Student projects / Internships
Positions for internships of 6 and 9 months are available for Master students interested in cell biology, biochemistry, cell biology of the neuron or biophysics. Interested candidates should send a letter of motivation and a short CV directly to the group leader(s). Please indicate in you letter on which project(s) you would like to work.
Internship Akhmanova lab
Internship Van Bergen en Henegouwen lab
Novel targets for personalized cancer therapy
Standard therapies for cancer include radiation, surgery and chemotherapy. To avoid side effects, recent developments are aiming at the application of targeted therapies using monoclonal antibodies. In our group we use antibody fragments (nanobodies) that are obtained from heavy chain antibodies present in animals from the Camelidae family. Nanobodies are ten times smaller than conventional antibodies (molecular weight of only 15 kDa), and bind with high affinity and specificity to different targets. These unique, naturally raised antibody fragments are selected in the process of phage display and can be functionalized by direct conjugation to fluorophores or effector molecules. Because of their size tumor penetration is better than the larger monoclonal antibodies. The nanobody-based therapy is an excellent system that can be used for the development of personalized medicine.
Cancer is the result of multiple perturbations in the network of functional interactions between proteins. Recent large scale comparisons between normal and cancer genomes have demonstrated that cancer genomes may have hundreds of genomic alterations. In this project we will use large genomic databases for searching mutations that are present in the extracellular domains of plasma membrane proteins from cancer cells. These mutated proteins will be used as novel tumor targets to which nanobodies binding to these tumor specific mutated proteins will be generated.
This project will be performed in collaboration with dr. Can Keşmir from the division of Theoretical Biology and Bioinformatics and dr. van Bergen en Henegouwen from the division of Cell Biology. We are looking for a highly motivated master student who is interested in the analysis of large data bases for the search of novel tumor targets, and wishes to combine this with phage display selections of nanobodies against these targets. Further information can be obtained from dr. Can Keşmir (firstname.lastname@example.org) or dr. P.M.P. van Bergen en Henegouwen (email@example.com).
Internships Kapitein lab
Computational analysis of microscopy images and movies
In the last 20 years technological advancements drastically changed the field of the modern biological microscopy. It became possible to observe and record structures and processes in unprecedented environments, on nanometer scales and at very high rates. Introduction of genetically-encoded fluorescent labels allowed labeling of individual organs, cells and molecules inside living organisms. Recent developments of microscopy techniques made it possible to record in high-resolution and in three dimensions a beating of heart, work of a brain or the development of a whole organism. Currently modern microscopy needs to deal with huge amounts of visual data presented in digital form. The efficient analysis of these data represents an unprecedented challenge.
In our lab we employ a number of microscopy techniques ranging from live confocal 3D to superresolution to study the structure and behavior of proteins at the sub-cellular level in cultured cells and in neurons. Using our setups we can generate data flows of up to 1 Gb per second. These images and movies should be efficiently analyzed. More specifically by analysis we mean development and implementation of algorithms for feature extraction (dots, lines, etc), intensity quantifications, patterns recognitions and visualization of results. To make analysis fast at such big volumes of data, these algorithms needs to be adapted to work on GPU and preferably written in Java. We are looking for an enthusiastic student who would develop software analysis workflow in collaboration with experimental scientists. Programming experience is a requirement and basic knowledge of mathematics and physics is a plus. If you are interested, please e-mail Lukas Kapitein (firstname.lastname@example.org) or Eugene Katrukha (email@example.com).
Internship Kole lab
Brain cells store and retrieve information by means of electrical excitability. The primary electrical event underlying the temporal- and rate coding schemes of single neurons is called the action potential. Over the last decade, high-resolution electrophysiological and imaging studies, including the findings from our laboratory (Kole et al., Neuron, 2007; Hallermann et al., Nat Neurosci, 2014), demonstrated that within neurons the action potential initiation site is spatially constrained to the axon initial segment. This unique domain is defined by a dense actin-spectrin filament network anchoring voltage-gated ion channels regulating voltage threshold and integrative properties of neurons. More recent developments in our group focus on newly identified ion channels and the contribution of glial cells to action potential generation. Using live electrophysiological and imaging methods together with high-resolution anatomical and computer simulations we characterize the structure-function relationships of channels and cellular structures and determine their contribution to the computational features of single neurons.
In our group we have a position available for a highly motivated master student, either for a computational or experimental project. Experience with electrophysiological recordings or live imaging would be an advantage but is not required. In the internship, students will be trained in the current physiology techniques. For more information and contact (firstname.lastname@example.org).
Internship Post lab