Research groups

[Page is still under construction!] Below you will find (for now) some of the research groups where you could do an internship.

Biomolecular Mass Spectrometry and Proteomics

Professor: Albert Heck
Interest area: Massa spectrometrie
Website: https://www.hecklab.com/

The study of all proteins that form the basis of life is called proteomics and is central to our research group Biomolecular Mass Spectrometry and Proteomics. The technique applied to research on the proteome, as the name of the research group suggests, is Mass Spectrometry (MS). Mass spectrometry is a technique that allows the characterisation of molecules in cells by breaking down molecules into ions and determining the mass-to-charge ratio. Do not be afraid of the complex theory behind the operation of this mechanism, many people in our research group do not deal with this on a daily basis. By using MS, interacting proteins and other biomolecules in cells can be identified. There are various specialisations within the research group and there is room for bachelor and master students who want to do an internship. The second year course Mass Spectrometry and Analysis gives a good introduction to our research area. Check out the website https://www.hecklab.com for more information about the people within the research group and current published articles.

Cellular Protein Chemistry

Professor: Stefan Rüdiger, Ineke Braakman
Interest area: Controlling protein damage, Protein Folding in the ER
Website: https://www.uu.nl/en/research/cellular-protein-chemistry

The section of Cellular Protein Chemistry is investigating how proteins in cells can reach their correct folding state, how helper proteins called chaperones help with this (Prof. Ineke Braakman and Dr. Peter van der Sluijs) and how these chaperones work exactly (Dr. Stefan Rüdiger). It uses, among other things, radioactive pulse chase and microscopic techniques to measure the kinetics of folding and transport processes of medically relevant model proteins, namely the envelope proteins of influenza and HIV virus, the LDL receptor (cholesterol uptake), and CFTR (Cystic Fibrosis), to be unraveled in living cells. To investigate how Hsp90 assists in the folding of substrate proteins, aggregation tests and fluorescence measurements are used to determine where and how the interaction takes place between the two. The research is not simple, but it is very challenging. If you want to know more, feel free to visit the east wing of the Kruyt building on the seventh floor.

Crystal and Structural Chemistry

Professor: Piet Gros, Eric Huizinga
Interest area: Protein Crystallography
Website: https://www.uu.nl/en/research/crystal-and-structural-chemistry

Within the Crystal and Structural Chemistry group, the 3-dimensional structure of proteins and protein complexes is studied with a focus on membrane-related and biomedical relevant processes. The group is divided into various subgroups with specific research themes such as the complement system (Piet Gros), blood clotting (Eric Huizinga) and communication between Glia cells and neurons (Bert Janssen), see the website for further subgroups. Molecular recognition and communication between multi-modular protein complexes play a major role in all these processes. To understand these processes, insight into the 3D structure of the protein complexes involved is crucial; it gives us an insight into the molecular interactions involved in recognition, provides insight into structural changes and leads to an understanding of the molecular mechanisms. The methods used for 3D structure elucidation are: protein crystallography, cryo-electron microscopy and cryo-electron tomography. The lab also consists of protein purifications and biochemical and biophysical analyses to determine protein quality, stability, functionality and protein interactions.

NMR spectroscopy

Professor: Marc Baldus, Alexandre Bonvien
Interest area: NMR spectroscopy
Website: https://www.uu.nl/en/research/nmr

Many students think NMR spectroscopy is complicated research. The theory behind NMR is indeed tricky, but most of us are not concerned with it on a daily basis. NMR spectroscopy is a technique for obtaining structural biological information. In the NMR spectroscopy research group, there are several divisions engaged in their own ongoing research. The research in the group of Dr. Hugo van Ingen focuses on the molecular basis of chromatin function, essential for the regulation of gene expression, replication and DNA damage repair. Marc Baldus employees conduct research on membrane proteins and complexes, but also on materials such as catalysts. Markus Weingarth’s group is working on peptides that prove very effective against multi-resistant bacteria, because of a unique affinity mechanism they run a very small chance of developing resistance. The staff of Prof. Alexandre Bonvin are, among others, working on the Haddock program that translates structural biological information (obtained by NMR) into models of biomolecular complexes. So very varied projects, but all very interesting.

Membrane Biochemistry and Biophysics

Professor: Antoinette Killian, Eefjan Breukink, Toon de Kroon
Interest area: Membranes
Website: http://mbb.science.uu.nl/

The research of the Membrane Biochemistry and Biophysics research group focuses on the molecular mechanisms behind processes involving biological membranes. Interactions between membrane proteins and lipids are essential for membrane biogenesis, membrane organisation and membrane function. The aim of the research is to unravel the molecular mechanisms underlying membrane assembly, organisation, homeostasis and function, with special emphasis on the lipid-protein interactions involved. Biophysical techniques used in this study include fluorescence spectroscopy, circular dichroism, preparation of model membranes, calorimetry (DSC, ITC), solid state NMR, thin layer chromatography, and mass spectrometry. These techniques are used in conjunction with peptide and protein synthesis/expression/purification, cloning, site-directed mutagenesis, use of microarrays, biomembrane isolation and treatment methods.

Cryo-Electron Microscopy

Professor: Friedrich Förster, Tzviya Zeev-Ben-Mordehai
Interest area: Structural Biology, Membrane Fusion
Website: https://www.uu.nl/en/research/cryo-em

Within the Cryo-Electron Microscopy research group, they are interested in the molecular organisation of biochemical processes and biomolecules within the cell. Research into these processes is done by using cryo-electron microscopy (EM). Cryo-EM is a technique that allows you to look at extreme magnifications of cells and its components, in which the sample (a biomolecular complex) is cooled to cryogenic temperatures in an aqueous environment. Cryo-EM makes it possible to make three-dimensional images of the biomolecular complexes to be studied in physiological conditions at extremely high resolution! For internships, there are opportunities for you to gain knowledge and training on protein expression and purification, cell cultures, molecular Cryo-Electron Microscopy/Tomography, Image processing and programming!

Chemical Biology and Drug Discovery

Professor: Geert Jan Boons
Interest area: Drug research
Website: https://www.uu.nl/en/research/chemical-biology-and-drug-discovery

The Chemical Biology and Drug Discovery (CBDD) group focuses on the chemical and chemo-enzymatic synthesis of complex biomolecules and employs these in analytical, biophysical and cell-biological experiments. Insights thus obtained can lead to new approaches for the treatment of diseases with unmet needs. CBDD is also interested in answering questions related to understanding, as well as influencing, carbohydrate-protein and peptide-protein interactions that underlie infections, cancer, and immunological and neurological disorders. Especially modified peptides and peptidomimetics, as well as carbohydrates and glycoconjugates, are synthesized and their properties examined. Research projects are often multidisciplinary and can have synthetic organic, chemical biological, analytical, and biological aspects. The research group is part of the Utrecht Institute for Pharmaceutical Sciences, as well as the Bijvoet Centre for Biomolecular Research.

Theoretical biology and bioinformatics

Proffessor: –
Interest area: –
Website: https://bioinformatics.bio.uu.nl/

The new theoretical techniques applied in the Theoretical Biology and Bioinformatics research group make it increasingly possible to study complex biological systems (consisting of interactive building blocks such as molecules, cells and organisms). The research group is divided into a Theoretical biology unit (led by Rob de Boer) and a Bioinformatics unit (led by Berend Snel), each with its own biological focus. What the research groups have in common is that they use computer biological techniques ranging from bioinformatics and mathematical modeling to computer simulation. These techniques are used, for example, for the study of the immune system, virus infections, evolutionary developments, genetic networks and genome evolution. The first-year biology course Systems Biology provides a good introduction to the role of theoretical research in biology. If this appeals to you, and you are interested in an internship, you can read further at http://tbb.bio.uu.nl for further information and an overview of the research that all members in our research group are conducting.

Developmental Biology

Professor: –
Interest area: –
Website: http://web.science.uu.nl/developmentalbiology/

This research group focuses on understanding the molecular processes that allow a fertilized egg to develop into a complex organism (human or animal). The most important questions include: How does cell division of stem cells lead to the formation of both new stem cells and differentiated cells? How do cells acquire the correct internal organization, and what happens when this is disrupted? What forms of translation regulation are important for controlling proliferation and differentiation? How do stronger cells compete with weaker cells to determine tissue formation? By gaining detailed insight into normal developmental processes, they also aim to better understand how the dysregulation of proliferation and differentiation contributes to developmental disorders and diseases such as cancer.

Cellular Dynamics

Professor: Anna Akhmanova
Interest area: –
Website: –

This research group falls under the research division “Cell biology, Neurobiology and Biophysics” (often abbreviated as Cell Biology), here they use other actions to arrange a thesis internship, read that here. In the Cellular Dynamics research group, they study the organisation of the cytoskeleton and various transport processes in the cell, which contribute to cell polarisation, differentiation, vertebrate development and diseases. There is a great focus on research into the microtubule cytoskeleton, for example which proteins interact with the two ends of the microtubules. During this research, high-resolution live-cell imaging and quantitative analysis of cytoskeletal dynamics and different methods that can identify protein-protein interactions (in vitro binding studies, pull-down assays, yeast-two hybrid screens and protein mass spectrometry) are used. identification). For example, the microtubule study uses Plus-end tracking proteins (+TIPs), a group of factors that interact specifically with the growing end of microtubules. For more examples of current research; see the website.

Animal Behaviour and Cognition

Professor: –
Interest area: –
Website: –

Animal Behaviour and Cognition (AB&C) conducts research on animals that live in social groups. The research mostly focuses on primates, but also includes birds and other animal species. This research contributes to how we as humans view and interact with animals. Thus, the research of AB&C finds applications in animal welfare and nature conservation. Animals in various habitats are studied to achieve this; in the wild, the zoo, and/or breeding colonies of biomedical research centers. In addition to fundamental scientific research, the AB&C group also focuses on education. Within the undergraduate biology program, AB&C provides courses in the study path Behavioural Biology, and within the Master’s programme Environmental Biology the group provides the Behavioural Ecology track.

Microbiology

Professor: –
Interest area: –
Website: –

At its core, the Microbiology group is about performing research on fungi and bacteria. The research is conducted in collaboration with companies, universities, and the UMC Utrecht. This research is both fundamental and applied and is of great societal importance, both in the biotechnological and medical fields. The group is divided into different projects, such as the Behavior Manipulating Fungi group, which investigates how pathogenic fungi can manipulate the behavior of insects so they can help the fungus spread better. In the so-called “zombie ant” model system, various omics analyses are being used to study which proteins and genes are involved. Microbiology is part of the Environmental Biology, Molecular and Cellular Life Sciences, and Bio-Inspired Innovation Master’s programmes. If you are interested in fundamental research or a more applied internship in microbiology, you’re always welcome to join this research group.

Plant-Environment Signaling

Professor: –
Interest area: –
Website: –

The Plant-Environment Signaling group (formerly known as Plant Ecophysiology) conducts research on the intricate interactions between plants and their environment. Specifically, the research focuses on the molecular and physiological mechanisms that underlie plant growth and development, as well as how plants adapt to a changing environment. The group’s research encompasses several areas, including plant development, biological timing, resilience to abiotic stress, and the processing of light cues associated with high planting density. Through their work, they aim to develop a scientific foundation for creating crops that are resilient and adaptable to future environmental changes.

Plant-Microbe Interactions

Professor: –
Interest area: –
Website: –

In nature, plants are attacked by a multitude of pathogens and pests that can cause major crop losses in agriculture. To protect themselves, plants can activate a sophisticated immune system. Moreover, they recruit beneficial microbes to their root system that help them to grow better and boost immune responses. The Plant-Microbe Interactions group aims to unravel at the molecular level how the plant immune system orchestrates interactions with beneficial microbes, pathogens, and insects. This provides a rational basis for developing sustainable strategies for disease resistance in next-generation crops that produce more with less input of fertilizers or pesticides. In 2022, they received the Spinoza Prize for our research.

Plant Stress Resilience

Professor: –
Interest area: –
Website: –

Plants are essential for our life. They represent a crucial source of food for both humans and animals. Plants, like all living organisms, sense environmental stresses such as flooding, increased salinity, temperature extremes, and oxygen deprivation. Plants exhibit a remarkable ability to react to these stresses, likely activating responses that would allow them to escape, tolerate, or cope with such conditions. The research group focuses on understanding how plants respond to these stresses. They aim to identify and discover the underlying molecular mechanisms and genetic factors that are essential to make plants able to react and resist. They are uncovering novel methods to modulate stress tolerance in different plant species, including crops. To do this they use a range of day-to-day tasks including plant phenotyping, regeneration of mutant plants, and a wide range of cutting-edge assays for testing responses to these stresses. M(B)LS graduates with a background in molecular biology and genetics could contribute to our research questions by joining our experimental design discussion, laboratory research, and data analysis. Eventually, M(B)LS can help us in our crucial role of translating scientific findings into practical applications, such as developing stress-tolerant crops for a more sustainable agriculture.

Translational Plant Biology

Professor: –
Interest area: –
Website: –

They translate fundamental scientific knowledge in plant biology, mostly in plant development and immunity, into technologies for crop improvement to help reduce the environmental impact of agriculture. For this they integrate molecular biology, genome editing, synthetic biology, and bioinformatics / artificial intelligence to investigate processes controlling plant architecture (Marcel Proveniers), disease resilience (Guido van den Ackerveken, Dmitry Lapin), and epigenetics (Jason Gardiner). They collaborate extensively with the crop breeding and Research & Development industry to co-develop technologies for sustainable agriculture. Chair of the group, prof. dr. Guido van den Ackerveken, leads several large national programs on this topic, e.g. CROP-XR and LettuceKnow. If you want to learn more about TPB research, contact us via email on the TPB group page or LinkedIn.

Genome Biology and Epigenetics

Professor: –
Interest area: –
Website: –

The research group Systems Biology of Gene Regulation (division of Genome Biology and Epigenetics) attempts to understand how information processing is regulated at the level of chromatin modifications and DNA sequence. A multitude of DNA sequence-dependent and -independent interactions coordinate the spatiotemporal recruitment of transcriptional regulators to the genome and are required for tissue-specific gene expression and cell identity. Interference or lack of specificity in this process can give rise to various human diseases. However, the underlying mechanisms that mediate these precise interactions are not fully explored. The group attempts to cover this gap by researching interactions between transcriptional and chromatin regulators with the genome, and how they impact biological processes. Towards this, the group combines various experimental and computational strategies, including genome and epigenome engineering, genome-wide studies, proteomics, single-cell measurements and computational modelling. This integrative approach allows this research group to understand gene regulatory mechanisms in a quantitative and functional manner.

Pharmaceutics

Professor: –
Interest area: –
Website: –

The research group Pharmaceutics is involved in the design and pre-clinical testing of tailor-made drug delivery systems for site-specific, time- and/or rate-controlled delivery of small molecular weight drugs, therapeutic proteins, nucleic acids, and antigens for therapy and prevention of life-threatening diseases such as cancer, inflammation, and infectious diseases. Examples include nanomedicines for targeted delivery of cytostatics to tumors, mRNA vaccines, synthetic vectors for gene therapy, and 3D scaffolds for tissue engineering applications. The combination of complementary fields of expertise brought together in the research program is unique and allows the development of novel drug delivery systems from scratch up to the preclinical testing phase. The research group has intensive collaborations with academic, industrial, and governmental groups. Research(ers) belonging to this group can be encountered by M(B)LS students in courses such as Genomes, Cells & Tissues and Future Medicines, and in the Master’s programme Drug Innovation.

Pharmacoepidemiology and Clinical Pharmacology

Professor: –
Interest area: –
Website: –

The division of Pharmacoepidemiology and Clinical Pharmacology contributes to a better understanding of the variability in medicines’ use and patient outcomes, both from a clinical and policy, as well as a methodological perspective. Despite extensive testing before marketing approval, variability in drug response (both efficacy and safety) is more the rule than the exception when medicines are used in daily clinical practice, i.e. in real life. The research program is inspired by societal needs to ensure that medicines deliver their full therapeutic potential. The program has a systems therapeutics focus, integrating various disciplines, dimensions, and phases of a product life cycle in order to learn about (rather than confirm) drug effects and their determinants both before and after initial marketing approval of the product. The primary conceptual anchors in the research strategy of the program are Epidemiological Methods, Clinical Pharmacology and Systems Therapeutics. Research is organized into three centers with a strong conceptual research strategy: the Centre for Pharmacoepidemiology, the Centre for Clinical Therapeutics, and the Centre for Pharmaceutical Policy and Regulation.

Pharmacology

Professor: –
Interest area: –
Website: –

Research in the Pharmacology group focuses on the basic mechanisms underlying non-communicable disorders (NCD) and their pharmacological manipulations via drugs, biologicals, and/or food components. The division aims to gain deeper insight into the pathways in which cells and mediators of the immune and/or central nervous systems get activated and how they interact, in order to develop new concepts for prevention and/or treatment of developed disorders with a strong focus on inflammation management. Furthermore, understanding the pathways that can be pharmacologically triggered to enhance repair and regeneration processes after organ injury, aiming at elucidating novel bio-inspired therapeutic strategies, are of interest. M(B)LS students participating in elective courses like FABA211 Airways or FABA212 Nutrition have touched upon such pharmacological topics. These practical, interdisciplinary and/or translational research topics make this department interesting for students of different programs, including M(B)LS students.