Publication date:
March 9th 2021
We are looking for a talented PhD student to study herpesvirus-host interactions in neuronal cells using an integrative structural biology approach. You will focus on the interaction of the herpesvirus fusion protein gB with Myelin Associated Glycoprotein using modern tools in structural biology such as cryo electron microscopy and mass spectrometry, as well asand biophysical and cell biological techniques. Moreover, you will construct interaction and imaging probes to identify additional interactors on the surface of neuronal cells and image gB-receptor interactions in a cellular context. The position is part of the Institute for Chemical Immunology (https://chemicalimmunology.nl/) and you will be co-supervised by Bert Janssen and Joost Snijder at Utrecht University.
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Publication date:
Feb 8th 2021
Protein lipidation is the covalent attachment of lipids to proteins. Despite the important role of this fatty posttranslational modification in health and disease, knowledge about these fatty modifications is lagging behind other posttranslational modifications, such as phosphorylation and acetylation. Biomolecular mass spectrometry and proteomics seeks a highly motivated, high-potential candidate for a PhD position in a research project studying the role of protein lipidation in neurological disorders. In this project, you will work at the interface of chemistry and biology. You will contribute to the development of new chemical biology and proteomics methodologies to study the regulation of protein lipidation, focusing on S-palmitoylation, aiming to reveal how these modifications affect brain proteins, especially those that are linked to neurological disorders.
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We are looking for a versatile and driven candidate, preferably with a background in chemical biology/molecular biology and who has:
Ideally, you also have:
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Publication date:
Jan 25th 2021
Regulatory T cells inhibit the response of conventional T cells to self- and foreign antigens. Regulatory T cells thereby prevent autoimmune reactions, but can also impede anti-tumour immunity. The activation of regulatory and conventional T cells requires that these cells undergo changes in their metabolism. The exact mechanisms underlying such metabolic switches differ between various T-cell types and are largely unknown. By mapping metabolic differences between T cells types, novel targets for therapeutic intervention can be identified, which could benefit patients suffering from for example autoimmune diseases or cancer.
In this collaborative project between Utrecht University and the Leiden University Medical Centre, you will combine mass spectrometry and metabolomics with immunology to study the metabolism of regulatory and conventional T cells. You will develop mass spectrometry methods to measure metabolic activities in human T cells and use these to identify targetable metabolic pathways in T cells. You will also become part of the ‘Institute for Chemical Immunology’, which brings together chemists and immunologist working across the Netherlands. You ideally have a background in metabolism or immunology. Hands-on MS experience is preferred, but not essential at the start.
Changes in metabolism are increasingly regarded as one of the hallmarks of cancer cells. Malignant cells rewire multiple aspects of their metabolism to fulfil the higher demand for energy, to produce building blocks for proliferation and to maintain their redox balance. Recent studies show that metabolism is further adjusted when cells become resistant to anti-cancer therapies. Metabolism thereby offers novel entry points that can potentially be exploited to overcome drug resistance in cancer.
In this interdisciplinary project, you will bridge mass spectrometry and metabolomics with cancer biology to study how metabolic changes contribute to drug resistance in cancer. You will develop innovative metabolomics methods to study metabolism in complex in-vitro model systems such as organoids, and apply these to identify novel targetable metabolic pathways in drug-resistant tumours. You ideally have a background in metabolism or experience in working with complex in vitro models. Hands-on MS experience is preferred, but not essential at the start.
We are looking for enthusiastic, highly motivated candidates, who are interested in undertaking an interdisciplinary project at the interface of Metabolomics, Metabolism and Immunology and/or Cancer Biology. You are hands-on, independent and have a passion for science.
You also have:
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Publication date:
Oct 1st 2020
As our new Technician you will assist in the general research projects, with emphasis on proteomics workflows consisting of sample preparation, chromatographic separation, and MS-based characterization and quantitation of peptides and proteins. In addition, you will support the group by measuring intact native proteins with specialized mass spectrometry instrumentation, like HDX, Orbi-traps and TOF’s. Part of your time will be spent managing and running a fee for service to biopharmaceutical companies, by solving ‘research’ questions using native mass spectrometry. You will support the proteomics research by maintaining analytical equipment such as the HPLC (RP, SEC, IEX, HpH), centrifuges, etc. Furthermore, you will maintain the stock of consumables and materials and where needed assist in testing and improving the used methodology and instrumental setup.
We are looking for a hands-on, flexible, self-motivated colleague who is also a team player, open minded and creative and last but not least: you are driven by knowledge and results through your passion and enthusiasm!
You also have:
In addition to the employment conditions laid down in the cao for Dutch Universities, Utrecht University has a number of its own arrangements. For example, there are agreements on professional development, leave arrangements and sports. We also give you the opportunity to expand your terms of employment yourself via the Employment Conditions Selection Model. This is how we like to encourage you to continue to grow.
Publication date:
Sept 3rd 2020
Signalling events between proteins, as well as protein localization, are highly and specifically regulated by the post-translational modifications (PTMs) that they can transiently harbour. Of these PTMs, phosphorylation, glycosylation and acetylation have been widely studied and characterized. Protein lipidation, the covalent attachment of a lipid group to a protein, is much less studied, but thought to be equally important. In addition to its well-established important role in fundamental biology, protein lipidation has been associated with multiple neurological diseases, including Huntington’s disease and Alzheimer’s disease.
In this project, you will work at the interface of chemistry and biology. You will develop new chemical biology and proteomics tools to study the regulation of protein lipidation, focusing on S-palmitoylation, aiming to reveal how these modifications affect brain proteins, especially those that are linked to neurological diseases. You have ideally a background in chemical biology, hands-on MS experience is preferred, but not essential at the start.
Publication date:
Sept 14th 2020
Immuno-oncology is a promising new area within the field of basic, translational and clinical cancer research and recent years have seen breakthroughs where (otherwise untreatable) patients have been cured by novel immunotherapies. Immuno-oncology focusses on understanding the relationship between the tumor and the patients’ own immune system, with the aim to target the cancer or microenvironment with antibodies or immune cells. Central to this approach is the identification of unique antigens presented by the tumor cells and immunological characterization of the tumor microenvironment (TME). Mass spectrometry provides the much-needed hypothesis-free window to discovery specific and novel tumor antigens, and reveal the intricacies of the tumor immunological landscape. In this position, you will participate in the PMC-UMCU-UU tumor immunology initative, and work alongside immunologists and clinicians in joint efforts, within the strong collaborative network of the immune-oncology research community in Utrecht. A background in proteomics and tumor immunology would be appreciated.
Publication date:
May 4th 2020
G Protein coupled receptors (GPCRs) are promising targets for treatment of cancer, as well as immune and inflammatory diseases. Next to small molecules, antibody therapeutics are recently found to modulate GPCR function with better specificity and longer lasting effects.
In this project, you will use combined techniques in mass spectrometry and cancer biology to study the mechanisms of novel antibody/nanobody therapeutics and bispecifics targeting GPCRs and GPCR oligomerisation. In this inter-disciplinary project bridging mass spectrometry, cell biology, and antibody/nanobody engineering, you will also become part of an extended research network collectively aimed at revealing the intricacies of GPCR signalling and rational perturbations for therapy. This ‘MAGNETIC’ consortium is funded by the NWO-ENW-PPS scheme, to develop the next-generation of GPCR-targeting pharmaceuticals. Applicants with prior knowledge in cell signalling are preferred; prior hands-on MS experience is not critical at the start.
Publication date:
April 21st 2020
Are you interested in developing a cutting-edge research program focused on developing and applying bioanalytical and biochemical approaches to investigate biological and disease processes?
Within the European consortium Epic-XS (https://epic-xs.eu) three different 2-year post-doctoral positions are available at Utrecht University, placed within the Heck-lab (https://hecklab.com), Altelaar-lab (https://altelaarlab.com/), and the Scheltema-lab (https://scheltemalab.com). The research emphasizes on the development of advanced mass spectrometry-based methods to address questions in proteomics and structural biology. The laboratory houses an excellent infrastructure, including a dozen state-of-the-art mass spectrometers, advanced separation technologies, bioinformatics, and laboratories for cell culture, biochemistry and molecular biology. The research group is vibrant and houses over 15 nationalities – Utrecht is a great place to be!
For all positions, the work is embedded in the European Proteomics program Epic-XS and participation in international meetings for this consortium is expected. The aim is to implement the developed technologies into the access sites, promoting collaborations.
The Scheltema laboratory focusses on the development and application of cross-linking mass spectrometry (XL-MS) to study protein-protein interactions. This technology utilizes small and agile reagents that covalently connect amino acids in close proximity. After proteolytic digestion, mass spectrometry can identify the connected amino acids. From these identifications distances constraints are derived that can be placed in in protein 3D structures, either known or directly predicted using this information. The structural details, at a resolution in the range of a few nanometers, allow resolving interaction interfaces between proteins. This can be done either in-vitro or in-situ in a close-to-native environment, making XL-MS an incredibly powerful approach for cell and structural biology.
For this position, you will join a team of dedicated researchers combining expertise in bioinformatics, biochemistry, mass spectrometry, and structural modeling on a variety of systems and organisms to answer cutting-edge questions in biological sciences. You are expected to apply size-exclusion chromatography and sucrose gradient ultracentrifugation to purify interesting protein assemblies, perform the cross-linking and mass spectrometry assays, perform data analysis and integrate the data into structural models. As part of the European Proteomics program Epic-XS you will interact and collaborate with international researchers and develop new methods for cross-linking mass spectrometry.
Recent illustrative work
Translational proteomics has made significant progress in recent years with improved protocols for the analysis of clinically important samples such as patient biopsy tissue material and different types of liquid biopsies. The analysis of patient tissue material allows the investigation of the disease state and the treatment response directly in the native in vivo environment and thereby provides valuable molecular disease information with high translational capacity. To make translational proteomics a main technology in clinical settings, several challenges need to be addressed. Here, we will focus on tissue biopsies, as the life in vivo setting, and extracellular vesicles (EVs), which potentially contain biomarkers for diagnosis and prognosis of disease conditions. Proteomics approaches will consist of high-end shotgun proteomics and targeted proteomics (e.g. DIA and SRM).
For this position, we seek a highly motivated biochemist or analytical chemist with proven expertise in mass spectrometry and clinical proteomics. You will join a team of dedicated researchers combining expertise in biochemistry, analytical chemistry, mass spectrometry and bioinformatics on a variety of systems to answer pressing clinical questions. As part of the European Proteomics program Epic-XS you will interact and collaborate with international researchers and develop new methods to translate proteomics results in clinically relevant information.
Recent illustrative work
In recent years we have been developing new mass analyzers and new fragmentation techniques targeted towards the direct analysis of intact proteins and protein complexes by native and top-down proteomics. Such analyses on the one hand allow us to directly probe stoichiometries and structures of large protein assemblies, like viruses and ribosome particles, on the other they make it possibly to identify and quantify distinct proteoforms of proteins highly modified by post-translational modifications such as phoshoproteins and (plasma) glycoproteins. Introducing charge detection single particle mass spectrometry and ECD and UVPD fragmentation on Orbitrap platforms has provided us with an unprecedented toolbox to discover so far little explored relevant parts of the proteome.
For this position, we seek a highly motivated biochemist or analytical chemist with proven expertise in biomolecular mass spectrometry. Having your own project, you will join a team of dedicated researchers combining expertise in bioinformatics, engineering and instrument development, biochemistry, analytical chemistry, and structural biology, and work on a variety of systems and organisms to answer cutting-edge questions in biological sciences. As part of the European Proteomics program Epic-XS you will interact and collaborate with international researchers and develop new methods for native mass spectrometry and top-down proteomics.
Recent illustrative work
