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UPDATE ON THE 2021 Systems Biology lab INTERNSHIPS (Bachelor and Master) – January 2021
To comply with VU Corona regulations, the Systems Biology group established a maximum number of experimental internship students that can be safely hosted in the lab.
For the period from February 2021 to July 2021 all experimental positions are filled. However, theoretical internships are still available.
Summer experimental and theoretical internship positions are available.
Students can do various types of projects in our lab. We supervise bachelor and master internship projects but you can also find supervisors for your literature thesis. Practical internships can be in the wet lab (here termed experimental) , can be computational (here termed theoretical) or can consist of a combination of those two. All of them qualify as ‘research internships’ in virtually all of the study programs.
Below is a list of projects that we thought of. If you are interested in one, just contact the person that is associated to that project. But there are options beyond this list. Check the Team and the Projects pages and click on the different team members to see their lines of research. If you are interested in a specific topic that we work on, but do not see an internship within that project listed below, just contact the team member and check for the possibilities. This is especially relevant if you are looking for a literature thesis project – these are usually tailor-made based on your interests.
If you have general questions about internships in our department see the contact information at the end of the page
|Project title||Type of research||Supervisor(s)|
|Literature survey on how distinct dietary fibres can affect microbiome composition||Literature thesis (Bachelor or Master)||Prof, Remco Kort (firstname.lastname@example.org)|
|KeepFoodSimple ( https://keepfoodsimple.nl) is looking for a student Food Science or related fields of study who is interested in an internship studying the relation between type or chemical structure of food fibre and its effect on the composition of the microbioom. A further questions is: what is the effect of combinations of different types of fibre on the composition of the microbioom. Fibre in this context is defined as non-digestible oligo- and poly saccharides. This study will also include an evaluation of the various methods to establish microbioom composition. If possible this study will be linked to ongoing experiments on the relation between fibre type and microbioom composition.
This internship will be guided by prof. dr. Remco Kort, Microbiology, Free University Amsterdam and Fons Voragen Em. prof. of Food Chemistry, Wageningen University & Research. Start coming months.
KFS will pay a compensation of 250€ per month.
Literature survey on how distinct dietary fibres can affect microbiome composition
It is well known that dietary fibers have a positive effect on gut and metabolic health. They slow down gastric emptying and reduce sugar response after eating.
They thicken the contents of the intestinal tract, causing a better stool consistency which help removing potentially toxic metabolites from the colon.
The fibers are also important substrates for a wide range of gut bacteria. These bacteria produce various short chain fatty acids that strengthen the gut membrane, stimulate immune response and affect lipid, glucose and cholesterol metabolism in various tissues. Regular high consumption of dietary fibers result in a very diverse microbiome and it suppresses pathogenic bacteria that excrete carcinogenic metabolites.
These insights have led to a general recommendation to consume at least 30 to 40 grams of dietary fibers per day. However, food scientist and dieticians have not yet specified what particular type of fibre and what mix has the most beneficial health effect.
Various studies have shown that different types of fibers stimulate different groups of bacteria, leading to different metabolic effects. Arabinoxylans, for instance, stimulate growth of the bacterial genera Bifidobacterium and Akkermansia. This is much less so with inulin. Different types of pectins have different physiological effects. Rhamnogalacturonan 1 is well noted for its immune stimulating effects.
The objective of this study is to make a comprehensive survey on how all the major dietary fibers present in grains, beets & carrots, fruits, nuts, beans and vegetables affect microbiome composition and the resulting physiological and metabolic effects.
Please contact Remco Kort in case of any interest
|Understanding optimal resource allocation strategies in yeasts||Computational|
Bachelor (with strong interest in computational methods)/Master
|Optimal allocation of limited resources, such as nutrients, energy, or physical volume of the cell enables to sustain cell maintenance and growth of cells, and is critical for unicellular microorganisms to strive. Moreover, the optimal allocation pattern can be context-specific, heavily depending on the environment the microorganisms live in. Therefore, computational techniques are of great help in order to capture and analyse resource allocation strategies/patterns, preferably at genome-scale. Thus in this topic, we blend existing knowledge of biochemistry and microbial physiology together with different types of computational modelling to advance the understanding of the organization of metabolism of two major eukaryal model organisms: budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe.
Techniques: genome-scale metabolic modelling (both conventional and proteome-constrained) (PySCes CBMpy, COBRA etc.), kinetic modelling (COPASI), programming with Python and/or R for data analysis and visualization
|Metabolism in health and disease||Experimental or computational (combinations are possible)|
|The work in this topic aims to understanding control and regulation of metabolism to reveal selective drug targets in pathogens and other disease-causing cells. In addition, we also want to understand these aspects for healthy cells to make sure that interventions against the disease will not harm them. We work with the parasite Trypanosoma brucei and with liver cancer cells in the wetlab, but also do research on the parasite Schistosoma mansoni, on head- and neck cancer and blood cell precursors in the dry-lab (always in collaboration with experimental labs
Techniques: Wetlab: cell culture, metabolite measurements, enzyme assays. Dry lab: kinetic modelling (COPASI, PySCes (python-based), genome-scale modelling
|Using CRISPR/CAS to create mutant yeast strains||Experimental (Bachelor or Master)||Dennis Botman
|In the lab, mutants strains of micro organisms are used routinely to explore and elucidate cellular physiology. This also holds for yeast, where mutants are often created by using so-called auxotrophic markers. These markers are metabolic genes that are deleted and can be restored again by replacing the studied gene of interest for the auxotrophic marker. Auxotrophic markers themselves can already affect cellular physiology, thereby making this technique debatable. In order to make clean mutant strains, we want to set up and use CRISPR/CAS to make gene knockouts without using any markers (scarless). In this internship, you will use CRISPR/CAS to knock out specific genes important in our research in a fully WT strain without any auxotrophic markers (scarless). You will also perform whole genome sequencing and characterization of the mutant strains.|
|Using insect biosensors for food flavor development||Experimental (Master)||Herwig Bachmann
|Flavor is an important characteristic of food and our sensory perception of it, e.g. through
smell or taste, critically determines our dietary choices. Microorganisms are involved in the
production of a diversity of volatile and non-volatile molecules, in fermented products like
bread, cheese, wine, coffee and chocolate. We know that using different bacterial strains
during fermentations can result in alternate flavors. Being able to distinguish the olfactory of
gustatory profiles produced by specific strains of micro-organisms is, therefore, critical to
develop products with the desired flavor. GC-MS approaches have traditionally been used
map out the chemical properties of flavors produced by microorganisms, but not all chemical
compounds are equally well detected. To facilitate rapid and high-throughput screening of
different strains of micro-organisms, we therefore aim to develop a novel bioassay using
insects as biosensors. Several insect species are known for their excellent chemical detection
abilities, and multiple applications to use them as biosensors have been developed already,
e.g. for the detection of landmines.
In this project, we aim to use the parasitic wasp Nasonia vitripennis as a biosensor for the
detection of particular strains of microorganisms that are used in the fermentation process
of plant-based products that are currently under development to offer an alternative to dairy
products. For example, the concentration of aldehydes, alcohols and ketones, produced by
microorganisms is critical for a positive sensory perception and, hence, acceptance of these
products by human consumers. For this, we need to be able to screen large number of odour
and taste profiles produced by different strains of microorganisms.
Your role will be to develop and test the possibilities of the Nasonia wasps as a biosensor for
these profiles. For this, you will develop a bioassay in which you use associate conditioning to
train the wasps to respond to a specific chemical compound and then test their response to
a panel of different microbial strains.
Supervision by Herwig Bachmann (email@example.com; A-LIFE section Systems
Bioinformatics) & Katja Hoedjes (firstname.lastname@example.org; A-LIFE section Ecology & Evolution).
Internships are in principle open for students from other universities in the Netherlands or outside the Netherlands. We welcome for example ERASMUS students. Please note a few things:
If you are a non-VU student and from abroad you should contact Dr. Rob van Spanning (email@example.com) if you want to do an internship in our group, and indicate your preferred project(s), starting date, length of internship, and how you will support yourself (costs for food, accommodation), as we are unable to support you financially.
VU students and other Dutch students can contact the putative internship supervisor directly.