Measure
We can monitor molecules in complex samples or in single cells, from chemicals to metabolites, RNA or proteins. We have sensitive assays to measure the impact of molecules on biological functions, from growth to toxicity to endocrine disruption.
Methods
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Effect Directed Analysis (EDA)
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Analytical chemistry
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(Cell) Biology
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Single-cell
Effect Directed Analysis (EDA)
In effect-directed analysis, we combine chromatography for fractionation of complex samples, and split these fractions for simultaneous functional assessment (cell-based assay) and compound identification (using mass spec).
In this way we can identify bioactive compounds in complex samples such as environmental samples, snake venoms, foods or body fluids.
Analytical chemistry
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Techniques
Mass spec-based methods
We have advanced analytical methods for metabolomics, proteomics and glycomics for the analysis of human fluids, intracellular metabolites, tissues and cell culture media. We hyphen separation techniques as HPLC, CE and GC with high-end (tandem) mass spectrometry (high-resolution, ion mobility and UVPD/IRMPD). We also have MS-based imaging facilities.
Contacts: Pim Leonards, Govert Somsen, Sofia Moco
NMR and crystallography
We have 300 – 600 MHz NMR machines for compound identification and analysis of complex fluids for metabolite quantification.
For protein structure determination, the workflow includes liquid handling for sample crystallization, optimizing crystals, crystal handling including cryo-protection and storage. Diffraction analysis and data collection is done on an in-house, state of the art Bruker D8 Quest X-ray source attached to an cutting edge PhotonII detector including downstream software suits for structure determination.
Contact: Elwin Janssen (nmr.beta@vu.nl).
Techniques
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(Cell) Biology
AIMMS has an array of methods, model systems and assays to monitor the impact of molecules on biological function. These include
- multicellular systems such as Zebrafish (contact Wilbert Bitter), C elegans (contact Samantha Hughes), organ-on-a-chip (contact Paul Jennings)
- cellular systems such as iPSC cells (https://www.eye-openers.nl/nl/seethecast/anja-wilmes/), cell (co-)cultures, complex in vitro models (contact Timo Hamers), organoids (Anja Wilmes), bioreactors and microfluidic setups (Bas Teusink)
- biochemical assays, including (receptor) binding & enzyme assays (Iwan de Esch), (GPCR) signalling, nanobodies (Martine Smid), Seahorse analyzer for metabolic functions (Paul Jennings).
Single-cell
We have different methods to analyze biological states at the single cell level, largely based on fluorescent probes and biosensors in combination with flow cytometry and advanced (high content) microscopy. We collaborate closely with the AUMC technology center in the same O2 building. We combine these techniques with the cell-based methods. We have dedicated image-analysis tools and expertise based on AI/ML techniques to turn images into quantitative data.
Techniques
Metabolites
Fluorescent protein based biosensors allow the dynamic, continuous, measurement of specific metabolites at single cell and even cell-compartment resolution. We apply , test, improve and develop such biosensors in house. Examples are sensors for pH, cAMP, ATP and recently glucose.
Intracellular pH in yeast cells analyzed with dynamic flow cytometry reveals two distinct subpopulations. (contact: Johan van Heerden, Bas Teusink)
RNA
RNAs can be detected at a single molecule level with RNA-FISH, which counts single mRNA molecules in fixed cells. We have this technique operational for bacteria, yeasts and fungi, and mammalian cells. We can also measure RNAs with time-lapsed microscopy using (variations of) the MS2 system. (contact: Evelina Tutucci)
Example of RNA-FISH in yeast: CLN2 mRNA smFISH (yellow), Tubulin IF (magenta), DAPI (blue), DIC (gray)
Sample projects
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