MSc projects on offer

Gin, beer, and moonshine: New tests to detect methanol for home brewers and distillers

BSc or MSc project

Contact: dr. Pim de Haan, pim.de.haan@rug.nl

While ethanol is the main product when home brewers and distillers ferment high-starch materials such as wheat, potatoes, and rice, there often is a small quantity of methanol present. Methanol is far more toxic than ethanol, and it may cause neurotoxicity and blindness. In this project, you will develop a new assay to quantify traces of methanol in distillate, i.e. in the presence of large concentrations of ethanol. You will develop a test with a colorimetric read-out on paper based on the selective reaction between the dye, basic fuchsine, and methanol. Therein, the intensity of the resulting color is a measure for the methanol concentration. You will do control experiments using mixtures of methanol and ethanol, and home-brewed distillate samples, both with your new method and with conventional gas chromatography.

Techniques: Paper microfluidics, colorimetry, UV/Vis spectroscopy, gas chromatography.

3D Printing for Biochemical Assays (2 spots available)

Contact: Pim de Haan, pim.de.haan@rug.nl; Prof. Sabeth Verpoorte, e.m.j.verpoorte@rug.nl

Duration: 20 or 30 weeks (30 or 45 ECTS)

Relevant techniques: 3D printing (stereolithography, fused deposition molding); computer-aided design (CAD); microfluidics; biochemistry; UV spectrometry.

Summary: Immobilized enzyme reactors (IMER) have numerous applications in analytical chemistry and other fields. We propose to make a miniaturized IMER (µIMER) for analytical purposes, in which an analyte is enzymatically converted to a product. The enzymes are immobilized inside a 3D-printed cartridge, which allows for the system to be used multiple times. Immobilization of enzyme inside a microchannel leads to a very high local concentration of enzyme, which should significantly speed up reactions (Michaelis-Menten kinetics). The MSc student is expected to design, develop, and characterize such a microfluidic system with computer-aided design (CAD) and 3D printing, any other techniques available in our lab may be used as well.

Translational studies on mechanisms and treatment of Amanita Phalloides intoxications

Contact: B.G.J. Dekkers, dr. I.A.M. de Graaf and prof. dr. D.J. Touw

Duration: 9 months (masterproject)

Location: UMCG, department of Clinical Pharmacy and Pharmacology / RUG Department of Pharmaceutical Analysis

Start date: no preference

Background: Amanita Phalloides, also known as the death cap, is one of the most toxic mushrooms known to man. Every year patients are admitted at the UMCG with a (potential) intoxication with this mushroom. Key characteristics of this intoxication are hepatic and renal failure, but recently we found that hematotoxicity occurs as well in these patients. Several antidotes are available, but their use is mainly based on in vitro studies and case reports.

Approach: Within our group we have several ongoing translational projects studying the mechanisms of α-amanitin toxicity, the main toxin of the Amanita Phalloides, and the treatment of this intoxication. These projects include studies using liver and kidney slices and hematopoietic cells. In addition, we are setting up an assay to be able to detect  α-amanitin to aid diagnostic and study toxicokinetics of this toxin.

A salivary gland on a chip – studying epithelial-immune cell interactions in Sjögren’s syndrome

MSc Project:   Pharmacy / Biomedical engineering / Medical Pharmaceutical Sciences / Molecular medicine and innovative treatment

ECTS:  Preferably 45 ECTS; 30 is possible.

Supervisors: Dr. Gwenny Verstappen (Rheumatology and Clinical Immunology, UMCG, g.m.p.j.verstappen umcg.nl); Dr. Pim de Haan (Pharmaceutical Analysis, UG, pim.de.haan rug.nl).

Start date: Fall or Winter 2023

In Sjögren’s syndrome, functioning of the salivary glands is impaired due to a chronic autoimmune reaction. It is hypothesized that in the pathogenesis of primary Sjögren’s syndrome, the interaction between the epithelial cells of the glandular duct and various immune cells plays a key role [1]. Researchers in the UMCG are able to grow patient-derived salivary gland organoids. However, it is not yet possible to study the interaction between the salivary gland epithelium and patient-derived immune cells (e.g. B cells) in a dynamic setting that mimics the in vivo situation. In this master project, you will design an organ-on-a-chip [2] with salivary gland cells. The epithelial cells will be cultured in small channels, with immune cells supplied by different microchannels representing blood (or lymph) vessels. You will investigate the interaction between the cells, as well as influence these processes by adding inflammation-inducing agents. The ultimate goal of the salivary gland on a chip is to generate a screening platform for pharmacotherapeutic modulation of epithelial-immune cell interaction in Sjögren’s syndrome. This project is a collaboration between Rheumatology and Clinical Immunology (UMCG) and Pharmaceutical Analysis (UG), and you will work in both of these departments.

Skills you will learn: cell culturing; (live) cell staining; microfabrication.

[1] Verstappen et al. Nat Rev Rheumatol. 2021, https://doi.org/10.1038/s41584-021-00605-2.

[2] Leung, de Haan et al. Nat Rev Methods Primers 2022, https://doi.org/10.1038/s43586-022-00118-6.

A Model-based Approach to chart less common drug metabolism and excretion Pathways in Pregnancy (MAPP)

Supervisors:   dr. P. Mian and prof. dr. D.J. Touw (d.j.touw umcg.nl)

Duration: 9 months (masterproject)

Location: UMCG, department of Clinical Pharmacy and Pharmacology

Start date: no preference

Background: Pregnant women are generally excluded from clinical trials. As a result, there is a lack of maternal exposure data of drugs, which complicates the selection of the best treatment options and dosing when pharmacotherapy is indicated during pregnancy. At present, it is impossible to study the pharmacokinetics of each drug during every trimester of the pregnancy  and for each specific condition (eg. kidney function disorder) or the use of co-medication in the clinical setting. It is therefore necessary to mechanistically describe metabolism and elimination of drugs (taking into account transporters) to mechanistically reach evidence-based dosing.

Approach: In terms of maternal pharmacokinetics, many physiological changes have already been incorporated in the computer program models (PK-sim® or SimCYP®), such as changes in body composition and changes in concentrations of drug binding proteins in plasma, as well as up or downregulation of several drug –metabolizing enzymes (e.g. cytochrome-P-450 enzyme (CYP)3A4).  However, information on less common elimination pathways (e.g. phase II enzymes, such as Uridine 5'-diphospho-glucuronosyltransferase (UGT)) is lacking.  The project will focus on performing physiologically based pharmacokinetic-predictions for model compounds of UGT1A, by modeling a number of prototypical drugs (lamotrigin, paracetamol and raltegravir) and validating predictions against therapeutic drug monitoring data in pregnant women. These predictions will result in one way of mechanistically-based dosing for UGT1A eliminated drugs within the pregnant women!

The use of livers from surplus slaughterhouse animals (Sus domesticus, Pig) for drug toxicity and metabolism studies.

Supervisor: Inge de Graaf (i.a.m.de.graaf rug.nl) ; Eduard Post

Preferred start date: September-December 2023

Number of ECTS: 40/45

Precision-cut liver slices have been used for several decennia and have proofed their usefulness for studies on metabolism and toxicity of pharmaceutical drugs. Ideally, because of species differences and to avoid the use of laboratory animals, these slices are prepared from human livers. However, the supply of human liver tissue (usually tissue that was disapproved for transplantation or surgical waste material) is limited and unpredictable. In addition, results obtained are often highly variable and therefore difficult to interpret.

As an alternative to human and laboratory animal liver, we may use the livers of slaughterhouse surplus animals. Particularly porcine livers are regarded as having value due to their similarities to humans in terms of size, anatomy and physiology. However, the utilization of surplus slaughterhouse animals involves donation after circulatory death (DCD), which refers to the procurement of organs after irreversible cessation of circulatory function. Consequently, livers collected from abattoirs are exposed to (extended) warm ischemia, which may greatly affect the viability and functionality of the slices.

Recently, encouraging results have been reported using machine perfusion, which is a novel strategy for preservation of DCD grafts. Machine perfusion involves organ perfusion with a controlled flow of perfusate, thereby fostering the preservation of organ microvasculature, the delivery of oxygen and nutrients, and the elimination of toxic metabolic waste. Recent studies have shown that  normothermic machine perfusion substantially ameliorates the metabolic and functional parameters of DCD livers subjected to extended warm ischemia time (1 hour). In another study, it was demonstrated that porcine DCD livers, subjected to one hour of warm ischemia, exhibited a 100% seven-day survival rate when treated with normothermic extracorporal perfusion.

The aim of this student research project is to assess whether liver slices of slaughterhouse DCD livers from pigs, with or without normothermic extracorporal perfusion, maintain viability and reactivity against hepatotoxic compounds, such as acetaminophen, LPS and alpha-amanitin. The student will learn how to perfom machine perfusion and prepare and incubate liver slices and utilize biochemical and analytical assays to assess metabolism and toxicity.

The influence of the tissue microenvironment on drug action

M.Sc. research project (laboratory based)

Supervisor: Dr. Anika Nagelkerke, a.p.nagelkerke rug.nl; daily supervision of the project will be provided by one of the PhD students.

Number of students: Multiple projects are available. Please get in contact for further details.

Preferred start date: Flexible.

Project description

The cells in our bodies do not grow in a vacuum. Instead each cell is surrounded by a complex tissue microenvironment, with both biological properties (e.g. other cells) as well as physical characteristics (e.g. structural components like extracellular matrix). In recent years, it has been realized more and more that this environment is of great importance for cell behaviour, but importantly also response to therapy. As such, replicating the various parameters of the tissue microenvironment in laboratory models for disease is a key area of interest. Still, new technologies are needed to fully incorporate microenvironmental parameters in the laboratory models that are used to study disease and associated therapy efficacy.

In this project, you will further develop laboratory models that incorporate the tissue microenvironment. Parameters of interest are: gradients in oxygen, mechanics and microarchitecture of extracellular matrix, microbial factors and environments with established  comorbidities. Your project will focus on one of these. You will learn how to design and fabricate model systems. You will use basic cell culture techniques, including 3D culture and co-cultures, as well as various biomaterials and microfabrication technologies. You will use microscopic analysis to study the behaviour of the cultured cells in the model systems, e.g. by immunofluorescent stainings. One key area of interest is cancer and the tumour microenvironment that is associated with this, focussing especially on sensitivity to common chemotherapeutics in different environments.

Examination of mechanisms and effectiveness of antidote (combination) therapy of Amanita Phalloides intoxification

Supervisors: Inge de Graaf, Daan Touw

The mushroom Amanita phalloides is the cause of 90% of deadly mushroom intoxications in the Netherlands. The liver is one of its main targets, since it is one of the first sites of exposure after oral ingestion of the mushroom. Moreover, the liver highly expresses several OATPs (organic anion transporter proteins) that are involved in the cellular uptake of the mushrooms’ toxins, α- and β-amanitin. Once taken up in the liver, these compounds inhibit RNA polymerase II resulting in inhibition of protein synthesis and ultimately in induction of apoptosis. In patients with α- and β-amanitin intoxication, liver failure is often seen, but acute kidney injury also occurs.

In the clinic, patients who are intoxicated with Amanita phalloides toxins are treated with different antidotes or combination of antidotes that aim at preventing the uptake of the toxins in the liver cells. These antidotes include silibinin, N-acetylcystein and penicillin, or combinations hereof. Particularly silibinine and penicillin are chosen because of their ability to (competitively) inhibit OATP. However, there is only weak clinical proof of their effectiveness against the intoxication.

In this project, we aim to examine the effectiveness of the antidotes against liver toxicity caused by α- and β-amanitin. For this purpose, we will use precision-cut liver slices (PCLS), preferably from human origin to avoid translational issues (α- and β-amanitin intoxication is highly likely to be species specific). PCLS are mini-models of the liver that contain all different liver cells in their natural configuration and have been shown to maintain expression of several (drug) transporters during culturing. The student will use a newly developed ELISA (enzyme linked immunosorbent assay) method for analysis of α-amanitin toxins in liver slices that are treated with amanitin and the antidotes. These concentrations will be linked to changes in viability of the slices.

Techniques: ELISA, preparation and incubation of PCLS, biochemical assays for viability determination of PCLS.