Dr. Rok Podlipec

Through several years of research work in the field of experimental biophysics, I have been acquainted with numerous exciting topics focused on how biomaterials and harmful nanoparticles impact biological responses and devoted myself to the development of fluorescence microscopy techniques for the diagnostics of eye diseases. I am currently engaged in nanotoxicology and correlative microscopy research, where we discover new mechanisms and initial events e.g. the onset of chronic inflammation in lungs on in vitro models by a new combination of the most advanced optical, electron and ion microscopies.

Research programme: Experimental biophysics of complex systems and imaging in biomedicine
Training topic: New correlative microscopy approaches to detect early mechanisms of inhaled nanoparticles toxicity


One of the major challenges in the field of nanotoxicology remains the discovery and understanding of new mechanisms and initial molecular events that can lead to damage or even permanent consequences in cells and tissues as a result of exposure to various nanoparticles. Established experimental methods often do not allow a sufficiently good spatial and temporal resolution to identify and characterize the initial response of cells and tissues to nanoparticles that come into contact with them. New research approaches using in vitro models are increasingly gaining ground, replacing expensive and often irrelevant research on animals.

In the Laboratory of Biophysics, we have therefore developed a new research approach, where we use the most advanced microscopic techniques on the in vitro models, from lung tissue, brain to the bone, which enable tracking of individual nanoparticles and cell structures in real-time, even on the nanoscale. Due to the limitations of fluorescence microscopy in terms of spatial resolution, we have therefore introduced correlative electron and ion microscopies, which allow insight into the interaction between nanoparticles and the biological system on a molecular scale, and also provide us with information about the chemical properties of the system. With this approach, we recently successfully characterized structures of nanoparticles coated with proteins and lipids, revealed as the key triggers for the onset of chronic inflammation in the lungs (link), and discovered several plausible mechanisms of tissue inflammation due to damaged hip prostheses (link). The main principle of correlative microscopy is the identification and characterization of the same studied structures with several complementary techniques. Because electron and ion microscopy are performed in a high vacuum and the samples need to be transported, the preparation of the samples still presents a big challenge.


There is no shortage of challenges to new research approaches of correlative microscopy to detect early mechanisms of toxicity of environmental nanoparticles exposed to humans. The research program, therefore, consists of several parts: independent work on in vitro models on one of the most advanced fluorescence experimental systems, super-resolution STED microscopy equipped with additional spectroscopic modalities, development of sample preparation for microscopy in high vacuum, use of advanced scanning electron microscopy with the focused ion beam technique (FIB-SEM) for gaining insight into the interior of cellular structures, as well as coupling and the analysis of measurements of the interaction of nanoparticles with biological material. The young researcher thus thoroughly learns how to work on state-of-the-art optical and electron microscopes and becomes familiar with all sample preparation procedures, from fluorescent labeling of biological structures, and administration of various nanoparticles, to freezing and drying necessary for electron microscopy.

We are searching for a motivated candidate who is interested in experimental work and has a passion to learn in the interdisciplinary field of physics and biology, the approach becoming more and more valuable in discovering new mechanisms of the impact of nanoparticles on e.g. the development of disease states in the body.