a) CAG — explain abbreviation and the method b) Can this method be applied on a unique hot water spring sample? c) How would you adapt the method for the sample in b)? d) Long read sequencing can also be used in metagenomics for genome assembly, but there are still some drawbacks, give 2 of them.

Explain PIGEX, MIMS and repair protocols for paleogenomes in the context of this course (more than just the abbreviation).

(Guest lecture Marie Joossens) a) Same stool sample was sent by Tina Saey to two different companies for analysis (American Gut and uBiome), she received a different microbial composition by the two, what could have caused this discrepancy? b) Could you in theory get the same microbial composition? c) Is there one solution or not?

(Guest lecture Bart Devreese) a) Why is the label-free approach in comparative proteomics difficult to use if you have more than 4 samples? b) Which other method would you choose if you had to compare 4 samples?

(Guest lecture Geert Goeminne) a) Scopoletin was produced by overexpression in A. thaliana, why did we see another compound eluting in our analysis? b) Why would we implement the scopoletin pathway?

Case study on leucine dehydrogenase

(Guest lecture Magdalena Calusinska) a) Assay optimisation: Comparison of whole gut (WG) vs. luminal fluid (LF) and comparison of two rRNA depletion kits: RiboZERO (RZ) vs. MicrobeENRICH (ME), figures on slides are given on the exam, which conditions do you prefer and explain why b) How do they remove rRNA in the metagenomic pipeline? c) What parameter is mainly used to compare quantification of transcripts in different samples? Explain briefly how this is calculated