Major Research Project Molecular & Computational Toxicology (C, E, S)

URL study guide

https://studiegids.vu.nl/en/courses/2024-2025/XM_0026

Course Objective

The aim is to obtain experience in scientific research including the design and execution of experiments and to critically interpret and reflect on the experimental results. The project will be conducted within the field of molecular and computational toxicology, in one of the following settings:
- University or Academic hospital
- Research institute
- Company The internship can be performed either within the Netherlands or abroad.

Course Content

The specific content of the project depends on the available projects and timing of the internship, but roughly deals with one of the following areas of research:
- Biomolecular Simulation & Modeling (dr. Daan Geerke): computational methods are developed to characterize the interaction between compounds with different proteins and to predict their mode of binding and action. In close collaboration with the experimental colleagues within the division, a special focus is possible on predicting unwanted binding to drug-safety related proteins and/or the formation of metabolites by drug-metabolizing or biocatalytically active enzymes. The binding affinity and -selectivity of compounds and metabolites are calculated using efficient and accurate computational methods, and research on and development of improved biomolecular models or force fields is possible as well.
- In vitro cell toxicology (Prof. dr. Paul Jennings): Utilisation of cultured human cells, including primary cells, renal cell lines, hepatic cell lines and induced human pluripotent stem cells for investigating mechanisms of toxicity. Assays employed include, cytotoxicity assays, stress assays, differentiation markers, mitochondrial injury (Seahorse bioanalyser), barrier function, impedance (xCELLigence), fluorescent reporter assays, transcriptomics and biokinetics. Attention will be paid to setting up new research/experiments, using state-of-the-art experimental or computational techniques, and data analysis and interpretation.

Teaching Methods

Literature review, formulating a research question, conducting experiments and/or simulation, documentation (e.g. lab journal, adherence to protocols, appropriate meta tagging and documentation of workflows), data analysis, reporting on results in group meetings, a written thesis and final presentation within the research group.

Method of Assessment

Academic attitude, execution, oral presentation, and written thesis

Literature

Starting literature will be provided by the supervisor. The first 1-2 weeks of the traineeship will be spent on literature reading and preparation for the project.

Target Audience

Communication, Education, or Society variant of the following tracks of the master Drug Discovery Sciences: Molecular Toxicology, Computer-Aided Drug Design (computational projects).

Custom Course Registration

The number of internal (VU) internship positions is limited. Candidates are selected based on their motivation (in form of a motivation letter), and previous experience (outlined in CV). Please refer to the canvas site “Master Drug Discovery Sciences” for more information regarding this application procedure. Be aware that a selection procedure applies to most external positions as well. Before the start of the project an internship agreement, which includes a non-disclosure agreement has to be signed by all involved parties and the project proposal has to be approved by the VU supervisor via the online internship management system. See the “Master Drug Discovery Sciences Internship manual” for more information on the rules and regulation regarding internships. Contact potential VU supervisors from the group for more information on different projects (see Canvas community "Master Drug Discovery Sciences") If after reading the manual you still have questions regarding the process related to internships, admission, approval, etc., please contact the internship coordinator via [email protected].

Additional Information

The standard length of a major internship is 24 EC (4 months), which can be extended to 36 EC (6 months in total). Make sure you discuss your personal education plan with your master (track) coordinator well in advance. See the “Master Drug Discovery Sciences Internship manual” for more information (rules, regulations, tips, etc.) on the internship process. This manual can be found on the canvas community “Master Drug Discovery Sciences”.

Entry Requirements

Entry requirements with respect to attained courses and number of credits apply. See the Education and Examination regulations and the internship manual Drug Discovery Sciences. For questions, consult the internship coordinator well in advance ([email protected]).