Department of Medical Biology
In our department we provide MSc research projects of minimally 6 months. Students are supervised by dedicated scientists and participate in departmental scientific meetings and Journal clubs.
Molecular mechanisms of endothelial barrier breakdown in the eye and brain
Brain edema, or swelling of the brain, is a potentially life-threatening condition, and diabetic macular edema (DME), swelling of the retina, is a major cause of blindness. Both disorders are the result of, respectively, loss of function of the neuroprotective blood-brain barrier (BBB) and the blood-retinal barrier (BRB) of blood vessels. We have found that inhibition of an endothelial cell-specific protein can prevent endothelial barrier breakdown in vitro and in vivo. In the current project, we would like to further explore through which mechanism this happens. Click here for more info.
Techniques: Endothelial cell culture, lentiviral transduction, confocal imaging, live cell imaging, electron microscopy, western blotting, qPCR.
Contact
Dr. Ingeborg Klaassen: i.klaassen@amsterdamumc.nl
Development of a zebrafish model for the pathological breakdown of the blood-brain barrier
Loss of the proper function of the neuroprotective blood-brain barrier (BBB) is a critical and chronic event in numerous neurological disorders. Leakage of plasma proteins can lead to vasogenic edema and significant clinical problems such as neuronal morbidity and mortality. More research is needed to get more insight into the molecular and cellular processes in the pathological breakdown of the BBB.
The aim of our study is to develop a zebrafish model that can be employed to study pathological breakdown of the BBB. No such model presently exists. Two reporter lines with fluorescent labeled blood vessels, Tg(Fli1꞉EGFP and Tg(Kdrl꞉RFP), are in our possession and can be used in combination with fluorescently labeled tracer molecules to study vascular permeability. Breakdown of the BBB will be induced by several pathological conditions, including hypoxia, high VEGF, and high glucose that will be administered by addition to the embryo medium in which the larvae are maintained. After different time points fluorescent tracers will be injected intracardially, embryos will be mounted in 1% low-melting agarose and vascular leakage will be assessed by using time-lapse confocal microscopy. In addition, if time permits, reporter lines will be cross-bred with mutant lines to study essential genes that are involved in BBB breakdown or maintenance of an intact BBB. We will study this in great detail, not only using time-lapse confocal imaging, but also transmission electron microscopy to study ultrastructural cell components as tight junctions and caveolar vesicles.
Contact
Dr. Ingeborg Klaassen: i.klaassen@amsterdamumc.nl
Gene and (stem) cell therapy for cardiac rhythm regeneration
Cardiovascular disease is an increasingly common cause of death. In case of cardiac rhythm disease, an electronic pacemaker can be implanted. This ever more frequent procedure (300,000 a year in Europe alone) has severe limitations. Electronic pacemakers have limited battery life, and can break or become infected. In addition, electronic pacemakers do not adjust to increased demand for blood flow, e.g. during exercise or – in children – because of growth.
We are therefore looking into supporting patients with cardiac rhythm disease with a biological pacemaker. The Boink group wants to improve heart rhythm management by development of therapeutic viruses and (stem) cells as biological pacemakers. We have obtained in vivo proof-in-principle for therapeutic AAV (adeno-associated virus), and are now critically expanding our strategies for pre-clinical testing to include adenovirus and lentivirus, in several in vitro and in vivo models.
We provide Master student research projects of 6 or more months. Students become part of a dedicated team, and participate in ongoing research, including scientific meetings and conferences.
Techniques: DNA cloning and sequencing. Cardiac gene expression and knockdown (by RNAi, miRNA or lncRNA). Virus production and purification. Transfection and transduction of cell lines, stem cells, and primary cells. In vitro and in vivo cardiac models. Microsurgery. Microscopy, Western blot, Immune fluorescence and histochemistry, qRT-PCR.
Contact
Dr. Geert Boink: g.j.boink@amsterdamumc.nl
Dr. Harsha Devalla: h.d.devalla@amsterdamumc.nl
Dr. Max Medina Ramirez: j.m.medinaramirez@amsterdamumc.nl
Department of Anesthesiology
In our department we provide MSc research projects of minimally 6 months. Students are supervised by the PI and participate in departmental scientific meetings and Journal clubs. A brief description of the available projects is listed below:
Novel and optimal multimodal therapy against acute myocardial infarction
Acute myocardial infarction (AMI) remains one of the common causes of death and hospitalization worldwide. Improved treatment strategies for AMI are urgently needed for for the prevention of adverse cardiac remodeling and eventual heart failure. In this research line we explore several novel and high potential targets against acute infarction and combine them to gain maximal reductions in infarct size in animal studies, with a keen eye towards applicability towards the clinical arena.
Techniques: isolated perfused mouse hearts, in vivo cardiac infarction model rat, stabile isotope for cardiac metabolism, cell death parameter analysis, western blotting, spectrophotometric enzyme analysis.
Contact
Dr. Coert Zuurbier: c.j.zuurbier@amsterdamumc.nl
Unravelling the mechanisms of the effective diabetes medicine Empagliflozin
The kidney-targeted Empagliflozin (EMPA) caused a large reduction in heart failure hospitalization and cardiovascular death in diabetes patients (Zinman B et al, NEJM 2015). Surprisingly, the underlying mechanisms are largely unknown. In this project we try to unravel the cellular mechanisms and actions of empagliflozin in the heart and endothelial cell.
Techniques: isolated perfused mouse hearts, isolated endothelial cells, stabile isotope for cardiac metabolism, genetic manipulations of targeted genes, cell culture, cell physiology parameter analysis, western blotting, spectrophotometric enzyme analysis.
Contact
Dr. Coert Zuurbier: c.j.zuurbier@amsterdamumc.nl
Dr. Nina Hauck: n.c.hauck@amsterdamumc.nl
Development of a Human Induced Pluripotent Stem Cell Model of Diabetic Neuropathy
Diabetic neuropathy (DN) is a debilitating, progressive neurodegenerative disorder that preferentially targets peripheral sensory neurons. Although highly prevalent, no disease modifying therapy exists due to unsuccessful drug discovery caused by failing translation of animal models. The breakthrough discovery of human induced pluripotent stem cells (iPS) offers researchers a novel method of acquiring human sensory neurons to develop disease-specific models (Takahashi et al., Cell 2006). In this project, we build on our iPS-derived model of healthy sensory neurons to develop the first human model of DN to facilitate research in the fields of anaesthesiology, pain medicine, and beyond.
Techniques: culture and differentiation of human induced pluripotent stem cells, confocal microscopy, microelectrode array, colorimetric cytotoxicity assays.
Contact
Dr. Nina Hauck: n.c.hauck@amsterdamumc.nl
Effects of sodium glucose co-transporter 2 inhibitors on endothelial dysfunction induced by pathological mechanical forces
Diabetes impairs endothelium functions in both macro- and micro vessels, leading to development of multiple cardiovascular diseases. Clinical studies have shown that sodium glucose co-transporter 2 inhibitors (SGLT-2i’s) significantly improve cardiovascular outcomes in diabetic and non-diabetic patients. Previous studies in our laboratory employing resting human endothelial cells suggest that SGLT-2i’s directly exert anti-inflammatory and anti-oxidative effects. In the present project we develop two dynamic cellular models that mimic mechanical forces induced endothelial dysfunctions, including enhanced stretch and disturbed shear stress in order to investigate the direct effects of SGLT-2i’s on activated endothelium.
Techniques: isolated endothelial cells, cyclic stretch model, cell culture under flow, cell permeability assay, western blot, cell physiology parameter analysis, spectrophotometric enzyme analysis, live cell image, immunofluorescence microscopy.
Contact
Dr. Nina Hauck: n.c.hauck@amsterdamumc.nl
Department of Medical Biochemistry
In our department we provide MSc research projects of minimally 6 months. Students are supervised by dedicated scientists and participate in departmental scientific meetings and Journal clubs. A brief description of the available projects is listed below:
Immune mechanisms in cardiovascular disease
Macrophages are key immune cells in tissue homeostasis and host defence. They are also critical in cardiovascular diseases (CVD). We study the regulation of monocytes and macrophages in cardiovascular disease and particularly focus on epigenetic and transcriptional pathways regulating macrophage responses in disease. Hereby we aim to identify important novel tools and approaches to modulate inflammation and reduce the development of CVD.
We apply molecular biology techniques (cloning, CRISPR, QPCR, RNAseq, Chromatin-IP, bioinformatics) and cell biology tools (FACS, ELISA, pharmacological inhibitors, imaging) in mouse and human cell models.
Contact:
Prof. Menno P.J. de Winther (Vascular Immune Cell Biology): m.dewinther@amsterdamumc.nl
Website: www.macrophages.eu
Aortic Aneurysms: how to predict them and how to inhibit further dilatation
Aortic aneurysms are dilatations of the aorta, which result in prophylactic aortic surgery when the aneurysm grows beyond 5 cm in diameter. In Marfan Syndrome patients, aortic aneurysm growth and rupture is the main cause of mortality. It is difficult to predict which patient is at high risk of aneurysm development and rupture. We study aortic markers in human and Marfan mouse aortic tissue, to develop predictive tools for aneurysm growth and rupture. Moreover, we perform intervention studies in a Marfan mouse model to reveal new therapeutic approaches.
Techniques: cell culture vascular cells, histological analyses Marfan mice, mouse experiments treating Marfan mice.
Contact
Dr. Vivian de Waard: v.dewaard@amsterdamumc.nl
Nuclear Receptor Nur77 reduces the inflammatory response of macrophages
The orphan nuclear receptor Nur77 (NR4A1) regulates a large variety of cellular processes and macrophage inflammatory signaling. We study Nur77-mediated gene regulation by comparing genome-wide DNA binding (ChIP-seq) and gene expression profiles (RNA-seq) in RAW264.7 macrophages. In this research project the bioinformatic analyses of databases provide novel clues on the role of Nur77 in macrophages, which will be explored in follow up experiments.
Techniques: bioinformatics, cell culture macrophages (mouse, human, cell lines), gain-of-function and knockdown experiments, RNA/protein expression, Seahorse metabolism assays.
Contact
Prof. Carlie de Vries: c.j.devries@amsterdamumc.nl
Molecular regulation of lipid metabolism by LXRs and the ubiquitin proteasomal system
We are interested in elucidating the molecular mechanisms that govern cellular and whole-body lipid metabolism. Specifically, we focus on the role of the ubiquitin-proteasomal-system and of the nuclear receptors LXRs herein. We have identified several new genes that play a role in controlling sterol and fatty acid metabolism in cells and are using biochemical, cellular biological, and mouse models to investigate their function. In particular, we are aiming to understand the role of these genes in cardiovascular and metabolic disease.
Techniques: Culture of primary cells and cell lines, Genetic manipulation of cells and mice using CRISPR/Cas9- and transfection-based methodology, Molecular biology, Biochemical assays, functional genetic screens.
Contact
Prof. Noam Zelcer: n.zelcer@amsterdamumc.nl
Vascular Microenvironment and Integrity
We are interested in understanding how endothelial cells respond to mechanical changes induced by physiological dynamics taking place within the vessel wall. In particular we search for novel molecular events taking place at endothelial cell-cell junctions (VE-cadherin complex) and cell-extracellular matrix adhesions (integrin complexes). These are crucial structures that preserve vascular barrier function, and are tightly controlled during vascular development, angiogenesis and transendothelial migration of inflammatory cells. More information about the research can be found on the Huveneerslab website.
Techniques: Live fluorescence microscopy, endothelial cell culture, image analysis, shRNA-mediated knockdowns, biomechanical assays and biochemistry.
Contact
Dr. Stephan Huveneers: s.huveneers@amsterdamumc.nl
Department of Radiology
For duration and conditions of the project, please contact the Principal Investigator.
Clinical implementation of state-of-the-art 4D flow MRI for cardiovascular diagnostics
4D flow MRI is an advanced non-invasive technique for visualization of blood flow. Clinical implementation of this technique is innovative and provides new insights into the function of heart valves, heart chambers and major blood vessels. This technique is particularly promising for the investigation of heart valve dysfunction.
This project focuses on the clinical implementation of 4D flow MRI. The candidate will specialize in 4D flow MRI (both scanning and post processing). With this knowledge and skills the candidate will conduct studies on the clinical value of 4D flow MRI in the context of mitral regurgitation.
Contact
Dr. Nils Planken: r.n.planken@amsterdamumc.nl
Department of Pathology
In our department we provide MSc research projects of minimally 5 months. Students are supervised by dedicated scientists and participate in departmental scientific meetings and Journal clubs. A brief description of the available project is listed below:
The Heart-Brain connection
In our research group we are interested in the connection between the heart and the brain. Despite the capacity of the brain to adapt cerebral blood flow to its own demand, systemic hemodynamic changes such as the function of heart, aorta and cerebral arteries may reflect on the cognitive functioning. In this project we study the molecular regulation of (extra- and intra-cranial) endothelial cells in protecting the brain against hemodynamic changes to understand their function in cardiovascular induced brain pathologies.
Techniques: we perform immunohistochemistry and imaging combined with quantitative molecular techniques.
Contact
Prof. Mat Daemen:m.j.daemen@amsterdamumc.nl
Dr. Dorien Hermkens: d.m.hermkens@amsterdamumc.nl
Biomedical Engineering and Physics
For duration and conditions of the project, please contact the Principal Investigator.
Development of a rat model for silent brain infarcts
Brain infarcts have overt and devastating consequences. However, small infarcts may occur much more frequently with aging and several cardiovascular diseases, and remain relatively unnoticed. We speculate that accumulation of small infarcts ultimately leads to cognitive impairment. In this project the student will help to develop a rat model for small infarcts by infusing microspheres into the cerebral circulation. Capillary perfusion is analyzed post mortem from brain sections. Potential recovery is studied by comparison of perfusion at day 1, day 7, and day 28 after microsphere infusion.
Techniques: Surgery, histology, 3D capillary analysis, immunohistochemistry.
Contact
Prof. Ed van Bavel: e.vanbavel@amsterdamumc.nl
Dr. Erik Bakker: n.t.bakker@amsterdamumc.nl