This year’s symposium is hosted by our chairman: Rao Vutukuri. Rao will connect all the lectures of the different speakers during our symposium and guide us during the day.
The following nine researchers will give a short lecture on a topic in their field:
Prof. Serge Lemay
Serge Lemay is a professor at bioelectronics (BE). The subject of his talk will be:
Plastic fantastic: single polymers as labels for biosensing
Gobert Heesink (PhD)
Gobert Heesink works as a 4th year PhD-candidate at Nanobiophysics (NBP). In his PhD project, he studies the etiology of Parkinson’s disease (PD) at its earliest stages by focussing on the behaviour of alpha-synuclein (αS) and how that is impacted by the cellular protein quality control (PQC) system. αS is an IDP involved in membrane remodelling and trafficking in the brain, but it is also the constituent of large fibrillar aggregates that are the hallmark of PD. There appears to exist a delicate equilibrium between maintaining health and preventing disease. To understand how the PQC system manages to keep this in balance, they aim to answer fundamental questions regarding αS. His talk will be about how they adress these questions:
From Molecules to Disease: Investigating the Early Biomolecular Interactions in Parkinson’s Disease
Prof. Wiendelt Steenbergen
Wiendelt Steenbergen is professor in Biomedical Photonic Imaging (BMPI) in the Faculty of Science and Technology and Vice-dean Research in the same faculty. In 2000 he was appointed assistant professor in biomedical optics and broadened his scope to low-coherence interferometry and photoacoustic and acousto-optic imaging for biomedical purposes. In 2010 he became full professor and group leader of the Biomedical Photonic Imaging group.
Laser speckle: hindrance or help?
“In its very early days the laser was regarded as a nice solution for unknown problems. Likewise laser speckle, a phenomenon associated with the coherence of light, was initially regarded as mainly annoying. In this talk I will show the opposite.
First I will show the speckle phenomenon as such in a situation in which speckles cannot be overlooked. But there are much more situations in which speckles are visible, once you know how they are formed. Once you know it, you see them everywhere. Finally I will introduce you to the methods that my research group develops to make speckles beneficial for patients.”
Dr. Carsten Wloka
After graduating with a diploma in biochemistry from Berlin in 2011, Carsten Wloka pursued a PhD in cell biology at the University of Pennsylvania, where he studied the mechanisms of cell division. Intrigued by the emerging field of bio-nanopore technology, and following the love of his life, he moved to the University of Groningen and worked with Oxford Nanopore Technologies to research biological nanopores as a Postdoc/Scientist. Since February 2024 he works as an assistant professor at the BIOS lab-on-a-chip group at University of Twente. The title of his talk is:
Biological Nanopores as Electrical Transducers for Real-Time Metabolite Quantification
Dr. Maria Carla Piastra
Maria Carla Piastra develops mathematical models to simulate normal and abnormal neuronal activity at different levels. From brain activity measured with scalp and intracranial EEG systems to neuronal network activity measured in vitro with microelectrode arrays (MEA) devices. Within this framework, she is involved in several (open-source) software development initiatives. Her main goal is to facilitate translational work between clinic and research, with a particular focus on epilepsy and stroke. With her Veni project, awarded in 2023, she will focus on the development of computational models for the treatment of refractory epilepsy with deep brain stimulation. She is an assistent professor at Clinical Neurophysiology (CNPH).
Biophysical computational models in neuroscience: an example in epilepsy treatment
Epilepsy is a chronic neurological disease that afflicts over 60 million people, worldwide. In 70% of the cases, patients can be effectively treated with antiepileptic drugs and for the remainder resective surgery can be an option. When both options are not viable or efficacious, deep brain stimulation (DBS) has emerged as an important treatment option. At present, DBS of the anterior nucleus of the thalamus (ANT) is a Class. Dr. Piastra evidences treatment for medically refractory epilepsy. However, DBS treatment effects are variable across patients, without knowledge of mechanisms or biomarkers that may account for this variation.
Dr. Avishek Das (Postdoc)
Dr. Avishek Das is a Postdoctoral Researcher interested in understanding nonequilibrium self-organization in living and autonomous systems. Currently in the group of Prof. Pieter Rein ten Wolde, he is exploring how information flow and feedback constrains bacterial performance during chemotaxis. They seek to rationalize bacterial behavior as autonomous machines navigating noisy nutrient gradients by using environmental information most effectively. Previously during his PhD with Prof. David Limmer at the University of California Berkeley, he designed novel numerical paradigms for the optimal control of nonequilibrium materials. Our approach yielded new and efficient algorithms to sample rare fluctuations and reactive events in nonequilibrium simulations.
Are bacterial cells limited by information about their stochastic environment?
Dr. Avishek Das will discuss the application of a novel computational technique, Path Weight Sampling (PWS), to address whether the fitness of chemotactic bacterium Escherichia coli is limited by information. PWS can exactly calculate the directional flow of information in simulations of any stochastic network even with nonlinearity and feedback. With PWS, they find that information and its usability separately constrain chemotactic performance. They rationalize their findings in terms of the design and interdependence of the sensing and response motifs in E. coli.
Prof. Jan Lipfert
Jan Lipfert is a professor in Molecular Biophysics at Utrecht University. His talk will be about :
Using physics to understand and fight viruses
“The COVID-19 pandemic has highlighted how viruses can cause human disease, with dramatic and global consequences. Here, I will present two projects where we have used single-molecule approaches to investigate aspects of the life cycles of two notorious viruses: SARS-CoV-2 and HIV.
In the first project, we have developed a tethered-ligand assay to investigate how SARS-CoV-2 attaches to human cells. Our assay comprises the tip of the Spike protein and the human receptor protein ACE2 connected by a peptide linker. We then use single-molecule force spectroscopy method to directly measure the strength of the virus-cell interaction. We find that SARS-CoV-2 (which causes COVID-19) can withstand higher forces compared to SARS-CoV-1 (which was responsible for the 2002/03 pandemic), which helps explain the different infection patterns of the two viruses (Bauer, Gruber, et al. PNAS 2022). Investigating the current variants of concern, we find differences in force stability that help rationalize the epidemiology of the different variants (Bauer, Gruber, et al. Nature Nanotech 2024).
In a second line of research, we investigate the interactions of HIV integrases, a key enzymes of the virus, with DNA. We find that, in addition to it well known catalytic role, integrase serves an unexpected structural role and can efficiently condense DNA into biphasic-biomolecular condensates (Kolbeck, et al. bioRxiv 2024 and De Jager, et al. bioRxiv 2024).”
Stijn van der Ham (PhD)
Stijn van der Ham is a 3rd year PhD-student in the Active Soft Matter group led by Dr. Rao Vutukuri. Soft matter physics presents captivating challenges in understanding the dynamic self-organization of living matter, active particle transport in complex fluids, and bio-membrane mechanics. Stijn van der Ham contributes to the group’s efforts to uncover the underlying principles governing these phenomena using experimental model systems.
Exploring Particle-Lipid Membrane Interactions Using Giant Unilamellar Vesicles
“Biological cell membranes play a critical role as barriers, separating the cell’s interior from the external environment. They form the first point of contact with foreign bodies, and are crucial in numerous cellular processes, including reshaping, protection, and transport across the membrane. In my research, I exploit giant unilamellar vesicles (GUVs; ~10-100 µm) as a model system to investigate complex membrane processes such as endocytosis and phagocytosis.
Endocytosis and phagocytosis involve the uptake of particles into cells, a process that requires the membrane to wrap itself around the particle. GUVs serve as a nice biomimetic model for investigating passive engulfment, a process where particle wrapping is driven by generic physical interactions like particle adhesion. Our studies find that the particle wrapping process is dictated by the balance between the elastic free energy penalty and adhesion free energy gain.
In my talk, I will illustrate this concept through experiments on the engulfment dynamics of both rigid anisotropic particles and flexible soft particles by GUVs.”
Dr. Kasia Tych
Dr. Kasia Tych works in the Biomolecular Sciences and Biotechnology Institute (GBB). Her research involves single-molecule characterisation of proteins using mass photometry (iSCAT), force spectroscopy and fluorescence with the optical tweezers and optical microscopy.
Shedding Light on Protein Folding and Dynamics: Unveiling Molecular Mysteries with Optical Tweezers
“Understanding the dynamics of proteins is essential, as these molecular machines orchestrate the vast array of processes vital for life. Optical tweezers, a ground-breaking technology, have emerged as a highly valuable tool in unravelling the enigmas of protein folding and dynamics. Optical tweezers enable precise manipulation and measurement of individual biomolecules with high sensitivity and resolution.
In this talk, I will showcase how optical tweezers can be used in the field of protein biophysics, giving examples from my research group where we have been characterising a molecular chaperone, Hsp90, as well as transmembrane transport proteins such as the ABC transporter OpuA. Through real-time manipulation and observation, we unveil the intricate pathways and kinetic mechanisms governing protein folding, protein-protein interactions and conformational dynamics, shedding light on the fundamental principles underlying biological function.”