Molecular Biology and Microbial Food Safety

The mission of the 'Molecular Biology and Microbial Food Safety' group is to carry out both fundamental and applied oriented research in specific areas in microbial food safety and molecular and cellular microbiology that are of importance to the food and pharmaceutical industries. The group focuses on the molecular biology and physiology of the interactions between microbes and their biotic and abiotic environment as it pertains to microbial food safety and human health.

Molecular Microbial Physiology

The general aim of the 'Molecular Microbial Physiology' group is to discover the properties that allow living (microbial) cells to catalyze a large array of concurrent chemical fluxes and information flows, and how these collaborate to provide single individual cells with the typical characteristics of a living organism, i.e. an entity that shows multiplication, adaptation and evolution. In this research we focus on questions related to the mechanisms by which microbes respond to environmental signals, and the translation of these signals into physiological responses.

Molecular Cytology

The central research theme in the 'Molecular Cytology' group is self-organization and signalling in living cells. Self-organization is the intrinsic property of matter to organize itself in a (dynamic) structure, whereas signalling implies the activity of gene-products to control a local activity which can alter the local cellular architecture (e.g. driving morphogenesis). In order to achieve a certain 3D architecture in cells, these two important mechanisms work in concert. In the research group, both mechanisms are studied with emphasis on membrane-related architecture of living cells using advanced microscopy tools.

Nuclear Organisation

Synthetic Systems Biology and Nuclear Organization

Living organisms only persist because their components are networking continuously at all levels of organization, in both time and space. Systems Biology is the new exciting science aiming to discover the principles of Life that determine how functions emerge from the interactions. For the proper functions to emerge, the networking between molecules controlling life must be complex and to the point. In order to understand existing biological functioning and to design entirely new and exciting functions and Life, this group engages in the precise acquisition of dynamic molecular and structural information and the building of mathematical models. One of our missions is to unravel the functioning of the eukaryotic genome in its natural environment, i.e. the cell nucleus. Of key importance is the notion that gene expression in eukaryotes is controlled at multiple hierarchical levels: the individual gene, the epigenetic level, and the 3D folding of the chromatin fiber in the interphase nucleus. Combining a wide variety of techniques, including state-of-the-art microscopic imaging and biochemical analyses, we investigate the interplay between these regulatory levels in the context of gene control.

Epigenetic Regulation of Gene Expression

The aim of the 'Epigenetic Regulation of Gene Expression' group is to understand epigenetic regulation of gene expression in terms of cell differentiation and human disease. Research is focused on unravelling the function of multiprotein complexes, such as the repressing Polycomb group (PcG) proteins. PcG proteins form multimeric protein complexes that are part of a cellular memory system responsible for the inheritance of gene activity to progeny cells. The action of PcG complexes is delimited by the presence of genomic elements, STAR elements, which counteract PcG mediated repression. Combining a variety of techniques, including novel developed genetic screens, we study the dynamic interplay between these two, functionally antagonistic systems. Our knowledge of epigenetic gene regulation has important biotechnological implications to improve a range of transgenic applications.

Molecular Plant Pathology

The overall mission of the ‘Molecular Plant Pathology' group is to unravel the molecular basis of disease and disease resistance in plants. For in depth research on the molecular basis of susceptibility and resistance we focus on interactions between soil borne pathogens and their hosts, using the interaction of the fungus Fusarium oxysporum with the tomato plant as a model. Our specific interest is focused on basal and induced defence mechanisms of the host and on virulence and avirulence factors of the pathogen.

Plant Physiology

Research within the ‘Plant Physiology' group is focused on signalling in plants at different organisational levels. Signal transduction cascades are studied that help plants cope with biological and environmental stress conditions: phospholipids signalling, the role of plant volatiles in plant-insect and plant-plant communication and the regulation of scent biosynthesis in tomato and petunia.

Cellular and Systems Neurobiology

The ‘Cellular and Systems Neurobiology' group has organized its research around a few well defined topics in the realm of neuronal excitability, a prominent property of the nervous system and its components. The core approach in the group is a functional electrophysiological one (from patch-clamping to in vivo). Most of the experiments are supported by computer modelling, focusing on single cell excitability in relation to the direct chemical surrounding of the neuron as well as on the adaptive strategies for excitability that optimize the working range of active neurons. In the latter case the consequences of single cell strategies are extrapolated to larger neuronal networks. The combination of theoretical and experimental work has proven to be very fruitful in the scientific setting of SILS.

Cognitive and Systems Neuroscience

The global research aim of the ‘Animal Physiology and Cognitive Neuroscience' group is to elucidate how neuronal networks distributed across the prefrontal cortex, temporal cortex and striatum cooperate in a number of cognitive processes, including learning and memory consolidation, attention and sensory integration. This aim is pursued using a variety of techniques and at various aggregate levels, ranging from the sub-cellular to macroscopic and behavioural domain. Nonetheless, most of the research focuses on the level of systems physiology.

Molecular Neuroscience

Within our laboratory we study the molecular biology that is behind developmental mechanisms in the central nervous system.

In our research team we endeavor to understand the molecular programming of specific neuronal groups within mdDA neurons and the cortex. To this end we have identified transcription factors that play key roles in these processes, as Pitx3, Lmx1b and Nurr1 for mdDA neurons. To study developmental processes we use complex gene transfer models as in-utero electroporation and whole brain ex-vivo cultering, to track these neurons as they leave the ventricular zone and start differentiating and move to there final position where they send out axons and receive inputs from other systems. A combination of these techniques with more classical genetic models ( Nurr1-ko, Pitx3-ko, Pitx3-Cre driver …) provide us with the essential tools to answer our research questions

Structural and Functional Plasticity of the Nervous System

Our main interest is structural plasticity in relation to stress and disease. In addition to apoptosis, we focus on the regulation of adult neurogenesis and its relevance for depression and dementia. Even though we do have an interest in neurogenesis in other brain areas, particular in the cortex and during early development, our primary focus is the hippocampus since it is not only affected in both these disease conditions but is also very sensitive to stress hormone action and implicated in learning and memory. The hippocampus is furthermore unique as it contains stem cells that continue to generate new neurons in adult animals, including humans, a process called "adult neurogenesis"

Biosystems Data Analysis

Measurements on biological systems generate an abundance of data. These data have to be transformed to information (summarized) and presented to the user (visualized). One way of doing both simultaneously is by using models. The general aim of the ‘Biosystems Data Analysis' research group is to develop and validate methods for summarizing and visualizing complex biological data.

van Leeuwenhoek Centre for Advanced Microscopy - FNWI

The goal of the van Leeuwenhoek Centre for Advanced Microscopy-FNWI is to boost Life Sciences research using (optical) microscopy techniques. This expertise centre facilitates molecular cellular studies by providing support in translating biological questions into microscopy approaches and by providing state-of-the-art microscopy (training) infrastructure for researchers. Because of this integrated expertise and advanced instrumentation, the centre has triggered significant collaborative research projects both within and outside SILS.

Mass Spectrometry of Biomacromolecules

The group ‘Mass Spectrometry of Biomacromolecules' develops mass spectrometry to understand biology at the molecular level. The research combines mass spectrometry with biomolecular and organic chemistry. Focus lies on four research themes, which are carried out in close collaboration with other groups within and beyond SILS, i.e., (i) systematic analysis of protein-protein interactions, (ii) post-transcriptional regulation of gene expression, (iii) host-fungal pathogen interactions, and (iv) identification of clinical biomarkers. The research group develops innovative, mass spectrometry-based experimental approaches that are designed for these research areas, but are also more widely applicable.

Micro Array Department and Bioinformatics

Microarray technology has become a well-established tool in the analysis of genome-wide gene expression studies. The expertise centre ‘Micro Array Department' operates as a technology and bioinformatics core facility for scientists within the University of Amsterdam, and as a service provider for external academic and industrial customers. The bioinformatics research group focuses on analysis of transcriptomics data. The expertise centre is always open to collaboration or participation in projects concerning microarray technology or analysis.