Molecular developmental biology

Molecular biology - Finding the protein interactome of a novel DNA motif, and finding the interactors of those binding proteins.

Chloë Kaal, chloekaal@hotmail.com 
A novel DNA motif was discovered, which is frequently found in core promotors, and thus important for gene expression. Using a DNA pull down the proteins that specifically bind the novel motif can be found. The found proteins were not that well studied. To find the interactome of those proteins, they were tagged with GFP. After that a GFP pull down can be done to find interaction partners of the proteins, and possibly predicting their function.

Learned techniques 
Culture cells, nuclear extraction, DNA pull down, CRISPaint, GFP pull down, Paqman.

Tips 
For this internship you have to apply early (definitely before september if you want to start in april), because it is popular. First come, first served. It is a challenging internship, but definitely a lot of fun when you like molecular biology.

 

Molecular and developmental biology (RIMLS) - Induction of M cell differentiation in an intestinal epithelial monolayer

Carlijn Friedrichs 
Nowadays, it is possible to study intestinal epithelial cell types in organoids. One of those cell types is the Microfold cell, which is important for uptake of antigens from the intestinal lumen in order to activate the immune system. Studying this function cannot be done in the organoids, because the intestinal lumen is not accessible. In this project, I made a monolayer (2D) from the organoids (3D), in which the apical side/intestinal lumen is accessible. For this, it is important to check whether it is possible to enrich for M cells in this model, and to check if these enriched M cells can function well. The M cell differentiation was induced by adding RANKL to the medium. On the other hand, another M cell differentiation inducer was made, which is the effector protein of Salmonella typhimurium. At last, both inducers would be compared in the new 2D model.

Learned techniques 
Cell culture of intestinal organoids (3D) and monolayer (2D). RNA isolation, cDNA synthesis and RT-qPCR. Immunostainings. Plasmid miniprep. Designing primers/plasmids for cloning (SnapGene). 

Tips 
Look for internships that really fits your interests. And send your motivation to more research groups, because not all of them will respond and if all of them do, then you can choose the best one. If they don't respond, don't hesitate to send them a reminder!

 

Molecular developmental biology - Relevant Transcription Factors in iPSC to Cardiomyocyte differentiation

Jelle Verploegen, jelle.topaas9@hotmail.com 
Using bioinformatic tools to combine scRNAseq data with ATACseq data from differentiating Cardio Myocytes from different timepoints to gain insight into relevant Transcription Factors in differentiation.

Learned techniques 
Programming in Python, big data analysis, unix shell scripting.

Tips 
Start looking as early as possible to find something that suits you.

 

Molecular developmental biology - Studying cardiomyocyte maturation by comparative transcriptomic approaches

Floor Hurkens, floorhurkens@live.nl 
During my internship I tried to improve a previously used protocol to differentiate human embryonic stem cells in the direction of mature cardiomyocytes. To check if the differentiation went well, I used different transcriptomic approaches. For one of the approaches, nuclei from cardiomyocytes have to be extracted. I tried to set up a protocol for that as well during my internship.  

Learned techniques 
Cell culture of human embryonic stem cells, differentiation of human embryonic stem cells, RNA extraction, cDNA synthesis, RT-qPCR, nuclei isolation, Western blotting.

Tips 
Start searching for an internship in time and enjoy your internship, because it is over before you know it!