===12 Januari 2024===

# Discuss how you can obtain interesting parameters from a Hill plot and a Scatchard plot (graphs and equations not given). Discuss the interpretation of the Hill plot and Scatchard plot for the binding of O2 to hemoglobin (graphs given).
# Usually the mean square displacement is used for the analysis of diffusion. a) Why the mean square displacement instead of the mean displacement? b) Explain why the mean square displacement is proportional to time and use the following equations: x(i) = x(i-1) +/- l, <x(i)²> = sum of x(i-1)² +/- 2lx(i-1) + l² and t(N) ~ N. c) Give the relationship between the mean square displacement and the diffusion coefficient in 1D, 2D and 3D. Give 3 parameters that change the diffusion coefficient (hint: D=kT/f and f=6*pi*viscosity*r).

===30 Januari 2023===

# Bespreek de informatie die je uit een Hill plot en een Scatchard plot kunt halen (grafieken en vergelijkingen niet gegeven). Bespreek de Hill plot en Scatchard plot van O2 binding aan hemoglobine (grafieken gegeven).
# Bespreek hoe DNA binding proteïnen specifieke bindingen kunnen maken met DNA. Gebruik hiervoor onderstaande structuren van de basen.

===13 Januari 2023===
# How can we determine rate constants for the situation: first and second step equally fast. Suppose you have measured λ1 and λ2 of the exponential decay, how can we determine the rate constants? S = k'1+k-1+k2+k-2 and P = k'1k2+k'1k-2+k-1k-2 is given.
# Discuss Fluorescence Correlation Spectroscopy, what information can we deduce with this technique. What adapation can we use to study the interactions of molecules?
(graph with EL, E and EL* are given, graph of S and P vs L0 is not given)

===3 September 2022===
#Discuss how DNA binding proteins specifically bind to DNA. Use the structures of the base pairs shown below.
#How can we determine rate constants for the situation: first and second step equally fast. Suppose you have measured λ1 and λ2 of the exponential decay, how can we determine the rate constants? S = k'1+k-1+k2+k-2 and P = k'1k2+k'1k-2+k-1k-2 is given.

===31 Januari 2022===

# Bespreek de informatie die je uit een Hill plot en een Scatchard plot kunt halen (grafieken en vergelijkingen niet gegeven). Bespreek de Hill plot en Scatchard plot van O2 binding aan hemoglobine (grafieken gegeven).
# Bespreek hoe DNA binding proteïnen specifieke bindingen kunnen maken met DNA. Gebruik hiervoor onderstaande structuren van de basen.

===24 Januari 2021===

# Leg uit hoe je de rate constants kan bepalen wanneer je te maken hebt met de volgende reactie: fast binding followed by slow conformational change.
# Bespreek hoe DNA binding proteïnen specifieke bindingen kunnen maken met DNA. Gebruik hiervoor onderstaande structuren van de basen.

===23 Januari 2020===

# Leg uit hoe je de rate constants kan bepalen wanneer je te maken hebt met de volgende reactie: fast binding followed by slow conformational change.
# Bespreek FCS. Wat kunnen we ermee doen. Hoe kan je FCS uitbreiden om proteine interacties na te gaan.

===13 Januari 2020===
#Bespreek de kinetische afleiding voor de massa en nummer concentratie. Aan de hand van deze formules bespreek de grafiek voor polymerisatie, bespreek nucleation, approach to plateau en reaching to the plateau.
#Bespreek hoe DNA binding proteïnen specifieke bindingen kunnen maken met DNA. Gebruik hiervoor onderstaande structuren van de basen.

===14 januari 2019===
# Bespreek de informatie die je uit een Hill plot en een Schatchard plot kunt halen (grafieken en vergelijkingen niet gegeven). Bespreek de Hill plot en Schatchard plot van O2 binding aan hemoglobine (grafieken gegeven). (Mondeling)
# Hoe binden proteïnen aan de buitenkant van DNA streng? Is de major of de minor groove hiervoor belangrijker? (schriftelijk)

===15 januari 2018===

# Leg uit hoe je de rate constants kan bepalen wanneer je te maken hebt met de volgende reactie: fast binding followed by slow conformational change.
# Bespreek FCS. Wat kunnen we ermee doen. Hoe kan je FCS uitbreiden om proteine interacties na te gaan.

===11 januari 2016===
# Bespreek de binding equation, binding partition function en degree of association. Bespreek hierbij de Hill plot en de Scatchard plot. Leg dit ook uit voor multiple binding sites. Hoe is het voor 'echte' situaties? Gebruik O2 en hemoglobine.
# De kinetica van self assembling van actine uitleggen. Hierbij gebruik maken van Mass Concentration, Number Concentration en Critical Concentration. Wat is treadmilling? Geef grafieken weer.

===12 januari 2015===
# Discuss Treadmilling in the formation of Actin Filaments. In your defense, include and explain the terms 'Mass Concentration', 'Number Concentration' and 'Critical Concentration'
# Discuss Fluorescent Correlation Spectroscopy, what information can we deduce with this technique. What adapation can we use to study the interactions of molecules?

===17 januari 2013===
Mizuno(mondeling)
# Bespreek de analyse self-assembling van myosine aan de hand van druk. Gebruik in je bespreking massaconcentratie, nummerconcentratie en kritische concentratie. Waarom kan 'pressure jump' gebruikt worden voor de analyse van de self-assembly?
# Bespreek MD(mean displacement), MSD(mean square displacement) en D(diffusion coefficient)bij random walk. Bespreek het verband tussen MSD en D. Waarom word meestal MSD gebruikt in plaats van MD?
Engelborghs (schriftelijk)
# Bespreek de binding van een restrictie-enzyme aan DNA. Hoe beïnvloeden de zoutconcentratie en de lengte van het DNA de kinetica? Geef de gepaste vergelijkingen en grafieken en bespreek.
# Hoe kan je, gebruik makend van de linked function theorie de denaturatie van DNA door ureum beschrijven?

===14 januari 2013===
Mizuno(mondeling)
# Bespreek de kinetica van actine polymerisatie. Gebruik de gepaste figuren en formules. Gebruik zeker massaconcentratie, nummerconcentratie en critica concentration
# Bespreek MD(mean displacement), MSD(mean square displacement) en D(diffusion coefficient). Bespreek het verband tussen MSD en D. Waarom word meestal MSD gebruikt in plaats van MD?
Engelborghs (schriftelijk)
# Hoe kan je, gebruik makend van de linked function theorie, ion condensation op DNA kwantitatief bespreken?
# Geef en bespreek 2 manieren om de dissociation rate(stond in vet) constant te bepalen voor een ligand L in een EL complex.
===18 januari 2011===
Enkel 1 en 2 mondeling.
# Bespreek hoe je de diffusieconstantie bepaalt met FCS.
# Hoe hangt de bindingssnelheid van een restrictie-enzyme af van de zoutconcentratie en lengte van DNA.
# Microtubuli-oscillaties bij hoge concentratie microtubuli.
# Linked function concept toepassen op denaturatie van proteïne door ureum.

===29 januari 2010===
Enkel 1 en 2 mondeling.
# Sigmoidale bindingscurve: haal maximum informatie uit grafiek.
# Counter ion condensation: ontwerp een experiment om exact de hoeveelheid counter-ionen te bepalen.
# Microtubulus-oscillaties
# Artikel over Random walk op DNA (rad51). (artikel voor te bereiden voor het examen, ter vervanging van de presentaties).
===12 januari 2009===
# Microtubulus-oscillaties en effect van tubuline-GMPPNP
# welke info haal je uit kinetische studies?
# counter ion condensation
# linked function concept in proteïne stabiliteit

===26 augustus 2008===
# In een oplossing met microtubuli wordt het GTP vervangen door een niet hydrolyseerbaar analoog GMPNPP (of zoiets). Wat gebeurt er?
# Hoe wordt de lengte van de myosine polymeren gereguleerd in vitro (in oplossing dus).
# Hoe kan er experimenteel aangetoond worden dat DNA omgeven worden door tegenionen.
# Een farmaco product bindt met proteïne, tijdens de bindingskineticastudies wordt er een lineare grafiek verkregen, maar het afgesneden stuk op de Y as is echter te klein om concludeerbare resultaten uit af te leiden. Welke informatie ontbreekt? Hoe zou je die wel kunnen bepalen?

===14 januari 2008===
# Proteïnen kunnen ontvouwen worden door het toedienen van ureum. Stel een model op via het 'linked function' concept om de invloed van ureum kwantitatief te beschrijven. (Of zoiets, ...).
# Wat beïnvloed de snelheidsconstante voor de specifieke binding van een restrictieenzyme aan DNA?
# Je hebt een ligand dat een signaal uitzend bij binding. Wanneer je de grafiek van de geobserveerde snelheidsconstante extrapoleert (naar L=0) bekom je een waarde die kleiner is dan de experimentele fout op de meettechniek. Hoe kun je de dissociatie-snelheidsconstante van L bepalen?
# Stel de partitiefunctie op voor één stuk DNA met een gap van 9 en een gap van 11 roosterpunten met een ligand dat bindt op 5 roosterpunten.