Physics and Engineering

The Diz-Muñoz group uses atomic force microscopy and live cell imaging to characterise and modify mechanical properties of cells and tissues. We also aim to develop non-contact techniques to measure and control such properties.

This will allow us to pursue a comprehensive understanding of the specific contribution of different force inputs (e.g. adhesion, membrane tension, contractility, stiffness) for cell polarization. Moreover, this will provide an avenue to assess how these inputs affect signaling and set a framework to theoretically describe the complex reality of cell migration.

Selected publications

Our team develops instruments and methods for X-ray scattering experiments within the EMBL/ESRF Structural Biology group and contributes to the development of the EMBL@PETRA-III beamlines in Hamburg.

Our core activity is to develop High precision diffractometers and automated sample environments for MX and SAXS beamlines. Recent example is a sample changer based on a 6 axis industrial robot and patented EdgeDewar (Picture). This system called FlexED8 holds up to 252 miniSpine samples holders in 7 pucks maintained in an ice free environment. The Flex technology is being adapted to equip the ESRF MX beamlines and coupled to our CrystalDirect harvester developed in collaboration with the Grenoble HTX lab.

Our technical expertise in high precision mechanics, cryogenics, optics, electronics and software, associated with the scientific input provided by the Synchrotron Crystallography Team ensures the success of our instruments. Most of them are transferred to industry and commercialised worldwide with the support of EMBLEM, the commercial and technology transfer arm of EMBL.

Selected publications

Engineering and physics are essential in two areas of our work.

1. To identify and characterize cell division genes systematically, we need novel high throughput methods. In our group we:

• constantly engineer both software and hardware to automate advanced microscopy and single molecule methods and,
• apply machine vision approaches to increase throughput and decrease bias in these experiments.

2. In order to interpret protein dynamics inside cells we need to understand their rheology. To this end we are interested in the physical properties of the microenvironment in the cell nucleus, which we probe by biophysical methods and model in computer simulations.

Selected publications

Research carried out at the EMBL Hamburg Unit utilizes the extremely brilliant Synchrotron radiation X-ray intensity produced by particle accelerators at DESY for structural investigations in biology. Experiments are carried out in Small angle solution scattering (SAXS) and X-ray crystallography (PX).

Each of these methods has specific instrumentation needs and our groups design, construct, build and commission the appropriate equipment. Our activities include mechanical engineering, vacuum technology, X-ray optics, data acquisition and control electronics and software. Because of the wide spectrum of skills and competences required our group members include physicists, mechanical, electronic and software engineers as well as skilled technicians in these fields.

EMBL is building and will operate three beamlines on one of the world leading synchrotron radiation sources, PETRA III. In this context major challenges and opportunities in the field of beamline instrumentation, sample handling, control electronics and software have to be mastered.

Selected publications

Progress in biology is driven by technology. High throughput sequencing and microscopy require sophisticated statistical and computational operations in order to exploit their potential. To understand (and, eventually, manipulate) biological systems, all available data about them needs to be integrated into computable maps and mathematical models. Ideas and techniques from physics, mathematics, statistics, computer science and engineering are the crucial drivers for our research.

Selected publications

The Synchrotron Crystallography team works in close collaboration with the Structural Biology Group of the European Synchrotron Radiation Facility (ESRF in the design, construction and operation of macromolecular crystallography (MX) and biological small angle X-ray scattering (bioSAXS) beamlines.

In addition, we are responsible for the management of the CRG beamline BM14 at the ESRF, which is operated in partnership with the Indian government and ESRF. We also participate in the development of instruments, software and novel methodologies for sample handling and data collection strategies, which is carried out in close collaboration with the Papp team.

Finally the team is active in a number of collaborative projects with other synchrotrons in Europe, such as EDNA and the kappa working group.

Selected publications

The Prevedel group develops new optical approaches and techniques to non-invasively image dynamic cellular processes in living tissue. To advance the frontiers of deep tissue microscopy we integrate concepts from diverse physical fields, such as wavefront engineering, photo-acoustics and computational imaging.

At the same time, we engineer innovative optical and mechanical hardware solutions for our microscopes to adapt them to particular samples and imaging conditions. In order to interpret our recordings, we also develop custom software to automate the extraction of relevant parameters from our data.

Selected publications

In order to investigate biological questions that were previously inaccessible because of the limited resolution of light microscopes, we are developing novel superresolution microscopy tools. The design and implementation of advanced microscopes is crucially based on physics and engineering such as optics, mechanical and electrical engineering, image analysis and software development.

Currently we are developing the following tools:

• Automated localization microscope for high-throughput superresolution imaging of entire proteomes.
• Robust three-dimensional superresolution microscopy with isotropic resolution.
• Superresolution microscopy with single-plane illumination.
• Microfluidics for superresolution microscopy.

Selected publications