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 2022

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 influence of the tumour 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.

Project description: Despite decades of research, cancer remains a disease that is challenging to treat. To generate a better understanding of the disease, cancer cells themselves have been studied in great detail. However, in recent years, it is realized more and more that also the environment in which the cancer cells reside is of great importance for their behaviour and response to therapy. As such, replicating the various parameters of the tumour microenvironment in laboratory models for cancer is a key area of interest. Still, new technologies are needed to fully incorporate the microenvironment in the laboratory models that are used to study cancer and associated therapy efficacy.

In this project, you will further develop laboratory models for cancer in which the tumour microenvironment is incorporated. Parameters of interest are: gradients in oxygen, mechanics 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 for cancer. 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. Sensitivity to common therapeutics in different environments will be evaluated using live cell imaging.

Development of a novel human in vitro lab on a chip system for cancer neuroscience studies

Supervisors: Dr. Mihaly Balogh (m.balogh rug.nl), Prof. Reinoud Gosens

Starting date: based on discussion (academic year 2022/2023)

There is continuously growing attention on the less understood interplay between cancers and the nervous system, including peripheral neurons (a new emerging scientific field: “cancer neuroscience”). As an apparent example, clear evidence shows shared systemic processes involved in both the development of cancer and neuropathic pain. In addition to their roles in tumor growth, some of the chemokines (e.g. complement 5 (C5), or the CXCR3 receptor, and its ligand CXCL10) also play important roles in the development of neuropathic pain, including chemotherapy-induced peripheral neuropathy (CIPN). Despite these observations, very few studies have investigated sensory neuronal dysfunction directly induced or influenced by tumor growth or how the tumor induced alterations might influence neurons.

We have already shown – for the first time in an in vivo preclinical setting –  that the development of colon cancer indeed leads to significant systemic sensory neuronal dysfunction in mice. These alterations include a significant decrease in the epidermal nerve fiber density of mice, in addition to mitochondrial dysfunction and altered Ca²⁺-homeostasis in the dorsal root ganglia of tumor bearing animals. These changes interestingly also underlie symptoms of CIPN. That is, colon cancer development seems to be leading to similar neuronal damage as in the case of CIPN, even without introducing any form of chemotherapeutic treatment. These observations seem to be extremely important for future studies aiming to determine risk factors of severe CIPN development (develops in about 30% of colon cancer patients).

The main aim of the project is to develop a fully new, completely human in vitro lab on a chip system to investigate the direct neuronal-cancer interactions.

Human pluripotent stem cells will be developed into sensory neuronal cells and co-cultured with human colorectal cancer cells by the utilization of our novel two-compartment lab on a chip system. The candidate would directly investigate the effects of human, HCT-116 colon cancer cells (and their released mediators) on neuronal growth and functions (e.g. axon growth) and also how the tumor growth is altered by the presence of neuronal mediators.

By the end of the proposed project, the candidate has successfully contributed to the development of a novel in vitro system for cancer neuroscience studies.

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.