Chemika Examenwiki - Gebruikersbijdragen [nl]

Plant Development and Metabolic Regulation

2024-02-08T14:09:21Z

R0631937: /* 31/01/2024 */

[[Categorie: Mabb]]

== Vakinformatie ==
Plant development and metabolic regulation

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0G45AE.htm

== Examenvragen ==

===31/01/2024===

Explain the formation of root hair cells

Apical dominance: fill in scheme + explain

Briefly discuss

coincidence model in Ara and rice

sweet immunity

CTR mutant related to ethylene

SMR1 and ratio stomata/ pavement cells

===25/01/2024===

- explain COP/DET

- explain figure about vasculature formation

briefly discuss:

a) Role of T6P during flowering

b) Hormone/sugar signals for outgrowth of rose bud

c) role of miR172 in floral organ identity

d) drought tolerance of WT, smr1, SMR1 over expressing lines. which mechanisms are in play?

===30/08/2022===

- explain the formation of root hair cells (7)

-Discuss clonal analysis and average cell numbers (5)

briefly discuss: (8, 2 each)

a) ABCE floral system

b) Sweet immunity

c) BHP role in root cells fate

d) what happens when QC cells get Lazer ablated? and how can we visualise that?

===03/02/2022===
COP/DET

Roothair formation, positioning, growth

Smaller questions:
a)coincidence model

b)Give 3 shoot apical meristem mutants and the phenotype

c)sweet immunity

d)Influence of miRNA and sugar on stress and development. Role of SPL and DELLA.

===22 januari 2021===
COP/DET en mutanten die hielpen bij dit te onderzoeken

regulation G1/S and S/M transition.

Small questions
a)Sweet immunity

b)hoe kan je invertase enzym activiteit bepalen in een plant extract

c)Wox figure explain

===22 januari 2021===
wortelhaarvorming uitleggen

COP/DET

a) sweet immunity

b)de rol van suikers & mirna in maturatie van plant

c)hoe kan je invertase enzym activiteit bepalen in een plant extract

===17/01/2019===
COP/DET

regulation G1/S and S/M transition.

Explain briefly:
a) sweet priming

b) polarity in Fucus

c) explain the figure: WOX

===17/01/2019===
Apical dominance: fill in scheme + explain

roothair formation

Smaller questions:
a) coincidence model in Ara and rice

b) sweet immunity

c) influence of miRNA and sugar on stress and development

Plant Development and Metabolic Regulation

2024-02-08T14:09:07Z

R0631937: /* 31/01/2024 */

[[Categorie: Mabb]]

== Vakinformatie ==
Plant development and metabolic regulation

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0G45AE.htm

== Examenvragen ==

===31/01/2024===
Explain the formation of root hair cells
Apical dominance: fill in scheme + explain

Briefly discuss

coincidence model in Ara and rice

sweet immunity

CTR mutant related to ethylene

SMR1 and ratio stomata/ pavement cells

===25/01/2024===

- explain COP/DET

- explain figure about vasculature formation

briefly discuss:

a) Role of T6P during flowering

b) Hormone/sugar signals for outgrowth of rose bud

c) role of miR172 in floral organ identity

d) drought tolerance of WT, smr1, SMR1 over expressing lines. which mechanisms are in play?

===30/08/2022===

- explain the formation of root hair cells (7)

-Discuss clonal analysis and average cell numbers (5)

briefly discuss: (8, 2 each)

a) ABCE floral system

b) Sweet immunity

c) BHP role in root cells fate

d) what happens when QC cells get Lazer ablated? and how can we visualise that?

===03/02/2022===
COP/DET

Roothair formation, positioning, growth

Smaller questions:
a)coincidence model

b)Give 3 shoot apical meristem mutants and the phenotype

c)sweet immunity

d)Influence of miRNA and sugar on stress and development. Role of SPL and DELLA.

===22 januari 2021===
COP/DET en mutanten die hielpen bij dit te onderzoeken

regulation G1/S and S/M transition.

Small questions
a)Sweet immunity

b)hoe kan je invertase enzym activiteit bepalen in een plant extract

c)Wox figure explain

===22 januari 2021===
wortelhaarvorming uitleggen

COP/DET

a) sweet immunity

b)de rol van suikers & mirna in maturatie van plant

c)hoe kan je invertase enzym activiteit bepalen in een plant extract

===17/01/2019===
COP/DET

regulation G1/S and S/M transition.

Explain briefly:
a) sweet priming

b) polarity in Fucus

c) explain the figure: WOX

===17/01/2019===
Apical dominance: fill in scheme + explain

roothair formation

Smaller questions:
a) coincidence model in Ara and rice

b) sweet immunity

c) influence of miRNA and sugar on stress and development

Advanced Biological Data Analysis

2024-01-29T17:43:24Z

R0631937: /* Examenvragen */

[[Categorie: Mabb]]

== Vakinformatie ==
Keuze-truncus vak voor master Biochemie (verplicht voor master Biologie), gegeven door Piet van den Berg, Tom Wenseleers & Hans Jacquemyn. Open boek examen waar je 2 datasets moet analyseren die gelijkaardig zijn aan die van de oefenzittingen. 10/20 voor het onderdeel van PVDB & TW. 10/20 voor het onderdeel van HJ.

Dit werd vroeger gegeven door professors Tom Wenseleers en Hans Jacquemyn. Het examen is schriftelijk open boek, en bestaat uit het ter plekke statistisch analyseren van verschillende datasets op de computer. Hierbij staat het deel gegeven door Wenseleers en Jacquemyn elk op 10 van de 20 punten.

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0F87AE.htm

== Examenvragen ==

===2024===

====Piet van den Berg & Tom Wenseleers====

Clownfish (Amphiprion spp.) are marine fish found in reefs in the eastern Indian Ocean and the western Pacific that have symbiotic relationships with sea anemones. They live in highly socially structured harems and are aggressively territorial.

In this study, the researchers were interested in understanding the aggressive behaviours of two species of clownfish:
- the common clownfish (A. ocellaris) and
- the orange clownfish (A. percula; variable ‘AmphiprionSpecies’ in the dataset)

They observed aggressive behaviours towards unfamiliar conspecifics of the fish at 24 different territories (indicated with ‘TerritoryID’ in the dataset), which each housed one or multiple clownfish harems. The researchers presented various males and females (variable ‘Sex’) from each territory with an unfamiliar conspecific, and then counted the number of aggressive behaviours that the fish exhibited in a timeframe of 5 minutes (‘AgressionEvents’).
Run a data analysis in R to answer the question below. Then write your answer on the next page of this document. Make sure your answer is clear and concise, and that your conclusion is supported by the data analysis that you performed. Paste the output (tables and figures) that is needed to support your argument to this document, but don’t paste code in this file (hand in your R script separately and make sure that it is clear). Make sure that your name is in the filename of both documents!

QUESTION: How does aggression depend on species and sex?
- Run models that consider all combinations of variables mentioned in the question above (including models that consider only single predictors).
- Also run a model that considers the interaction.
- Choose the best model.
- Check for overdispersion and continue with the appropriate model.
- For the purpose of this exercise, there is no need to do any other model diagnosis checks.
- Visualize the best model with an as good as possible visual representation. Write a clear conclusion (important!).

====Hans Jacquemyn====

Ecological processes are central to the formation of new species. When barriers to gene flow emerge between populations (e.g. shifts in flowering time, landscape changes), there is an increased likelihood that divergent selection and local adaptation will lead to the rapid formation of ecotypes, and potentially new species. However, it is often not clear to what extent populations have diverged genetically and morphologically. This may be particularly true for the orchid genus Epipactis. This genus contains a problematical complex of taxa among which species limits are difficult to define. As a result, different authors have treated the taxonomy of Epipactis in different ways, some recognizing the different taxa as distinct species, others considering them as minor intraspecific variants. In dune habitats in Belgium, plants that closely resemble the widespread Epipactis helleborine can be regularly encountered. The precise taxonomic position of these plants, however, is not clear and currently subject to debate; some regard it as a variety of E. helleborine (E. helleborine var. neerlandica), some as a subspecies (E. helleborine subsp. neerlandica), whereas others consider it as a distinct species (E. neerlandica).
In this study, 28 different morphological characters were measured for plants growing in dune and forest habitats to investigate to what extent dune and forest ecotypes differ morphologically. These characters were related to the size of the plant (traits T1–T14), leaf characteristics (T15–T16), and floral morphology (T17–T28).

1) Investigate whether the overall morphology differs significantly between plants of the forest and dune ecotype and identify the variables that most determine the morphological difference between the two ecotypes.

2) Illustrate graphically which variables best explain variation in morphology between both ecotypes.

3) Can you notice a significant difference in overall morphology between the different populations that were sampled and did these differences depend on the ecotype? Illustrate your answer with the appropriate graph.

===2024===

====Piet van den Berg & Tom Wenseleers====

Swifts are insectivorous birds belonging to family of Apodidae. Swifts resemble swallows in both morphology and niche, but the two families are only distantly related – their similarity is due to convergent evolution. They occur on all continents and those endemic to temperate regions are typically migratory. Swifts are particularly active during twilight (when their insect prey also tend to be more active) and can ascend to high altitudes when they are foraging.

In this study, the researchers wanted to know if swifts are influenced by the brightness of the moon during their foraging bouts. Specifically, they were interested to know if moon illuminance affected the altitude reached during their foraging bouts by swifts of three species: the common swift (Apus apus), the pallid swift (Apus pallidus) and the alpine swift (Tachymarptis melba). The researchers equipped the animals with sensors that allow to make rough altitude estimations. For a large number of foraging bouts, the researchers logged whether the bird reached a high altitude or not (‘high’ was defined as more than the mean plus a standard deviation of flight altitudes during the day; this is recorded under the variable “altbin” in the dataset: 1 for a high altitude and 0 for a low altitude). They also measured moon illuminance (“moon_illuminance”) during each foraging bout and included the species of the measured individual in the dataset (“species”). They had many measurements for each individual (the individual is indicated by “tag” in the dataset).
Run a data analysis in R to answer the question below. Then write your answer on the next page of this document. Make sure your answer is clear and concise, and that your conclusion is supported by the data analysis that you performed. Paste the output (tables and figures) that is needed to support your argument to this document, but don’t paste code in this file (hand in your R script separately and make sure that it is clear). Make sure that your name is in the filename of both documents! Exercise
QUESTION: How does moon illuminance affect flight altitude in the three species of swift?
- Run models that consider all combinations of variables mentioned above (including models that consider only single predictors).

- Also run a model that considers the interaction. Choose the best model.
- Check for overdispersion and continue with the appropriate model.
- For the purpose of this exercise, there is no need to do any other model diagnosis checks. Visualize the best model with an as good as possible visual representation.
- Write a clear conclusion (important!).

====Hans Jacquemyn====

Primula veris is a distylous plant species that can be found in forest and grassland habitats (Fig. 1). Populations of P. veris typically contain long-styled (L-morph) and short-styled (S-morph) plants. Due to the pronounced differences in environmental conditions (e.g. light conditions, soil moisture content) between forests and grasslands, we can expect that plants growing in these habitats display different growth characteristics.

Fig. 1 Example of Primula veris growing in grassland habitat.

To test this hypothesis, a large number of plant characteristics were measured:
• Leaf dry mass (Leaf_dry_mass) (g)
• Number of leafs (Leafs)
• Number of flower stalks (Flower_stalks)
• Average length of flowering stalks (Stalk_length) (cm)
• Total number of flowers (Total_flowers)
• Average number of flowers per flowering stalk (Average_flowers)
• Leaf surface area (Leaf_surface_area) (cm²)
• Leaf width (Leaf_width) (cm)
• Leaf length (Leaf_length) (cm)
• Number of stomata (Stomata)
• Specific leaf area (SLA) : ratio of leaf area to dry mass

Besides, information on the habitat (forest or grassland), morph type (short-styled (S) or long-styled (L)), and the population from which plants were sampled (Population) is provided as well.

1) Investigate whether the overall morphology differs significantly between plants from grasslands and plants in forests and whether this difference is significantly affected by morph type.

2) Which variables are most important in determining the difference in overall morphology between forest and grassland plants?

Illustrate your results with the appropriate figures. Please also explain in detail why you have chosen for a particular analysis technique.

===30 januari 2023===
====Piet van den Berg & Tom Wenseleers====
In this study, the researchers were interested in how dominance relationships affect food sharing in the wild. In 4,549 hours of observations, they recorded all instances where there was the possibility for sharing food (potential sharing events). This was the case when one individual had food (the “possessor”) and another individual begged to obtain some of it (the “potential partner”). They recorded whether the begging behaviour resulted in the possessor sharing food with the potential partner (“Sharing” in the dataset; 1 if food was shared, 0 if not). They gave each individual an identity tag and recorded these for both individuals in each potential sharing event (“Possessor” and “PotentialPartner” in the dataset) and they also recorded their dominance ranks (“DominancePossessor” and “DominancePotentialPartner”). Most individuals were observed in multiple potential sharing events.

QUESTION: How does dominance rank affect food sharing in chimpanzees?

Run models with the dominance ranks of the possessor and the potential partner as predictors. Consider all combinations (both ranks separately, both together, and a model that also includes the interaction). Choose the best model. Include the appropriate random effects structure in all models that you run. Check for overdispersion and continue with the appropriate model. For the purpose of this exercise, there is no need to do any other model diagnosis checks. Visualize the best model. Write a clear conclusion (important!).

====Hans Jacquemyn====
#The marsh orchid (Dactylorhiza sphagnicola) and the heat-spotted orchid (Dactylorhiza maculata) (Fig. 1) are two orchid species that are able to hybridize when they co-occur. In the Belgian Ardennes, both allopatric and sympatric populations of both orchids can be found and there are some indications that hybridization occurs in sympatric populations. In order to get better insights in the hybridization process, the morphology of a large number of plants was investigated in a large sympatric population where both species co-occurred. In total 28 morphological traits were measured (Table 1). The same characteristics were also measured for a large number of plants in allopatric populations (one for each species). The data have been summarized in two datasets. The dataset sympatric.xlsx contains all data for the sympatric population, the dataset allopatric.xlsx contains the data for the allopatric populations.
#* A. Investigate whether the two species can be unequivocally distinguished based on the measured characteristics?
#* B. Which traits are most important to distinguish the two species?
#* C. Are there indications that hybridization has occurred in the sympatric population? How can you deduce this from your analysis?

===17 januari 2020 NM ===
====Tom Wenseleers - oral (you receive the questions in an R file)====
# The provided data file contains detailed data on the survival of the passengers of the titanic (survived=0/1 for passengers that died or not) as a function of, amongst others, their age ("age"), their sex ("sex") and the price they paid for their ticket ("priceperticket").
#* A. Fit a model of passenger survival in function of age, sex & priceperticket with the appropriate error structure. Start with a model that takes into account all possible higher-order interaction effects and then use stepwise backward model reduction and calculate the best model based on the bayesian information criterion bic. Test for the possible presence of outliers & influential observations and remove those if necessary.
#* B. Make effect plots of all the predictors in your best model (on the link scale but using y axis response plot labels, using type="rescale") and interpret the results.
#* C. Calculate the log(odds ratio) to survive for male passengers of average age that paid for the most expensive ticket vs those that paid for the cheapest one. Do the same for female passengers. Did the log odds of them surviving go up in proportion to the price they paid for their ticket, or was there an unfair advantage for those that paid for the most expensive one?
Paste all R code + all tabular & graphical output & interpretation in a word document and do the same for the part of hans jacquemyn and hand it over to the assistant saved as lastname_firstname.docx & lastname_firstname.r (zip these two files as lastname_firstname_exam.zip)

====Hans Jacquemyn (in a Word document)====
#Orchids rely on mycorrhizal fungi to complete their life cycle. Recent research has shown that these fungi can be quite diverse and belong to different genera. Fungal communities are also likely to vary between orchid populations. Little,however, is known about the factors determining variation in fungal communities and whether this variation affects the population dynamics of orchids. It can be expected that differences in soil conditions have a significant impact on mycorrhizal communities and therefore impact on the population dynamics of the orchids. To test this hypothesis fungal communities were determined in a large number of populations of the terrestrial orchid Neottia ovata (Fig. 1). For each population a series of soil characteristics was measured and the change in population size was assessed by comparing the population size in 2003 with that in 2013. Data were collected in three separate plots in each population. The data have been summarized in two datasets, one that gives for each population the abundance (number of sequences) of all detected fungi (Neottia_fungi.xlsx), and one that gives an overview of the soil characteristics (Neottia_soil.xlsx).
#* The soil characteristics that were measured are soil moisture content (moist), organic matter (OM), phosphate concentration (P), nitrate concentration (NO3) and ammonium concentration (NH4). The last file also tells you whether a population has increased (1) or decreased in size (0) between 2003 and 2013.
#* A. Assess whether fungal communities vary among populations?
#* B. Investigate whether variation in fungal communities can be related to soil conditions. Which soil variables have the largest effect on fungal communities?
#* C. Investigate whether the observed changes in population size can be related to variation in mycorrhizal communities.

===17 januari 2020 VM ===
====Tom Wenseleers - oral (you receive the questions in an R file)====
# Researchers were interested to test if queen pheromones of the honeybee, which in that species are emitted by the queen to stop the workers from reproducing, would also inhibit the reproduction of either workers or queens in the bumblebee. They hypothesized that such cross activity might be observed in the event that these compounds exploit conserved physiological pathways linked with the regulation of reproduction. To test this hypothesis, the researchers exposed bumblebee queens and bumblebee worker groups (groups of 20 workers each) to either a blank solvent-only control or a solution of honeybee queen pheromones for a period of 2 weeks. Subsequently, they dissected the queens and workers and measured the size of the largest oocyte in their ovaries to be able to test for any effects on ovary development. For each of the worker groups, these measurements were averaged over all individuals. In terms of experimental design, genetic background was controlled for by doing the experiment in a paired fashion, whereby the worker groups exposed to each replicate control and queen pheromone treatment were derived from the same source colony and similarly, the queens exposed to each replicate control and queen pheromone treatment were taken to be sisters of each other (colony or sibgroup is encoded as variable "id" in the dataset). In your analysis, take into account this non-independence through the inclusion of a random effect term, and use a model with the appropriate error distribution.
#* Aim: Test whether honeybee queen pheromones inhibit ovary development and whether this effect is caste dependent. (cf. dataset "data.csv").
#* SPECIFIC QUESTIONS:
#** A. Display your data using "spaghetti plots", i.e. plot oocyte size in function of treatment, using two different panels for caste, and connect points that are measured from individuals from the same colony (for workers) or sib-group (for queens). Make this plot both using lattice's xyplot and ggplot2.
#** B. Fit a model of oocyte size (SIZE_OOCYTE) in function of TREATMENT and CASTE, either considering a possible interaction effect between both or not, taking into account possible random effects and use a model with the appropriate error distribution. Decide which model is best based on the AIC criterion. What is the name of the type of model you fitted? (in this case a linear mixed effects model was ok, since the distribution or errors was normal: lme() or lmer())
#** C. Make effect plots of the effects in your model and explain what these imply.
#** D. Carry out the relevant tests for the significance of the different effects. What do these tell you? Also carry out Tukey posthoc tests to test the effect of treatment for each of the two castes. What would the conclusion have been if you would have ignored the dependency in your data (variable ID, i.e. colony or sibship)? WOuld the effect of TREATMENT have been more or less significant then and why? (just do a normal lm here)
#** E. Test whether the residuals of your model conform to your assumed error distribution.

====Hans Jacquemyn (in a Word document)====
#The marsh orchid (Dactylorhiza sphagnicola) and the heat-spotted orchid (Dactylorhiza maculata) (Fig. 1) are two orchid species that are able to hybridize when they co-occur. In the Belgian Ardennes, both allopatric and sympatric populations of both orchids can be found and there are some indications that hybridization occurs in sympatric populations. In order to get better insights in the hybridization process, the morphology of a large number of plants was investigated in a large sympatric population where both species co-occurred. In total 28 morphological traits were measured (Table 1). The same characteristics were also measured for a large number of plants in allopatric populations (one for each species). The data have been summarized in two datasets. The dataset sympatric.xlsx contains all data for the sympatric population, the dataset allopatric.xlsx contains the data for the allopatric populations.
#*Given Vegetative traits: Plant height from soil level (cm), Number of cauline leaves, Lowermost leaf length (cm), Lowermost leaf maximum width (cm), Length of second leaf (cm), Maximum width of the second leaf (cm), Position of the second leaf greatest width (cm), Uppermost leaf length (cm), Uppermost internodium length (cm), Stem diameter under infl orescence (mm), Stem diameter above lowermost leaf (mm), Number of flowers, Inflorescence length (cm), Length of inflorescence axis between the bract insertion points of first and fifth flowers (cm)
#*Given Flower traits: Bract length (cm), Bract width (cm), Ovary length (cm), Lateral sepals length (cm), Lateral sepals width (cm), Petals length (cm), Petals width (cm), Labellum length (cm), Labellum lateral lobes length from base (cm), Labellum median lobe length (cm), Labellum width (cm), Labellum median lobe width at base (cm), Spur length (cm), Spur diameter at base (cm)
#* A. Investigate whether the two species can be unequivocally distinguished based on the measured characteristics?
#* B. Which traits are most important to distinguish the two species?
#* C. Are there indications that hybridization has occurred in the sympatric population? How can you deduce this from your analysis? Illustrate your answer with the appropriate figures and explain which analysis you have used and why.

===6 januari 2019===
====Tom Wenseleers - oral (you receive the questions in an R file)====

# Researchers were interested to test if queen pheromones of the honeybee, which in that species are emitted by the queen to stop the workers from reproducing, would also inhibit the reproduction of either workers or queens in the bumblebee. They hypothesized that such cross activity might be observed in the event that these compounds exploit conserved physiological pathways linked with the regulation of reproduction. To test this hypothesis, the researchers exposed bumblebee queens and bumblebee worker groups (groups of 20 workers each) to either a blank solvent-only control or a solution of honeybee queen pheromones for a period of 2 weeks. Subsequently, they dissected the queens and workers and measured the size of the largest oocyte in their ovaries to be able to test for any effects on ovary development. For each of the worker groups, these measurements were averaged over all individuals. In terms of experimental design, genetic background was controlled for by doing the experiment in a paired fashion, whereby the worker groups exposed to each replicate control and queen pheromone treatment were derived from the same source colony and similarly, the queens exposed to each replicate control and queen pheromone treatment were taken to be sisters of each other (colony or sibgroup is encoded as variable "id" in the dataset). In your analysis, take into account this non-independence through the inclusion of a random effect term, and use a model with the appropriate error distribution.
#* Aim: Test whether honeybee queen pheromones inhibit ovary development and whether this effect is caste dependent. (cf. dataset "data.csv").
#* Specific questions:
#** A. Display your data using "spaghetti plots", i.e. plot oocyte size in function of treatment, using two different panels for caste, and connect points that are measured from individuals from the same colony (for workers) or sib-group (for queens). Make this plot both using lattice's xyplot and ggplot2.
#** B. Fit a model of oocyte size (SIZE_OOCYTE) in function of TREATMENT and CASTE, either considering a possible interaction effect between both or not, taking into account possible random effects and use a model with the appropriate error distribution. Decide which model is best based on the AIC criterion. What is the name of the type of model you fitted? (in this case a linear mixed effects model was ok, since the distribution or errors was normal: lme() or lmer())
#** C. Make effect plots of the effects in your model and explain what these imply.
#** D. Carry out the relevant tests for the significance of the different effects. What do these tell you? Also carry out Tukey posthoc tests to test the effect of treatment for each of the two castes. What would the conclusion have been if you would have ignored the dependency in your data (variable ID, i.e. colony or sibship)? WOuld the effect of TREATMENT have been more or less significant then and why? (just do a normal lm here)
#** E. Test whether the residuals of your model conform to your assumed error distribution. (he wanted to see a histogram of the residuals)

====Hans Jacquemyn (in a Word document)====
# Evolutionary theory predicts that coexistence of two closely related plant species can have a major impact on floral morphology and plant mating systems. To test this prediction, floral morphology of a large number of individuals from both allopatric and sympatric populations of Common centaury (Centaurium erythraea) and Seaside centaury (C. littorale) (Fig. 1) were investigated along the Belgian coast. For each individual seven floral traits were measured (Table 1). (Data set: Centaurium.xlsx) (Table 1: ''Floral traits measured in allopatric and sympatric populations of Centaurium erythraea en C. littorale along the Belgian coast.'' (Given traits and variables were: Total length of the flower (mm), Total Petal length (mm), Petal width (mm), Ovary length (mm), Style length (mm), Length of the anthers (mm), Level of herkogamy (mm))
#* A. Investigate whether floral morphology differs significantly between flowers of Centaurium erythraea and C. littorale.
#* B. Illustrate graphically which variables best explain variation in floral morphology between both species and indicate which variable most determines the difference between the two species.
#* C. Can you notice a difference in floral morphology between allopatric and sympatric populations? Is this difference determined by the identity of the species? If yes, explain how and illustrate with the appropriate graph.
#* D. Based on your results, can you conclude that allopatric populations can as easily discerned from sympatric populations for C. erythraea as for C. littorale? And which floral traits are best suited to discern allopatric from sympatric populations?

Plant Development and Metabolic Regulation

2024-01-25T14:37:12Z

R0631937: /* 25/01/2024 */

[[Categorie: Mabb]]

== Vakinformatie ==
Plant development and metabolic regulation

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0G45AE.htm

== Examenvragen ==

===25/01/2024===

- explain COP/DET

- explain figure about vasculature formation

briefly discuss:

a) Role of T6P during flowering

b) Hormone/sugar signals for outgrowth of rose bud

c) role of miR172 in floral organ identity

d) drought tolerance of WT, smr1, SMR1 over expressing lines. which mechanisms are in play?

===30/08/2022===

- explain the formation of root hair cells (7)

-Discuss clonal analysis and average cell numbers (5)

briefly discuss: (8, 2 each)

A - ABCE floral system

B- Sweet immunity

C- BHP role in root cells fate

D- what happens when QC cells get Lazer ablated? and how can we visualise that?
===22 januari 2021===
#COP/DET en mutanten die hielpen bij dit te onderzoeken
#regulation G1/S and S/M transition.
#klein vraagje:
Sweet immunity
hoe kan je invertase enzym activiteit bepalen in een plant extract
Wox tekening
===22 januari 2021===
#wortelhaarvorming uitleggen
#COP/DET
#sweet immunity
#de rol van suikers & mirna in maturatie van plant
#klein vraagje: hoe kan je invertase enzym activiteit bepalen in een plant extract

Plant Development and Metabolic Regulation

2024-01-25T14:36:58Z

R0631937: /* 25/01/2024 */

[[Categorie: Mabb]]

== Vakinformatie ==
Plant development and metabolic regulation

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0G45AE.htm

== Examenvragen ==

===25/01/2024===

- explain COP/DET

- explain figure about vasculature formation

briefly discuss:
a) Role of T6P during flowering
b) Hormone/sugar signals for outgrowth of rose bud
c) role of miR172 in floral organ identity
d) drought tolerance of WT, smr1, SMR1 over expressing lines. which mechanisms are in play?

===30/08/2022===

- explain the formation of root hair cells (7)

-Discuss clonal analysis and average cell numbers (5)

briefly discuss: (8, 2 each)

A - ABCE floral system

B- Sweet immunity

C- BHP role in root cells fate

D- what happens when QC cells get Lazer ablated? and how can we visualise that?
===22 januari 2021===
#COP/DET en mutanten die hielpen bij dit te onderzoeken
#regulation G1/S and S/M transition.
#klein vraagje:
Sweet immunity
hoe kan je invertase enzym activiteit bepalen in een plant extract
Wox tekening
===22 januari 2021===
#wortelhaarvorming uitleggen
#COP/DET
#sweet immunity
#de rol van suikers & mirna in maturatie van plant
#klein vraagje: hoe kan je invertase enzym activiteit bepalen in een plant extract

Plant Development and Metabolic Regulation

2024-01-25T14:36:45Z

R0631937: /* Examenvragen */

[[Categorie: Mabb]]

== Vakinformatie ==
Plant development and metabolic regulation

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/G0G45AE.htm

== Examenvragen ==

===25/01/2024===

- explain COP/DET
- explain figure about vasculature formation

briefly discuss:
a) Role of T6P during flowering
b) Hormone/sugar signals for outgrowth of rose bud
c) role of miR172 in floral organ identity
d) drought tolerance of WT, smr1, SMR1 over expressing lines. which mechanisms are in play?

===30/08/2022===

- explain the formation of root hair cells (7)

-Discuss clonal analysis and average cell numbers (5)

briefly discuss: (8, 2 each)

A - ABCE floral system

B- Sweet immunity

C- BHP role in root cells fate

D- what happens when QC cells get Lazer ablated? and how can we visualise that?
===22 januari 2021===
#COP/DET en mutanten die hielpen bij dit te onderzoeken
#regulation G1/S and S/M transition.
#klein vraagje:
Sweet immunity
hoe kan je invertase enzym activiteit bepalen in een plant extract
Wox tekening
===22 januari 2021===
#wortelhaarvorming uitleggen
#COP/DET
#sweet immunity
#de rol van suikers & mirna in maturatie van plant
#klein vraagje: hoe kan je invertase enzym activiteit bepalen in een plant extract

Genoom-, proteoom- en metaboloomanalyse

2023-09-03T19:49:16Z

R0631937: /* 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, Robben, en Schoofs. Alles is gesloten boek.

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

==Examenvragen==
===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