Table 3. Overview of selected student projects in the PBL of week 2 of the 2020 and 2021 course editions.

Project	Aim	Organism(s)	Models (draft/context)	Databases and tools	Outcome(s)
P1: Engineering a synthetic pathway for maleate in E. coli	Building a model that includes all the necessary reactions for the maleate production and checking which other reactions of the model could be optimised to get a higher maleate production	E. coli	iEC1344_C [25] (BiGG Models)		Creation of an E. coli that was survivable and able to produce maleate. Identifying other reactions that could be optimised to increase the maleate production
P2: Impact of different diets on anxiety and depression in regards to serotonin levels	Evaluating the growth of 3 Clostridial species for holding a high 7α-dehydroxylation activity that strongly up-regulates serotonin production	Clostridium hiranonis Clostridium hylemonae Clostridium scindens Bacteroides fragilis Bacteroides uniformis	C. hiranonis TO-931 DSM 13275 C. hylemonae DSM 15053 C. scindens ATCC 35704 B. fragilis NCTC 9343 B. uniformis ATCC 8492 [26] (VMH models, AGORA reconstructions)		Reduced growth rate of C. hiranonis growth under an unhealthy diet, which might affect serotonin levels
P3: Genome-scale metabolic modelling of human CD4+ T cells	Building models for naive CD4+ T cells, Th1, and Th2 cells and performing a comparative essentiality analysis	H. sapiens	Recon3D	GSE22886 [27], GSE24634 [28], and GSE2770 [29]	Identified essential metabolic pathways for naive CD4+ T cells, Th1, and Th2 cells
P4: Exploratory study using a human alveolar macrophage or respective mouse model combined with the Zika virus	Performing single reaction deletion, after the reconstruction of the host virus model, to predict putative antiviral strategies that could be tested experimentally	H. sapiens M. musculus Zika virus	Human macrophage iAB-AMØ-1410 [30] Mouse model iMM1415 [31] Zika virus Biomass objective function [32]	DrugBank	Confirmation of the validity of the human virus model and reconstruction of other models using different hosts Identified potential targets for antiviral therapies
P5: Metabolic differences in high and low STAT3 expressing breast cancer	Comparison of metabolic reactions, genes, and metabolites in high and low STAT3 expression using expression data from breast cancer patients and a breast cancer cell line model	H. sapiens	MDA-MB-231: Context-specific breast cancer cell line models [33]	GSE62944 [15]	Phenylalanine and vitamin B6 metabolisms identified as unique in the low STAT3 expression model

Project title, aims, organisms of interest, used models, and data, as well as project outcomes, are briefly summarised. More detailed descriptions of the projects are given in S1 Appendix. These descriptions have been written by the individual student as part of the learning process.

PBL, project-based learning.