@conference{nokey,

title = {Advanced microfluidic strategies for droplet handling and biomedical applications},

author = {Piotr M. Korczyk and Sławomir Błoński and Damian Zaremba and Barbara Kupikowska-Stobba and Tetuko Kurniawan},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Microfluidics, a multidisciplinary area bridging physics, biology, and chemistry, has grown remarkably due to its ability to manipulate fluids at microscales [1]. Our work emphasizes the design and refinement of microfluidic devices that enable controlled droplet generation and manipulation [2,3], with practical applications in life sciences and chemical analysis.

By utilizing two-phase flows in confined channels, we engineer systems that exploit droplet-based transport, enabling precise sample encapsulation and reagent handling. Innovative passive control elements and capillary-hydrodynamic circuits are incorporated to guide droplet behavior without external actuation, offering compact and programmable platforms [4–7].

Algorithmic strategies complement our physical designs: digital droplet merging and splitting are used to achieve dynamic concentration control, improving reproducibility and flexibility of biochemical protocols [4,8].

Biomedical applications of our research include microfluidic chambers tailored for cell culture under biomimetic mechanical stress [9]. In collaboration with Université Grenoble Alpes, we investigated epithelial tissue mechanics, revealing how curvature modulates calcium signaling and gene expression. Another system, developed with the University of Oxford, allows us to measure oxygen unloading kinetics from erythrocytes using ultra-fast medium exchange and fluorescence microscopy [10].

These tools have proven effective in real-world scenarios, such as evaluating oxygen delivery efficiency during human kidney perfusion in transplant settings [11]. We demonstrate that red blood cell behavior, rather than blood flow alone, governs tissue oxygenation, contributing to a revised understanding of oxygen delivery metrics [12].

Our results underscore the potential of microfluidic systems not only as precise fluid manipulators, but also as transformative platforms for biological experimentation and diagnostics.





ACKNOWLEDGMENTS



This work was supported by the European Commission [grant HORIZON-ERC-POC No GAP 10118800] and the National Science Centre (Poland) [grants OPUS

No 2019/35/B/NZ2/03898. 

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Enhancing antiplatelet efficacy through bioenergetic modulation: combined inhibition of glycolysis and oxidative phosphorylation},

author = {Patrycja Kaczara and Anna Kurpińska and Olena Lytvynenko and Agnieszka Kij and Kamil Przyborowski and Katarzyna Rafa-Zabłocka and Stefan Chłopicki},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Blood platelets play a crucial role in the development of vascular thrombosis, a major complication in patients with cardiovascular and metabolic diseases. The primary strategy to reduce the risk of thrombotic cardiovascular events is antiplatelet therapy. However, this approach is not fully effective in patients with metabolic disorders, where platelets often exhibit hyperreactivity despite pharmacological treatment. This suggests that alterations in platelet energy metabolism may underlie this condition.

Platelet activation is an energy-demanding process that relies on dynamically regulated metabolic pathways, with energy derived from both glycolysis and mitochondrial oxidative phosphorylation (OXPHOS). Such bioenergetic plasticity allows rapid functional responses and can contribute to platelet hyperreactivity in metabolic disorders, often limiting the efficacy of antiplatelet therapies. In this study, we investigated whether mild interference with platelet energy metabolism could enhance the inhibitory effect of cangrelor, a P2Y12 receptor antagonist that does not directly affect bioenergetic pathways.

Washed platelets from healthy donors were treated with CORM-A1 (a carbon monoxide-releasing molecule that inhibits both glycolysis and mitochondrial respiration) or a combination of 2-deoxy-D-glucose (2DG, a glycolytic inhibitor) and oligomycin (an ATP synthase inhibitor) at low concentrations, in the presence or absence of cangrelor. Platelet aggregation was assessed using light transmission aggregometry, while the oxygen consumption rate (OCR) and the extracellular acidification rate (ECAR), reflecting real-time metabolic flux, were measured using Seahorse extracellular flux analysis. Intraplatelet ATP levels and reactive oxygen species (ROS) production were quantified using luminescence- and fluorescence-based assays. Targeted liquid chromatography-tandem mass spectroscopy (LC-MS/MS) analysis was employed to assess intracellular metabolites and eicosanoids.

Our results show that dual, partial inhibition of both glycolysis and OXPHOS significantly enhanced the antiplatelet effect of cangrelor. Although CORM-A1 and the combination of oligomycin and 2DG modulated platelet bioenergetics through distinct mechanisms, both strategies led to increased accumulation of adenosine, potentially responsible for the enhanced antiaggregatory effect of cangrelor. In contrast, reductions in ROS and eicosanoid production appeared to be consequences, rather than causes, of diminished platelet activity. Metabolomic profiling revealed that oligomycin alone shifted metabolism toward glycolysis and decreased aspartate. In contrast, 2DG increased erythrose 4-phosphate and aspartate levels, pointing to differential regulation of glycolytic and ancillary pathways. Changes in aspartate levels most clearly distinguished the effects of oligomycin and 2DG. However, under thrombin-stimulated conditions, combined treatment showed that the metabolic effects of 2DG predominated.  

These findings highlight the central role of bioenergetic pathways in platelet function and suggest that dual, partial inhibition of energy metabolism may represent a novel strategy to enhance antiplatelet therapies – particularly in metabolically dysregulated states.





ACKNOWLEDGMENTS



This study was supported by a grant from National Science Centre Poland [OPUS; 2021/41/B/NZ7/01426]

......},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Unravelling metabolic disruptions in MPAN disease – insights from patients fibroblasts},

author = {Agata Wydrych and Barbara Pakula and Patrycja Jakubek-Olszewska and Justyna Janikiewicz and Aneta M. Dobosz and Marta Skowrońska and Iwona Kurkowska-Jastrzębska and Bogusz Kulawiak and Monika Żochowska and Agnieszka Dobrzyń and Magdalena Lebiedzinska-Arciszewska and Mariusz R. Wieckowski},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Neurodegeneration with Brain Iron Accumulation (NBIA) is a rare inherited disease characterized by progressive symptoms associated with excessive and abnormal iron deposition in the brain. Out of the 11 described NBIA subtypes, the most frequently diagnosed are pantothenate kinase-associated neurodegeneration (PKAN), PLA2G6-associated neurodegeneration (PLAN), beta-propeller protein-associated neurodegeneration (BPAN), and mitochondrial membrane-associated neurodegeneration (MPAN). In our study, we focus on the MPAN subtype, which is caused by mutations in the C19orf12 gene and is one of the most common NBIA subtypes diagnosed in Poland.

The goal of our research is to identify the affected metabolic pathways in fibroblasts derived from MPAN patients with a mutation in the C19orf12 gene. Our experimental approach is based on growing fibroblasts under both basal and OXPHOS-promoting conditions to better visualize potential mitochondrial metabolic defects.

Fibroblasts derived from MPAN patients are characterized by impaired cellular and mitochondrial processes, such as reduced proliferation, altered metabolic activity, decreased oxygen consumption, and increased ROS levels, when compared with control fibroblasts. These alterations become more apparent under conditions that favor mitochondrial metabolism. Moreover, the exact role of the C19orf12 protein in cellular physiology, as well as the impact of mutations in the C19orf12 gene, will be evaluated using HEK-T clones with mutated C19orf12 gene. This will provide deeper insight into the pathomechanism of MPAN disease.





ACKNOWLEDGMENTS



The study is co-financed from the state budget from the Education and Science Ministry program entitled “Science for Society”. Project number NdS/537386/2021/2022, the amount of co-financing 1 900 000 PLN, total value of the project 1 900 000 PLN. Poland 

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Light-mediated activation of mitochondrial BKCa channel protects guinea pig cardiomyocytes against hypoxic injury},

author = {Joanna Lewandowska and Piotr Bednarczyk and Barbara Kalenik and Bogusz Kulawiak and Antoni Wrzosek and Adam Szewczyk},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Photobiomodulation is a non-invasive medical intervention based on the regulation of biological systems via illumination with infrared light (IRL). The therapeutic potential of IRL includes analgesic, anti-inflammatory, and cytoprotective effects, especially in ischemia-reperfusion processes. One of the proteins that absorbs IRL is cytochrome c oxidase (COX), located in the inner mitochondrial membrane, constituting complex IV of the mitochondrial respiratory chain. In the structure of COX, two copper centres can be distinguished, CuA and CuB, which absorb light from the red and infrared spectral range. The maximal absorption wavelengths change depending on the redox conditions: in an oxidising environment, they are 820 nm and 680 nm for CuA and CuB, respectively; in a reducing environment, they are 620 nm and 760 nm for CuA and CuB, respectively. Previous studies have shown that changes in COX activity affect the opening of the large-conductance Ca2+-activated potassium channel (mitoBKCa) [1]. In turn, it has been shown that stimulation of the mitoBKCa channel, like other mitochondrial potassium ion channels by chemical compounds, has a cytoprotective effect, especially in the case of hypoxia and ischemia-reperfusion injury [2]. 

As a research model, we have chosen cardiomyocytes isolated from guinea pigs and mitochondria isolated from them. The quality and purity of isolated mitochondria were confirmed by electron microscopy, functional and biochemical analysis. The Western Blot technique confirmed the presence of the α subunit forming the pore of the mitoBKCa channel. Patch-clamp studies revealed the presence of a functional channel with the characteristics of the mitoBKCa channel, including a conductance of about 130 pS, and a voltage dependence and sensitivity to Ca2+. Moreover, inhibition by paxilline (a classical inhibitor of the BKCa channel) was also observed. The patch-clamp experiments have also shown a regulation of mitoBKCa channel activity by IRL. Illumination with 820 nm light was able to restore mitoBKCa channel activity, which had dropped in response to 300 μM K3[Fe(CN)6]. Moreover, irradiation with 760 nm wavelength reactivated the channel inhibited by reducing agents - ascorbate and TMPD. To investigate the cytoprotective effect of IRL, the cardiomyocytes were subjected to three regimens before hypoxia: glucose deprivation, exposure to infrared light (820 nm), and a combination of both events. 

Our results show that in specified redox conditions 820 nm light regulates the activity of the mitoBKCa channel present in the mitochondria of guinea pig cardiomyocytes and that IRL exposure provides significant cytoprotection against subsequent hypoxic stress. 





ACKNOWLEDGMENTS



Study was funded by the Polish National Science Center grant MAESTRO No. 2019/34/A/NZ1/ 00352 to AS. 

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {The role of phase separation in regulating animal gene expression},

author = {Adam Kłosin},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Transcriptional condensates offer a new framework for understanding the organization of genomic activity. These protein-rich, sub-micrometre assemblies of transcription factors and RNA Polymerase II have been observed in mammalian embryonic stem cells and embryos of model organisms. However, their mechanism of formation and physiological function remain topics of debate. Using optical tweezers experiments, we recently demonstrated that a pioneer transcription factor can undergo surface condensation on DNA in a sequence-specific manner [1]. This involved a transition from a thin adsorbed layer to a thick condensed layer, characteristic of a prewetting transition. We are now investigating whether surface condensation could explain the formation of transcriptional condensates in a living animal. We have established C. elegans embryo as a model system, where we characterize several condensate-forming transcription factors and study their role in gene regulation during development and stress response. We found that genomic locations with a high local clustering of binding sites promote condensate formation. Deleting one such location reduced condensate numbers and altered the gene expression profile of several genes. Previous work on engineered condensates in mammalian cells showed that phase separation could buffer variation in cellular protein concentration [2].  Our experiments in C. elegans suggest that endogenous transcription factor condensates could act as buffers that regulate the level of available transcription factor and fine-tune the organismal response to stress. 

  



ACKNOWLEDGMENTS

 

The work in the Spatial Epigenetics Laboratory at the Nencki Institute of Experimental Biology is founded by NAWA Polish Return 2021 Grant (BPN/PPO/2021/1/00026), the ERC Starting Grant 2022 (101077099)  and EMBO Installation Grant 2022 and Max Planck Parnter Group Program

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Enhancing GōMartini 3 approach for the study of conformational changes in large-scale biomolecular assemblies},

author = {Adolfo Poma Bernaola},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Advances in structural biology, particularly through cryo-electron microscopy (cryo-EM), have enabled the high-resolution characterization of increasingly complex biomolecular assemblies. These developments underscore the need for computational methods capable of capturing biologically relevant conformational changes over extended timescales. While atomistic molecular dynamics (MD) offers detailed insights at atomic resolution, it is inherently limited to local structural fluctuations and often fails to capture the large-scale transitions commonly observed in biological systems. 

GōMartini 3 is a coarse-grained (CG) approach that enables the simulation of protein-membrane interactions, protein folding or unfolding under mechanical forces, and intrinsically disordered proteins. This method is well-validated for small protein systems, such as those composed of one or two well-structured chains, but its application to large macromolecular assemblies remains limited. 

Here, we present an enhanced approach for the study of such complex systems, which integrates information from atomistic MD into the GōMartini 3 model to better capture long-timescale dynamics [1]. Native contacts (NCs) identified from short atomistic MD trajectories are used to inform GōMartini 3, enabling the exploration of conformational transitions with reduced computational overhead. Benchmarking different NC selection strategies revealed that incorporating both high-frequency intra- and inter-chain contacts significantly improves structural flexibility and sampling efficiency. This approach successfully reproduces the conformational landscape of the SARS-CoV-2 spike protein, composed of ∼3000 residues, outperforming the standard implementation. The full framework is available as an open-source resource, offering a scalable tool for simulating complex biomolecular assemblies comprising thousands of residues over timescales reaching hundreds of microseconds.

...},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Back to first principles: models of intrinsically disordered protein conformations},

author = {Radost Waszkiewicz and Barbara P. Klepka and Anna Niedźwiecka},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {As much as 50% of proteins in eukaryotes are believed to be intrinsically disordered [1]. While recent breakthroughs in machine learning have enabled computational tools that rapidly predict protein structure from sequence alone—largely thanks to the Protein Data Bank’s archive of over 200,000 experimentally determined conformations—these structures represent only a subset of proteins: those with stable, well-defined folds. Predicting the dynamic conformations of intrinsically disordered proteins (IDPs) requires extrapolation beyond AlphaFold’s current capabilities and demands more information than the sequence alone can provide.

Data on IDPs remain sparse, and their conformations are sensitive to environmental factors such as ionic strength, temperature and molecular crowding, making model development and evaluation challenging. Because of their extended conformations, direct numerical simulation (both all-atom and coarse-grained) can be prohibitively expensive. Our recent work [2] shows that many phenomenological models of average molecular size overfit, particularly when predicting hydrodynamic size.

While several sequence-based corrections to Gaussian chain models have been proposed, we find that first-principles modeling consistently outperforms them, underscoring the central role of steric interactions in modeling fully disordered and multidomain IDPs. Furthermore, additional data on the dependence of conformation on ionic strength allow us to examine under what conditions screened electrostatic interactions significantly influence protein conformation and when they do not

...},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {The devil is in details – protein hdx reveals critical changes in dynamics underlying protein functional differences},

author = {Michał Dadlez},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {HDX provides unique insight into structural dynamics of proteins. It allows to monitor the relative frequencies of local or global unfolding events, which enable the exchange of main chain amides to solvent deuteria. Over the years HDX studies have shown that the half-lives of such opening events may span from sub-second times to hundreds of hours, so the dynamic axis of protein structurome is long, spanning several orders of magnitude. It has also shown that the dynamic component is quite well represented in typical proteins, and highly stable regions are rather and exception than a rule. Moreover, in some cases of protein variants of the same crystal structures, but different functionalities the detailed analyses of HDX results may provide dynamic rationale of their functional differences. 

Two such cases will exemplified in the presentation. 

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {In or out? GW182 SD joints the biomolecular condensates party in miRNA-mediated gene silencing},

author = {Michał K. Białobrzewski and Maja K. Cieplak-Rotowska and Zuzanna Staszałek and Marc R. Fabian and Nahum Sonenberg and Michał Dadlez and Anna Niedźwiecka},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {GW182 is a fuzzy, intrinsically disordered protein that plays a key role in processing bodies (P-bodies)1. These biomolecular condensates are responsible for degrading mRNA during post-transcriptional miRNA-mediated gene silencing2. The N-terminal region of GW182, called the Ago-binding domain (ABD), binds to Argonaute (Ago), a core component of the miRNA-induced silencing complex (miRISC). The C-terminal region, known as the silencing domain (SD), recruits the CCR4-NOT deadenylase complex to miRISC-targeted mRNAs and enables gene repression.

CCR4-NOT is involved not only in the miRNA-mediated silencing pathway. It also functions in a different post-transcriptional repression mechanism driven by tristetraprolin (TTP)3, an intrinsically disordered RNA-binding protein that targets AU-rich elements in the 3′ untranslated regions (UTRs) of cytokine mRNAs. Both GW182 and TTP recruit CCR4-NOT to silence gene expression, but they do so through distinct mechanisms. This functional overlap led us to explore whether the two silencing pathways might converge or compete with one another.

Interestingly, GW182 SD can repress gene expression even when tethered to mRNA independently of the ABD. While recent studies have revealed the role of the GW182 ABD in liquid-liquid phase separation (LLPS)4, the contribution of the SD to this process remains unclear. It is also unknown how other proteins that interact with GW182 might affect the P-body formation.

To address these knowledge gaps, we performed biophysical studies showing that the human GW182 SD can drive LLPS independently from the ABD. Phase diagrams reveal that this phase behaviour is temperature-sensitive and relies on π-π interactions between tryptophan side chains. We also observed that GW182 SD forms multiprotein liquid droplets with a fragment of the CNOT1 subunit of CCR4-NOT that specifically binds to GW182 SD. This interaction points to a host–client relationship5 between GW182 and CNOT1. Furthermore, the presence of TTP as a third component disrupts the formation of these condensates. This interference suggests that GW182 and TTP are in direct molecular competition for binding to the same region of CNOT1. This could indicate the possibility of the two post-transcriptional gene silencing pathways crossing over6.



ACKNOWLEDGMENTS

 

This work was supported by the NCN grants no. UMO-2016/22/E/NZ1/00656 to A. N. and no. UMO-2023/49/B/NZ1/04320 to M. K. B. The studies were performed in the NanoFun laboratories co-financed by ERDF within the POIG.02.02.00-00-025/09 programme

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Looking for molecular mechanisms of the cytoprotective role of NPAS4},

author = {Beata Greb-Markiewicz and Izabela Krauze and Piotr Kruszyński},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {NPAS4 (Neuronal PAS domain-containing protein 4), which belongs to the bHLH-PAS transcription factors, was discovered in hippocampal neurons [1]. Later, NPAS4 was shown to be induced by activity and stress in pancreatic β-cells for protection from endoplasmic reticulum stress, leading to the suggestion of NPAS4 as a therapeutic target in type 2 diabetes [2] and pancreas transplantation [3]. NPAS4 has neuroprotective effects in the damaged brain after ischemic stroke and has been proposed as a component of novel stroke therapies [4]. Also, NPAS4 has been proposed as a therapeutic target for depression, neurodegenerative diseases associated with synaptic dysfunction [5] and Alzheimer's disease [6]. Despite the presented important functions of NPAS4 and its potential therapeutic application, the mechanism of action of this protein, especially nongenomic way is not understood.

We believe that the multifunctionality of NPAS4 reported in the literature depends on the intrinsically disordered nature of its structure. The conformational plasticity of the long C-terminal region, predicted as IDR (intrinsically disordered region), its sensitivity to environmental changes and ability to interact with multiple partners, could explain documented multiple functions of NPAS4. Recently, the ability to form liquid-liquid phase separation (LLPS) has been proposed to be important for neuronal development and synaptic plasticity. Mutations in areas responsible for LLPS have been shown to lead to pathological aggregation and diseases such as autism or cancer. During this presentation, we will present attempts to clarify the links between NPAS4 and the development of neurodegenerative diseases.   





ACKNOWLEDGMENTS



This work was supported by a subsidy from The Polish Ministry of Science and High Education for the Faculty of Chemistry of Wroclaw University of Science and Technology.},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {How machine learning allows to reconstruct cardiomyocyte action potential from the surface of the body},

author = {Sebastian Wildowicz and Tomasz Gradowski and Elżbieta Katarzyna Biernacka and Karolina Borowiec and Olgierd Woźniak and Igor Olczak and Paulina Figura and Aleksandra Bedełek and Teodor Buchner },

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Motivation and Aim: Interpretation of certain electrocardiographic symptoms is still considered an art. Modern techniques, such as machine learning (ML) can be particularly useful, however following Wittgenstein, their abilities to interpret the world are set by the limits of the language, that has been used in learning process. Our aim is to demonstrate the usefulness of ML techniques based on PhysECG reconstruction model: a new paradigm of ECG interpretation, based on molecular theory of biopotentials. We want to show, that the features of the model have a clear bearing to underlying cardiac anatomy and physiology. Specifically, we show, how the local cardiomyocyte action potential (AP) can be quite reliably reconstructed from the surface ECG. We present the results of a pilot study [1], which are long from being reliably confirmed, on the clinical level, but on the technical level they generate promising results.

Novelty: Application of PhysECG algorithm allows to interpret the ECG within a different dogma. We decompose the passage of an activity wave through the ventricles into two mutually related but functionally disjoint processes: passage of the activation wavefront (P1) and cardiomyocyte response (P2). Starting the analysis from the electronic circuit analysis of the electrode setup, we show how to reconstruct the true unipolar potentials, that reach individual electrodes, and how they account to ECG lead, observed in clinic. 

Methods: We have used a ML model trained on 800,000 12-lead ECG recordings of MIMIC database, which contains healthy individuals and patients with various cardiological symptoms. The model performs a two-step reconstruction of the ECG, which is decomposed into activation functions (P1 process) and locally spatially averaged cardiomyocyte response (AP), resolved per electrode. As test data we have used 549 recordings of PTB database, including 80 patients of cardiological norm. For the pilot study we have used 51 recordings of Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) from National Institute of Cardiology.  

Main results: We confirm the result, that the Wilson potential is far from being constant and far from zero [2]. The analysis allows us to show correlation between QRS widening and T wave inversion: note, that in clinic the processes of depolarization and repolarization are often treated separately, due to complex spatiotemporal dynamics. We demonstrate a conceptual model of the QRS-T wave relation, showing, that there is a direct link between T wave inversion and wide QRS complex: note, that both these symptoms are observed in the ECG of ARVC patients. Finally, we show, that the possibility to perform a regional resolution of the AP reveals regional changes, which are potentially arrhythmogenic. We show that early results on the assessment of activation duration show correlation with the progression of the disease

.......},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Deep learning for medical diagnosis},

author = {Szymon Płotka},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Deep learning is increasingly redefining diagnostic workflows in medicine, particularly in radiology, where it enables automated, accurate, and scalable analysis of complex imaging data. This talk provides a high-level overview of deep learning approaches in medical diagnostics, with a focused examination of their application to pancreatic tumor detection using computed tomography (CT) imaging. Pancreatic cancer remains one of the deadliest malignancies, largely due to late-stage diagnosis and the subtle, often ambiguous appearance of tumors on imaging. We present recent developments in convolutional neural networks (CNNs) and hybrid architectures trained on CT datasets for the segmentation and classification of pancreatic lesions. These models have demonstrated the potential to detect tumors at earlier stages and differentiate between malignant and benign growths with increasing accuracy. The talk will also cover practical challenges, including limited annotated datasets, variability in scan protocols across institutions, and the need for clinically interpretable outputs. Strategies such as data augmentation, and model tuning are discussed in the context of improving performance and generalizability. We conclude by exploring the clinical implications of AI-assisted radiology, regulatory considerations, and pathways toward integration into real-world diagnostic settings. This session is intended for researchers and clinicians at the intersection of AI and healthcare, highlighting the opportunities and challenges of applying deep learning to high-impact diagnostic problems.

 



ACKNOWLEDGMENTS



Support from the Center for Machine Learning, University of Warsaw, IDUB Action 7.3.1, and from the Division of Biophysics, Faculty of Physics, University of Warsaw, 501-D111-01-1110102 funds.

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {From Rosenblatt’s perceptron to jumper’s Alphafold},

author = {Szymon Nowakowski},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Today, machine learning methods have become part of mainstream everyday use. In the natural sciences, they have emerged as standard research tools across many fields, significantly extending and complementing conventional approaches to modeling complex systems and processes. 

When Frank Rosenblatt introduced the first artificial neuron in 1958 [1], his inspiration came directly from biology. That biological grounding continued to shape the development of neural network architectures — for example, convolutional neural networks [2] were modeled after the structure of the cat’s visual cortex.

When John Jumper and Demis Hassabis presented AlphaFold2, their neural network model for predicting tertiary protein structure [3], the direction of inspiration had reversed. Their model was built not on biological intuition, but on abstract mathematical constructs such as tensors, attention mechanisms, and the transformer architecture, initially developed for natural language translation. These tools from the world of artificial intelligence were used to address one of the central challenges in biology: protein folding [4].

In this talk, I will outline key aspects of AlphaFold2’s inner workings, framing them within the broader historical shift from biologically inspired architectures to mathematically grounded paradigms — a transformation reflected even in the evolving terminology, as tensors replaced neurons along the way. This perspective will be set against the backdrop of recurrent cycles of enthusiasm in neural network research, each periodically constrained by the technological limitations of its time. 

This framing is especially relevant today, as society increasingly reflects on the boundaries, potential, and implications of artificial intelligence—in science, across societal structures, and in our individual lives.



ACKNOWLEDGMENTS

 

Support from the Center for Machine Learning, University of Warsaw, IDUB Action 7.3.1, 501-D111-20-0001370 funds. 



},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Computational insights into targeting Pteridine Reductase 1, a key enzyme from pathogenic trypanosomatids},

author = {Joanna Panecka-Hofman and Ina Pöhner and K. Uszyńska and Edyta Dyguda-Kazimierowicz and Rebecca C. Wade},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Pteridine reductase 1 (PTR1) is a folate pathway enzyme in trypanosomatid parasites that uses an NADP cofactor to reduce folates for DNA synthesis. It contributes to resistance against antifolate drugs like methotrexate (MTX), and thus is considered a promising anti-trypanosomatid drug target.

Using molecular docking simulations, we have developed two compound series combining 2-aminobenzothiazole and 3,4-dichlorophenyl moieties, resulting in several low-micromolar PTR1 and parasite growth inhibitors, less toxic than the parent compound [1]. One compound exhibited inhibition against both T. brucei and Leishmania species, which is relatively uncommon. Finally, computationally efficient quantum-mechanical calculations enabled us to elucidate the effects of halogen substitutions on inhibitor interactions with PTR1.

These efforts have also shown that drug development targeting PTR1 is hindered by a limited understanding of its structural dynamics, which we have studied using molecular dynamics simulations and related computational techniques [2,3]. We have uncovered an opening movement of the substrate loop that affects interactions of PTR1 with substrates, product, and the model inhibitor MTX. The dynamics of loop-ligand interactions appear critical for understanding binding mechanisms. These findings highlight factors influencing ligand binding to PTR1 and may support further PTR1-targeted drug design.





ACKNOWLEDGMENTS



This work was supported by the European Union’s FP7 grant New Medicines for Trypanosomatidic Infections (agreement no. 603240), the Klaus Tschira Foundation, the Polish National Science Centre (grant no. 2016/21/D/NZ1/02806), the BIOMS program at the Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, and the Department of Chemistry at Wroclaw University of Science and Technology. Computational resources were provided by the Interdisciplinary Centre for Mathematical and Computational Modelling (ICM), University of Warsaw (grant no. G70-13, GB70-11, GA73-25, GA84-38), the Faculty of Physics, University of Warsaw (infrastructure financed by European Funds: POIG.02.01.00-14-122/09), CSC - IT Center for Science Ltd., and the Wroclaw Center for Networking and Supercomputing (WCSS).

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {SimDNA: a coarse-grained method for DNA folding simulations and 3D structure prediction},

author = {Maciej Maciejczyk and Naeim Moafinejad and Michał J. Boniecki and Janusz M. Bujnicki},

issn = {2084-1892},

year  = {2025},

date = {2025-06-26},

urldate = {2025-06-26},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {DNA, the blueprint of life, primarily forms a double helix but can also create structures like junctions, triplexes, and quadruplexes. These structures are essential for cellular functions, including gene expression regulation, replication, and genome stability maintenance. 

Exploring DNA structure through methods like X-ray crystallography, NMR, and Cryo-EM spectroscopy is crucial but accompanied by challenges. These methods can be costly and time-intensive. X-ray crystallography captures static snapshots of DNA conformations, lacking dynamic insights. Moreover, NMR is restricted in its ability to analyze smaller DNA molecules, while achieving high-resolution Cryo-EM density maps is more common for larger biomolecules, such as those with 150 kDa. 

SimDNA is a new computational tool based on SimRNA [1] that addresses these challenges. It predicts DNA 3D structures using a coarse-grained representation and the Metropolis Monte Carlo sampling technique - a statistical mechanics method that efficiently explores conformational spaces of the molecule by sampling from Boltzmann distribution. 

This approach allows SimDNA to accurately fold various DNA forms, including duplexes, junctions, and non-canonical structures like triplexes and G-quadruplexes, even without external restraints. Furthermore, SimDNA enables guided simulations using data from experiments or other computational methods, providing a versatile tool for researchers. This flexibility allows user-defined restraints to focus simulations on specific interactions or structural configurations, facilitating the study of transitions between different DNA structures. Overall, SimDNA holds great promise for advancing our understanding of DNA behavior, offering insights into fundamental biological processes, and aiding in biomedical research and therapeutic development. 



 

ACKNOWLEDGMENTS



This research was funded by the European Research Council (GA 261351) to J.M.B. and by the RACE-PRIME project, performed within the IRAP programme of the Foundation for Polish Science, co-financed by the European Union under the European Funds for Smart Economy 2021-2027 (FENG).

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Mapping spatial organization of functional inputs in valence-related amygdalo-hippocampal circuits},

author = {Dario Cupolillo and Vincenzo Regio and Andrea Barberis},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

issue = {44 (suppl. A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {The formation of memories in response to aversive or rewarding stimuli is crucial in guiding avoidance or approach behaviors. Scattered, projection-defined neuronal populations within the basolateral amygdala (BLA) selectively activate during encoding and retrieval of memories associated with either positive or negative valence. Interestingly, BLA neurons projecting to the CA1 area of ventral hippocampus (vCA1) respond to both positive or negative predicting cues with no marked bias, suggesting that, within the whole responding population, two distinct subnetworks relay opposite information to vCA1. However, the mechanism by which vCA1 pyramidal neurons discern between positive and negative-related information remains unclear. The valence information might stay segregated within two distinct neuronal populations in vCA1, or it might also converge onto the same vCA1 neurons, which have the capability to specifically encode negative or positive valence.

We suggest that valence-activated BLA neurons contact vCA1 dendrites in a precise spatial organization that together with inhibitory synapses can generate unique valence-related spiking patterns in the postsynaptic neuron. To validate this hypothesis, we aimed at building a map of the spatial location of functional synaptic inputs from BLA, vCA3 and bistratified interneurons onto vCA1 pyramidal neurons. To this end, we have developed an automated procedure to perform single-spine calcium imaging in the whole vCA1 dendritic arbor exploiting custom made neural network algorithms combined with electrophysiology and optogenetics. This integrated approach allowed to reveal the unique distribution of BLA and vCA3 and inhibitory inputs onto the whole dendritic arbor of vCA1 pyramidal neurons....

},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Excitatory effects of metabotropic receptors in neocortical vasoactive intestinal polypeptide-expressing interneurons},

author = {Karolina Bogaj and Joanna Urban-Ciecko},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

volume = {44 (suppl.A)},

issue = {44 (suppl. A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {A deterministic model of nicotinic receptor function: a shift from stochastic paradigms},

author = {Ewa Nurowska and Krzysztof A. Meissner},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

issue = {44 (suppl. A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {We recently presented a novel deterministic model for the operation of the nicotinic acetylcholine receptor (nAChR) [1], offering an alternative to traditional stochastic (Markovian) models [2]. To validate the model predictions, we used ultrahigh-resolution single-channel recordings of the nACH receptor [3]. Unlike these models, the new approach assumes that receptor gating is fully determined by agonist binding, with no random transitions or delays. The model assumes that the agonist molecules bind to the receptor alternately and repeatedly (Fig.1A,C). After dissociating from the receptor, the agonists remain within the binding pocket and participate in subsequent binding events. The receptor remains open as long as at least one agonist molecule is bound (Fig.1C). Thus, prolonged openings occur through repeated binding of both agonist molecules.

The model also accounts for brief openings, which happen when only one agonist molecule is involved in activation, or when the receptor is partially desensitized. We define a partially desensitized receptor as one with a C-loop in the closed (down) position. (Fig.1B). Such a receptor can still open briefly if an agonist binds at the site where the C-loop remains in the open (up) position.

In the Markov models, conformational transitions from the resting state to the open and desensitized states are triggered by an increase in the agonist affinity. In deterministic model the binding site affinity remains constant regardless of whether the second site is occupied or whether the receptor is in the open or closed state.

We provide exact mathematical formulas linking agonist binding times to receptor with measured receptor opening times. This enables quantitative validation of the model and connects directly measurable macroscopic properties with microscopic parameters characterizing receptors. 

Furthermore, the model suggests that receptor kinetics can be modulated without direct binding of a modulator molecule, pointing to a novel form of non-classical modulation [4]. The model can help assess whether an ionotropic receptor behaves deterministically....

},

key = {Plenary lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Structure-function relationship of the GABA type A Receptor},

author = {Michał A. Michałowski and Katarzyna Terejko and Karol Kłopotowski and Jerzy W. Mozrzymas},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Polish Biophysical Society and Adam Mickiewicz University},

volume = {44 (suppl.A)},

issue = {44 (suppl. A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {The γ-aminobutyric acid type A receptor (GABAAR) is a pentameric ligand-gated ion channel responsible for mediating inhibitory neurotransmission in the central nervous system. Dysfunction of GABAAR is implicated in several neurological and psychiatric disorders. Despite substantial progress in understanding GABAAR  architecture and function, the molecular details of its activation mechanism remain incomplete [1]. We aimed to identify and temporally map structural elements of the α1β2γ2 GABAAR subtype that facilitate the transition from the agonist-bound to the fully open channel state. We applied single-channel recordings with high temporal resolution to wild-type and a wide array of single-point mutants targeting different structural regions of the receptor, followed by kinetic modeling and Φ-value analysis [2] to determine the contribution of each residue to gating transitions.

Mutations were introduced in functionally distinct receptor regions, including the agonist binding site, extracellular-transmembrane domain interface, and ion pore, allowing us to compare their effects on dose-response characteristics and gating kinetics. Notably, mutations in the binding pocket - such as β2E155, β2F200, α1F45 and α1F64 - produced significant right shifts in EC50 values, consistent with disrupted ligand binding but also significantly affected the receptor gating. Conversely, mutations in regions distant from the binding site, especially in the N-terminal region (β2F31, α1F14), at the domain interface (β2V53, β2P273, α1H55, α1P277) and  transmembrane helices (β2H267, β2E270 β2L296, α1G258, and α1L300), predominantly altered channel opening and closing kinetics without major changes in agonist affinity. 

A particularly striking result was that some mutations at the domain interface—such as α1R220 and β2R216 in the β10-M1 linker and α1D54, β2E52 in loop 2 resulted in a near-complete loss of function despite normal membrane expression. This suggests that these residues are essential for the conformational coupling between extracellular and transmembrane domains. On the contrary a number of the ion pore lining residues mutations (β2T256, β2L259, α1T260, α1L263) induced the spontaneous activity of the receptor underlining a labile conformation of the channel gate.

Using Φ-value analysis, we reconstructed a sequential map of conformational changes leading from extracellular domain top to agonist binding through domain interface to pore opening (Fig. 1), supporting a model where early events localize near the binding site and later transitions propagate through the domain interface into the transmembrane helices. Small range of all obtained Φ-values suggest that movement of the respective receptor structures is highly synchronized. This corresponds well with significant effects of almost all of investigated single point mutants on the receptor gating, multiple conjugated interactions between respective residues and also exceptionally broad variety of modulators affecting GABAAR gating.  All those data supports the allosteric character of the receptor.....

},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {The effects of 17β-estradiol and progesterone on the BK channel activity in human glioblastoma cells},

author = {Anna Lalik and Beata Dworakowska and Anna Sekrecka-Belniak and Klaudia Skutnik and Michał Wojcik and Kamil Niezabitowski and Jakub Kraus and Paulina Trybek and Agata Wawrzkiewicz-Jałowiecka},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

issue = {44 (suppl. A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Sex differences in glioblastoma incidence and progression suggest a regulatory role of steroid hormones, including 17β-estradiol (E2) and progesterone (P) [1], but the exact mechanism of action is not yet understood.  In this study, we examined how E2 and P influence the expression and functionality of large-conductance voltage- and Ca²⁺-activated potassium channels (BK) channels and evaluated their impact on cell viability and cycle progression in human U87-MG glioblastoma cells.

U87-MG cells were treated with two E2 and P concentrations (i.e., E2: physiological-like 0.0018 μg/ml and pharmaceutical 1.8 μg/ml; P: physiological-like 0.025 μg/ml and pharmaceutical 25 μg/ml) for 24–48h. Cell viability was assessed using the CCK-8 assay. RT-qPCR was used to measure the expression of BK α and β (1–4) subunits. Promoter regions were screened for hormone-responsive elements using the online program AliBaba2.1. Functional activity of gBK channels was evaluated via single-channel patch-clamp method. The recordings were obtained at varied membrane voltages (–50 mV to +75 mV with 25 mV step) and analyzed by kinetic, correlation and nonlinear methods. Flow cytometry was used to assess the effects of E2 and P effects on the cell cycle.

Both E2 and P induced a concentration-dependent inhibition of BK channel activity in U87-MG cells, with a well-pronounced reduction in open-state probability (pop), especially under depolarized conditions, as shown for exemplary potential of 50 mV in Table 1. .....

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Atomic-resolution structural insights into naturally-crystalline proteinaceous mosquitocides},

author = {Jacques-Philippe Colletier},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

volume = {44 (suppl.A)},

issue = {44 (suppl. A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {As the vector of malaria, Dengue fever and filariasis, the mosquito is arguably the organism most threatening to human health. Chemical mosquitocides are cost-effective, but they also affect crustaceans, bees and fish, and extensive application results in resistance in the field. Notably, the recent spread of resistance to pyrethroid insecticides threatens efforts to control malaria. To date, the most environmentally-safe alternative to control mosquito populations remains the application of proteinacous mosquitocides produced in the form of naturally-occurring nanocrystals by entomopathogenic bacteria. Notably, Lysinibacillus shapericus (Ls) produces the binary toxin Tpp1Aa/2Aa (formerly known as BinAB) while Bacillus thuringiensis israelensis (Bti) produces a cocktail of four naturally-crystalline proteinaceous toxins (Cyt1Aa, Cry11Aa, Cry4Aa, Cry4Ba). The structures of these proteins long remain elusive due to both the minute size of the natural crystals and the difficulty to recrystallize the toxins in vitro after their dissolution. We will report on the in vivo protoxin structures of Ls Tpp1Aa/2Aa as well as Bti Cyt1Aa and Cry11Aa, which we solved by applying serial femtosecond crystallography to the naturally-occurring nanocrystals [1-3]. We will present results from structure-guided mutagenesis, which afforded the identification of residues that affect crystal size, pH sensitivity and toxin folding, thus providing insights into each toxin’s bioactivation cascade. Altogether, our results open avenues for development of new, rational strategies for improved mosquito control, e.g. by development of recombinant bacterial insecticides combining potent larvicidal proteins of different origins [1-3]. ...},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {BKCa channel as a novel modulator of DNA damage response in human bronchial epithelial cells exposed to particulate matter},

author = {Kamila Maliszewska-Olejniczak and Agata Kustra and Wojciech Szymański and Adrianna Dąbrowska-Hulka and Monika Żochowska and Bogusz Kulawiakand and Piotr Bednarczyk},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

volume = {44 (suppl.A)},

issue = {44 (suppl. A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Although particulate matter (PM) is a well-recognized genotoxic environmental agent, the molecular mechanisms underlying its harmful health effects remain poorly understood. The respiratory epithelium, as the primary site of PM deposition, acts as a protective barrier and is enriched in potassium channels that are essential for maintaining airway surface liquid homeostasis. In human bronchial epithelial (HBE) cells, large-conductance calcium-activated potassium (BKCa) channels—located at the apical plasma membrane and within the inner mitochondrial membrane play a key role in this regulation.

In this study, we investigated the potential involvement of the BKCa channel in the cellular DNA damage response (DDR) following PM exposure [1]. While DDR pathways have been extensively characterized, the role of ion channels in these processes remains largely unexplored. To address this, we employed BKCa-depleted HBE cells (HBE ΔαBKCa) as a physiological model [2].

Exposure to standardized PM (SRM-2786) in HBE ΔαBKCa cells resulted in decreased clonogenic survival, elevated ROS levels, PARP1-dependent apoptosis, cell cycle alterations, and an increase in DNA double-strand breaks compared to wild-type (HBE WT) cells. qPCR analysis revealed upregulation of genes involved in both single-strand break repair (SSBR), such as OGG1 and XRCC1, and double-strand break repair (DSBR), including XRCC3 and PARP3, suggesting a compensatory activation of DDR pathways.

In conclusion, this study provides the first evidence of a critical role for the BKCa channel in modulating the DNA damage response to particulate matter in bronchial epithelial cells ....

},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Structure-guided stabilization of membrane-active peptides as a strategy to combat antibiotic resistance},

author = {Monika Wojciechowska and Małgorzata Lobka and Izabela Siekierska and Joanna Trylska},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Polish Biophysical Society and Adam Mickiewicz University},

volume = {44 (suppl.A)},

issue = {44 (suppl. A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {The emergence of multidrug-resistant bacteria poses a serious global health challenge and necessitates the search for alternative antibacterial agents. Membrane-active peptides (MAPs), including antimicrobial peptides (AMPs) and cell-penetrating peptides (CPPs), are promising molecules due to their fast mode of action and low propensity to induce resistance. However, their use is limited by poor structural stability, susceptibility to proteolytic degradation, and possible toxicity toward mammalian cells.

Our work focuses on improving the antibacterial properties of MAPs by stabilizing their biologically active conformations, particularly α-helices (Fig. 1). We employed a hydrocarbon stapling strategy that involves the incorporation of two (S)-2-(4′-pentenyl)-alanine residues into the peptide sequence and covalent side-chain cross-linking. This modification locks the peptides into a helical conformation and enhances their structural integrity. Using this method, we successfully modified a range of peptides, including anoplin (a naturally weak AMP) [1], a CPP - (KFF)₃K [2], and de novo designed amphipathic peptides rich in lysines and leucines [3]. Stapled versions of these peptides showed significantly improved antibacterial activity, with MIC values ranging from 2 to 4 μM against both gram-positive and gram-negative strains. The stapled anoplin exhibited a 16-fold increase in activity and substantially enhanced proteolytic stability [1]. Similarly, stapled (KFF)₃K gained membrane-permeabilizing properties and potent antimicrobial function [2]. Structural studies confirmed that these peptides adopt membrane-active α-helical conformations. Importantly, none of the stapled peptides exhibited hemolytic activity or cytotoxic effects on mammalian cells [1-3].

In a further step, we designed and synthesized conjugates of the stapled peptides with aminoglycoside antibiotics, such as neomycin and amikacin, using both reducible and non-reducible linkers. These conjugates retained or exceeded the antibacterial activity of the parent compounds and were effective against resistant bacterial strains, highlighting the synergistic potential of peptide–antibiotic hybrids [4].

In conclusion, our strategy of stabilizing secondary structures has proven highly effective in improving the antimicrobial performance and therapeutic potential of MAPs, offering a promising platform for the development of next-generation antibacterial agents ....



},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Bicarbonate transport correction drives clinical benefit of Elexacaftor/Tezacaftor/Ivacaftor in F508del-CF},

author = {Miroslaw Zajac and Agathe Lepissier and Yashoda Yalal and Elise Dreano and Aurelie Hatton and Isabelle Sermet-Gaudelus},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

volume = {44 (suppl.A)},

issue = {44 (suppl. A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Cystic fibrosis (CF) is caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR), an epithelial ion channel essential for maintaining airway surface homeostasis through the coordinated transport of chloride (Cl⁻) and bicarbonate (HCO₃⁻) into the airway surface liquid (ASL). Defective CFTR disrupts this ion balance, leading to ASL dehydration, impaired mucociliary clearance, and progressive lung disease. The Elexacaftor/Tezacaftor/Ivacaftor (ETI) triple modulator therapy has demonstrated substantial clinical benefits in people with CF (pwCF) carrying the F508del mutation, primarily attributed to restored Cl⁻ transport. Emerging evidence indicates that ETI-mediated Cl⁻ correction is further modulated by airway inflammation. However, the effect of F508del-CFTR rescue on transepithelial electrogenic HCO₃⁻ secretion — a critical determinant of ASL pH, viscosity, and host defense — remains incompletely characterized, limiting our understanding of the full therapeutic potential of CFTR modulators.

We aimed to characterize CFTR-mediated transepithelial bicarbonate (HCO₃⁻) transport following F508del-CFTR rescue, both at baseline and under inflammatory conditions. The extent of CFTR functional correction was correlated with clinical outcomes in people with CF.



Methods 

Primary human nasal and bronchial epithelial cells from people with CF (pwCF) carrying at least one F508del-CFTR allele were treated with Elexacaftor/Tezacaftor/Ivacaftor (ETI), both alone and in combination with TNF-α and IL-17 to model an inflammatory microenvironment. CFTR-mediated transepithelial bicarbonate (HCO₃⁻) and chloride (Cl-) transport was assessed by using short-circuit current (Isc) measurements in Cl⁻-free and HCO₃⁻-free buffer systems, respectively. 

Results

ETI treatment significantly increased F508del-CFTR–dependent bicarbonate (HCO₃⁻) and chloride (Cl⁻) short-circuit currents (Isc) to a similar extent. The Isc HCO₃⁻ / Isc Cl⁻ ratio in ETI-treated F508del cultures was comparable to that observed in wild-type (WT) epithelia. Exposure to TNF-α and IL-17 further enhanced ETI-corrected CFTR-mediated HCO₃⁻ and Cl⁻ transport, without altering their relative permeability ratio. No significant differences in Cl⁻ or HCO₃⁻ transport correction were observed between F508del homozygous and heterozygous primary cultures. At the individual patient level, the extent of HCO₃⁻ transport correction correlated with improvements in FEV₁, while Cl⁻ transport correction was associated with changes in sweat chloride concentration.

Conclusions 

ETI restores chloride (Cl⁻) and bicarbonate (HCO₃⁻) transport at similar rates across the airway epithelium, with selectivity akin to wild-type CFTR. Both CFTR-dependent HCO₃⁻ and Cl⁻ transport independently and additively influence pulmonary disease severity in CF. Incorporating bicarbonate transport assays into clinical trials may enhance the evaluation of modulator efficacy and aid in optimizing personalized treatment strategies for CF ....

},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Metallic nanoparticles as potential modulators of anticancer therapy},

author = {Grzegorz Gołuński and Patrycja Bełdzińska and Marcin Zakrzewski and Barbara Galikowska-Bogut and Natalia Derewońko and Katarzyna Bury and Marzena Jamrógiewicz and Dariusz Wyrzykowski and Rafał Sądej and Jacek Piosik},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

volume = {44 (suppl.A)},

issue = {44 (suppl. A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Cancer is one of the greatest challenges faced by medicine. World Health Organization estimates that cancer’s incidence and death toll approached 20 and 10 million, in 2022, respectively, with the most common being lung, breast, colorectum, and prostate cancers [1].

Although heterogeneity of the disease requires individual approach to each patient, chemotherapy remains one of the most commonly used treatment regimens. Despite its undeniable efficacy, factors such as cancer cells resistance and severe side effects of the therapy significantly limit the potential benefits for the patient. Researchers all around the globe are trying to address these concerns aiming for the therapy combining maximized efficiency with minimal complications of the therapy[2].

Nanomedicine is one of the disciplines heavily involved in this research. The unique properties of  nanomaterials, including metallic nanoparticles, make them excellent candidates for the modulators of the classic anticancer drugs used in chemotherapy. The nanoparticles may be used both as the theragnostic agents and drug delivery vessels increasing selectivity of the anticancer drug, reducing cancer cells drug resistance, and contributing to the anticancer activity of the treatment regimen [3]. 

Therefore, we decided to evaluate the metallic nanoparticles potential to modulate the activity of the anticancer drugs. In our research we employed number of physicochemical methods to analyze interactions between selected metallic nanoparticles and anticancer agents, starting from spectroscopic methods via dynamic light scattering and atomic force microscopy to calorimetric methods. Subsequently, we assessed influence of nanoparticles on the anticancer drugs biological activity in the Ames mutagenicity test, MTT and alamarBlue cytotoxicity tests, and 3D Matrigel test.

Obtained results indicate direct interactions between metallic nanoparticles and anticancer drugs from anthracyclines group. However, there was no conclusive evidence on the cisplatin interactions with nanoparticles. Nevertheless, employed biological assays revealed significant influence of analyzed nanoparticles on the biological activity of all investigated anticancer drugs. Notably, the mutagenic activity of all tested was reduced while cytotoxic activity against chosen cancer cell lines was either not affected or elevated. Moreover, in case of the non-cancerous cell lines we observed protective effects of the tested nanoparticles against evaluated anticancer drugs.

Summing up, the results of our research indicate direct interactions between most of anticancer drugs and metallic nanoparticles. Furthermore, observed interactions affect biological activity of the drugs increasing their anticancer potential and selectivity. Similar effect was observed in case of cisplatin, where no direct interactions were confirmed....

},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Proteins: new avenues for the design of optical biosensors},

author = {Sabato D’Auria},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Since several years, researcher have acknowledged the importance of integrating biological molecules into the design of artificial devices.  Biosensors are a combination of signal transducers and biomolecules, and they have a fundamental role in medical diagnosis, food safety and environmental control.  The compactness, portability, high specificity, and sensitivity are the motives that the design of biosensors is considered to have a high potential in all analytical practices.  Consequently, modern biotechnological strategies are exploiting the use of proteins, enzymes and antibody as components of sensors for analyses of high social interest. In particular, the idea is to take advantage of the extremely wide range of selective affinities sculpted into the various biomolecules by natural biological evolution. The number of potential molecules specifically recognized by different biomolecules is enormous and it sorts from small molecules to macromolecules (including protein themselves). The advantages of using proteins as components of biosensors are presented},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {What Vesicles Remember: Nanoscale Traces of Cellular Identity in Plasma Membrane Models},

author = {Katarzyna Pogoda and Karolina Chrabąszcz and Natalia Piergies},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Cell-derived plasma membrane vesicles are among the most physiologically relevant model systems for studying native membrane composition and architecture [1]. Structural abnormalities in cell membranes are a hallmark of tumor cells and often accompany neoplastic transformation. Changes in membrane composition can significantly affect its biophysical properties, contributing to increased resistance to anticancer therapies [2]. However, the lack of specific biophysical or biochemical profiles for cancer cell membranes persists, primarily due to limited methods for nanoscale and spatial characterization of such thin and flexible structures. 

In this study, we propose the use of atomic force microscopy working in force spectroscopy mode to analyze the nanoscale mechanical properties of plasma membrane vesicles derived from normal (microglia) and cancerous (glioblastoma) cell lines (Fig. 1A). For the first time, we demonstrate that the mechanical properties of plasma membrane vesicles (Fig. 1B) closely resemble those of the cells from which they originate (Fig. 1C). Furthermore, we describe differences in the biomolecular composition of these vesicles using FT-IR spectroscopy combined with principal component analysis (PCA). Finally, we show that integrating atomic force microscopy with infrared spectroscopy for the study of native plasma membranes reveals pronounced local heterogeneity that would otherwise remain undetected (Fig. 1D).

...},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Probing the impact of cannabidiol on cellular lipid dynamics via vibrational spectroscopy},

author = {Karolina Chrabąszcz and Agnieszka Panek and Katarzyna Pogoda},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Lipids, once considered merely as cellular energy reservoirs, are now recognized as dynamic regulators of numerous biological processes, including signal transduction, membrane remodeling, and cellular stress responses.[1] Increasing evidence points to their important role in the development of anti-cancer therapy resistance, including radioresistance. Malignant peripheral nerve sheath tumors (MPNST) are among the most radioresistant types of tumors, with limited treatment options and poor prognosis.[2]

In our study, we investigated the effects of cannabidiol (CBD)—a non-psychoactive compound with anticancer and neuroprotective potential—on the radiosensitivity of normal and cancerous cells of the peripheral nervous system. Our findings reveal that CBD sensitizes MPNST cells to ionizing radiation, while simultaneously protecting normal Schwann cells from radiation-induced damage.[3] Mechanistic insights obtained from vibrational spectroscopy strongly suggest that lipids are key modulators of this differential response.

Using a combination of Raman, FT-IR, and nanoscale AFM-IR imaging, we demonstrated distinct changes in the levels, distribution, and conformation of cellular lipids—especially cholesterol and its esters as well as  phospholipids—in both cell types. The high-resolution chemoselective maps obtained by AFM-IR revealed localized lipid accumulation and modifications that correlate with the observed radiobiological effects.

To precisely track lipid alterations at the molecular level, we employed spectroscopically active probes in the form of deuterated lipids, whose unique C–D stretching vibrations appear in the cell-silent region of the spectrum (2000–2300 cm⁻¹), avoiding overlap with endogenous cellular signals.[4] This allowed us to selectively monitor the dynamics and distribution of cholesterol modifications in both cell lines, and its interaction with CBD.

These results highlight the pivotal role of lipid metabolism in modulating cellular responses to therapy and demonstrate the power of combining label-free vibrational spectroscopy with active molecular probes for uncovering treatment-induced biochemical changes. Our approach provides new insights into CBD-mediated modulation of radioresponse and suggests that lipid-targeting strategies could enhance therapeutic outcomes in tumors like MPNST.

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {The lasing spectroscopy in studies on protein aggregation linked with neurodegenerative diseases},

author = {Piotr Hanczyc},

isbn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {There is a growing imperative to detect neurodegenerative diseases at their earliest, pre-symptomatic stages if we are to intervene effectively. In these disorders, small, diffusible assemblies of misfolded proteins - amyloid oligomers [1,2], and specific types of fibrils strains [3] are now recognized as the principal culprits driving neuronal damage. While Thioflavin T (ThT) fluorescence has long been a staple for monitoring protein aggregation, it struggles to capture the fleeting, early-stage oligomeric species, and its signal is vague in terms of fibrils structure. Further obscured by subtle microviscosity changes around the assemblies. By contrast, exploiting optical gain through lasing of ThT-labeled oligomers dramatically amplifies these weak emissions, offering a level of sensitivity far beyond conventional fluorescence. We developed a multi-parametric assay that combines enhanced ThT fluorescence, Fabry-Perot cavity lasing, and machine-learning-driven image analysis. By embedding ThT-stained samples in an optical cavity under pulsed excitation, we induce narrowband lasing (FWHM ~2 nm) that amplifies viscosity-modulated emission into sharp spikes. This approach not only reveals the structural rearrangements that accompany disease progression but also discriminates between distinct aggregation states and fibril strains via their characteristic lasing thresholds. It shows that lasing should help with early diagnosis and strains recognition of neurodegenerative diseases, potentially before clinical symptoms emerge, which could improve patient outcomes through timely therapeutic intervention. ...



 

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {The Mobility of EGFP Chromophore: Environmental Influence on Fluorescence Lifetime and Anisotropy DECAY},

author = {Joanna Krasowska and Anna Modrak-Wójcik and Zygmunt Gryczyński and Ignacy Gryczyński and Beata Wielgus-Kutrowska},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Fluorescent proteins (FPs) are nowadays widely used in a variety of spectroscopic methods, especially as biological markers for in vitro and in vivo imaging. [1,2]. One of the interesting applications is monitoring changes in the anisotropy of the green fluorescent protein (GFP) fluorescence in cells and tissues [3,4]

All FPs share common features: the cylindrical form, composition of 11 β-sheets, an α-helical segment buried inside the barrel and the fluorescent chromophore formed autocatalytically from 3 amino acids. [5]

We performed comparative studies on EGFP (F64L/S65T-GFP) fluorescence properties in different environment – from various solutions to molecule entrapped in the poly (vinyl alcohol) (PVA) film (Table 1). 

In contrast to small organic fluorescent molecules stiffened in polymer matrices [6], the immobilisation of EGFP in the PVA film results in a shorter fluorescence lifetime and rotational correlation time (j), as well as lower initial anisotropy (R0). Interestingly, increasing the viscosity of the solution does not affect any of EGFP fluorescence properties.

We suggest that the fast anisotropy decay in PVA film  is due to an increase in the mobility of the EGFP chromophore inside the protein after rearrangement of hydrogen bonds during PVA drying.

These findings shed light on the role and importance of structural water in GFP. The revealed unique fluorescent properties of GFP may be used to the development of novel applications in its use as a molecular marker. ....



},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {From Cells-on-a-Chip to Organ-on-a-Chip – new devices and tools for preclinical studies},

author = {Agnieszka Żuchowska and Patrycja Baranowska and Magdalena Flont and Agnieszka Gnyszka and Weronika Świtlik and Zuzanna Iwoń-Szczawińska and Dominik Kołodziejek and Joanna Konopka and Oliwia Tadko and Paweł Romańczuk and Aleksandra Szlachetka and Gabryiela Ułanowicz and Elżbieta Jastrzebska and Zbigniew Brzózka },

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {One of the main goals of cell engineering is to develop advanced, three-dimensional (3D) cell and tissue models that mimic tissue physiology in vivo [1]. Thanks to the use of microsystems, it is possible to mimic the spatial growth of cells, the complex composition of the extracellular matrix or control intercellular interactions in laboratory conditions.

The intensive development of miniaturization, which has been going on for several years, has made it possible to use modern technological solutions in chemical and biological research. Lab-on-a-chip systems are one of new microfluidic technologies that enable the creation of advanced 2D and 3D cell cultures in laboratory conditions [1]. Microfluidic cell culture has significant advantages over conventional macroscopic cell culture techniques and has the potential to improve knowledge in many fields of medicine, biology and chemistry.

Currently, preclinical drug research is based on several commonly used cell models, including two-dimensional (2D) and three-dimensional (3D) models cultured under standard conditions (static cultures, culture plates). Therefore, to reproduce the correct ratio of cell model volume to the external environment and flow conditions, a new approach to the generation and culture of in vitro cell models called the Organ-on-a-Chip (OoC) systems, has been proposed. The real challenge is to choose which cell model would be most suitable for modeling a particular organ using OoC technology.

The lecture will present several applications of cell engineering developed in our research group, i.e. the development and testing of new drugs and testing the effectiveness of various combinations of anticancer therapies (2), the Islet-on-chip system for creating islet cell cultures (3,4).

....},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Electrochemical biosensors for multiple biomarkers detection},

author = {Iwona Grabowska},

isbn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {The interest in biosensor technology has been constantly growing over the last few years. Designing biosensors capable of detecting two or more analytes in a single measurement remains a significant challenge [1, 2]. Electrochemical methods are frequently used for this purpose, mainly due to the ability to apply two or more different redox labels, each characterized by independent and distinguishable electrochemical signals. Additionally, alongside antibodies, aptamers have been increasingly used as bioreceptors in the construction of such sensors [2]. In our group, we have joined this research line, and within this presentation we report on (I) multianalyte sensing platforms for cardiac biomarkers through the development of aptamer-based electrochemical sensors for brain natriuretic peptide (BNP-32) and cardiac troponin I (cTnI) [3] and (II) simultaneous detection of low density lipoprotein (LDL) and malondialdehyde-modified low density lipoprotein (MDA-LDL) based on the approach involving the formation of two types of specific immunoconjugates consisting of monoclonal antibodies: anti-LDL or anti-MDA-LDL, together with redox-active molecules: ferrocene and anthraquinone, respectively, coated on magnetic beads (MBs) [4]. In the first example, commercial gold-screen printed electrodes were modified electrophoretically with polyethyleneimine/ reduced graphene films. Covalent grafting of propargyl-acetic acid integrates proparyl groups onto the electrode, to which azide-terminated aptamers can be immobilized using Cu(I)-based “click”-chemistry. To ensure low biofouling and high specificity, the cardiac sensor was modified with pyrene anchor carrying poly(ethylene glycol) units. In the case of BNP-32, the sensor developed shows a linear response from 1 pg mL-1 to 1 µg mL-1 in serum; for cTnI, linearity is observed from 1 pg mL-1 to 10 ng mL-1, as required for early-stage diagnosis of heart failure. In the second example, the decrease in redox molecules current in the concentration range of 0.001-1.0 ng mL-1 for LDL and 0.01-10.0 ng mL-1 for MDA-LDL, registered by square wave voltammetry (SWV), was observed upon the formation of complexes between LDL or MDA-LDL and the appropriate immunoconjugates. The detection limits were estimated to be 0.2 ng mL-1 for LDL and 0.1 ng mL-1 for MDA-LDL.  ...},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Electrochemical RNA-based aptasensor for neomycin detection in milk samples},

author = {Katarzyna Kurzątkowska-Adaszyńska and Aleksandra Adamicka and Agnieszka Jackowska and Iwona Grabowska},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {The overuse of antibiotics in livestock, particularly in dairy cows, has raised significant concerns due to its direct contribution to the emergence of antibiotic resistance in humans. Antibiotic treatments, widely used to prevent and manage bovine mastitis, can promote the selection of resistant bacterial strains that can disseminate through the food chain, the environment, and direct contact with farm workers. This growing public health issue results in antibiotic-resistant infections that are increasingly difficult to treat, leading to higher morbidity, mortality, and economic burdens. Among commonly used veterinary antibiotics, neomycin is frequently administered in veterinary therapy for farm animals. Therefore, the development of simple and cost-effective methods for neomycin detection in food products is of paramount importance.

This study presents the development of a novel electrochemical aptasensor for detecting neomycin in cow’s milk. A 2'-O-methylated ssRNA aptamer (APT) was employed as the recognition element and covalently immobilized onto a gold electrode surface, accompanied by co-deposited thiolated molecules (c-DTMs). The influence of different immobilization strategies and c-DTMs on the sensitivity of an impedimetric aptasensor for neomycin detection was systematically investigated. Electrochemical impedance spectroscopy (EIS) was employed, using Fe(CN)63-/4- redox probes, to evaluate sensor performance. Three distinct immobilization approaches were compared: (i) co-deposition (one-step) – simultaneous immobilization of APT and c-DTMs; 

(ii) sequential (two-step) – APT deposition followed by c-DTMs immobilization; and (iii) a hybrid method involving co-deposition followed by sequential modification. The tested c-DTMs included 

6-mercaptohexan-1-ol, 4-mercaptophenol, mercapto-polyethylene glycol, and mercaptosulfobetaine methylacrylate.

Our findings demonstrate that the one-step co-deposition of APT and c-DTMs leads to the highest sensor efficiency for neomycin detection. Among the tested c-DTMs, 4-mercaptophenol provided the most effective reduction of nonspecific interactions, thereby improving sensor selectivity. The aptasensor’s performance was assessed by monitoring changes in electron transfer resistance upon neomycin binding, recorded using EIS in the presence of Fe(CN)63-/4 redox couples. The developed aptasensor exhibited high sensitivity, achieving a low detection limit of 36.3 nM in a 10-fold diluted cow’s milk sample. Moreover, it demonstrated excellent selectivity for neomycin, effectively distinguishing it from structurally similar aminoglycosides (kanamycin and streptomycin) as well as tetracycline antibiotics (tetracycline and oxytetracycline).

The proposed electrochemical aptasensor provides 

a user-friendly, scalable, and cost-effective solution for detecting neomycin in milk samples. Its high sensitivity and specificity make it a promising tool for food safety monitoring and quality control in the dairy industry.





ACKNOWLEDGMENTS



This research was funded by the National Science Centre, Poland, grant number 2020/37/B/NZ9/03423, and the Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences in Olsztyn



.....},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Monitoring of the mitochondrial network in a cellular model of Parkinson's disease under the influence of Mdivi-1},

author = {Julia Anchimowicz and Damian Woźnica and Piotr Zielonka and Sławomir Jakieła},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Mitochondrial fragmentation is an early hallmark of dopaminergic neurodegeneration in Parkinson's disease (PD)1-3, yet there is a lack of quantitative, long-term assays for evaluating mitochondria-targeted therapeutics. Here, we present an integrated, reusable microfluidic culture chamber (Fig.1) with fully automated, on-stage fluorescence microscopy, which can track the mitochondrial network of living neurons for ten days — from SH-SY5Y differentiation through toxin injury to pharmacological rescue.

Differentiated SH-SY5Y cells were challenged with the Parkinsonian toxin MPP⁺ and subsequently treated with five concentrations of the dynamin-related protein 1 inhibitor Mdivi-1. The microfluidic device delivers programmable pulses of culture medium, BioTracker 488 Green Mitochondria Dye, toxin, and drug with sub-microlitre precision while maintaining a temperature of 37 °C. Custom software triggers time-lapse imaging and streams data directly to ImageJ/MiNA4 for skeletonisation of the mitochondrial network (Fig.2).

In three repeated biological studies, we observed 

a 42% decrease in the median mitochondrial branching length (MBL) after exposure to MPP⁺ (p < 0.001). Mdivi-1 caused a concentration-dependent restoration of MBL, reaching the highest values at a concentration of 40 µM (p < 0.01) (Fig.3); total branching length and network area reflected this trend. These results confirm that MBL is a sensitive, information-rich indicator of mitochondrial health and demonstrate that acute mitochondrial fragmentation can be reversed pharmacologically.

Our platform enables the high-throughput, longitudinal interrogation of mitochondrial dynamics under precisely controlled microenvironments. We anticipate that coupling this assay with patient-derived neurons will accelerate the discovery of disease-modifying drugs and inform mitochondrial gene-therapy strategies for PD and related neurodegenerative disorders. ....

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Studies in yeast revealed a molecular mechanism of neurodegenerative diseases linked to mt-Atp6 mutations},

author = {Roza Kucharczyk and Emilia Baranowska and Alain Dautant and Katarzyna Niedzwiecka and Jean-Paul di Rago and Deborah Tribouillard-Tanvier and Hubert Dominique Becker},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Mutations in the mitochondrial MT-ATP6 gene lead to a deficiency or absence of ATP the energy-rich molecule synthesized in mitochondria by ATP synthase and consequently result in mitochondrial diseases. The number of identified variants continues to increase due to the widespread use of next-generation sequencing (NGS) in patient diagnostics, with 962 entries currently listed in the MitoMap database. Assessing the functional consequences and pathogenicity of these variants remains challenging, particularly when they are found in only a small number of patients or coexist with wild-type mitochondrial DNA in cells and tissues (heteroplasmy), a common phenomenon. Taking advantage of the genetic tractability of Saccharomyces cerevisiae and the high instability of heteroplasmy in this organism, we constructed over twenty yeast strains bearing mutations in the ATP6 gene equivalent to those identified in patients. These mutations affect highly conserved residues of subunit a (Atp6) of ATP synthase, a protein essential for proton translocation across the mitochondrial inner membrane, which is coupled to ATP synthesis. Their effects on the function and biogenesis of yeast ATP synthase were analyzed using biochemical and molecular biology techniques. Thanks to the recent availability of high-resolution structures of yeast ATP synthase, we also investigated the structural consequences of these substitutions in silico and proposed molecular mechanisms of pathogenicity for five of the mutations. Furthermore, the identification of genetic suppressors for some of these mutations located in distal regions of the Atp6 protein that restored enzymatic activity provides a promising starting point for the development of small molecules that could be used to treat these currently incurable diseases.

I will also report on the engineering of a yeast strain expressing a new type of split-GFP, termed Bi-Genomic Mitochondrial Split-GFP (BiG Mito-Split-GFP). In this strain, the sequence encoding the non-fluorescent GFP1–10 fragment (the first ten β-strands) was integrated into the mitochondrial genome and is thus translated by the mitochondrial machinery, while the complementary fragment (GFPβ11) is fused to a nuclear-encoded protein of interest, translated in the cytosol. The self-assembly of this bi-genomically encoded split-GFP occurs exclusively in mitochondria, and only when the protein of interest is present in the matrix. Therefore, BiG Mito-Split-GFP provides a definitive method for confirming the localization of a given protein within the mitochondrial matrix.





ACKNOWLEDGMENTS



Financed by National Science Center of Poland: 2016/23/B/NZ3/02098, 2018-31-B-NZ3-01117.

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Puzzling path of potassium influx into mitochondria – the story of mitoK_{ATP}},

author = {Piotr Koprowski},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Mitochondrial ATP-sensitive potassium channels (mitoKATP), first described over three decades ago, seem to play an important role in cardioprotection. Yet, despite extensive efforts, their molecular identity remains unresolved. Initial mitoplast patch-clamp recordings revealed a K⁺ conductance inhibited by matrix ATP and glibenclamide, suggesting a mitochondrial counterpart of sarcolemmal KATP channels [1] . This led to the hypothesis that mitoKATP comprises a Kir6.x-type pore-forming subunit and a sulfonylurea receptor (SUR2A). However, knockout of Kir6.1/6.2 failed to eliminate mitochondrial K⁺ fluxes, prompting a search for alternative candidates.

Three main hypotheses currently dominate. The first posits that the renal potassium channel isoform ROMK2 (Kir1.1), which contains a mitochondrial targeting sequence, forms the channel pore [2]. Overexpression of ROMK2 in cardiomyocytes induces an ATP-inhibited, diazoxide-activated K⁺ current and improves resistance to ischemia–reperfusion injury. In our studies, purified ROMK2 reconstituted into planar lipid bilayers generated single-channel activity consistent with mitoKATP properties [3]. The channel was activated by diazoxide and inhibited by ATP/Mg²⁺ and glibenclamide. In other studies, a 55-kDa mitochondrial splice variant of SUR2A was shown to co-assemble with ROMK2, and SUR2A-55 overexpression enhanced mitoKATP activity and cardioprotection in vivo. However, genetic studies produced conflicting results: cardiomyocyte-specific ROMK deletion did not abolish cardioprotection, whereas global ROMK knockout worsened injury.

A second model proposes a dedicated mitochondrial KATP complex formed by CCDC51 (pore-forming) and ABCB8 (regulatory). A reconstituted CCDC51–ABCB8 channel recapitulates mitoKATP pharmacology, including diazoxide activation and ATP/glibenclamide inhibition. CCDC51 knockout abrogates diazoxide-induced K⁺ uptake and eliminates preconditioning-induced cardioprotection, strongly supporting this complex as a functional mitoKATP entity [4].

A third hypothesis suggests that the F1Fo-ATP synthase may function as a K⁺ channel under stress conditions. Fo subunit can conduct K⁺ along with protons, potentially acting as a latent uniporter during ischemia. Curiously, K+ transport via purified ATP synthase exhibits pharmacology of the mitoKATP channel [5].

Despite these advances, it remains unclear what is the molecular identity of  mitoKATP. An important question is whether multiple mitoKATP entities or regulatory modes exist (potentially unifying Kir/ROMK and CCDC51/mitoSUR paradigms), and how this knowledge can be harnessed therapeutically. Resolving the mitoKATP mystery will guide new strategies for safeguarding mitochondria under stress.





ACKNOWLEDGMENTS 



This work was partially supported by National Science Centre grant No. 2023/49/B/NZ1/02415

.....},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Innovative applications of known antioxidants: lipid nanocarriers with α-tocopherols - DSC and AFM analysis},

author = {Andrzej Dudek and Bartosz Pruchnik and Małgorzata Serowik and Teodor Gotszalk and Hanna Pruchnik},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Based on literature and our preliminary studies, tocopherols—like cholesterol—can be used to create liposomal nanocarriers with favourable properties, such as uniform size, controlled shape, and high homogeneity, which support their stability and effectiveness in therapeutic applications [1]. The wide biological activity of tocopherols, especially α-tocopherol, makes them appear to be a competitive component of lipid nanocarriers to cholesterol.  

The α-tocopherol derivatives can affect the mechanical and structural properties of the lipid bilayer of the nanocarriers, hence the precise determination of these changes is crucial for therapeutic applications of liposomes with tocopherols as a drug delivery system

....},

type = {Poster},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Next-Generation Cell Sheet Engineering via Smart Polymer Brush Coatings},

author = {Yana Shymborska and Andrzej Budkowski and Yurij Stetsyshyn},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {The future of regenerative medicine hinges on smart materials that enable precise, non-invasive control of cell behavior. In our work, we develop and characterize advanced temperature- and pH-responsive polymer brush coatings tailored for cell sheet engineering - platforms that not only support robust cell culture but also allow for gentle, enzyme-free detachment of intact cell layers.

We have synthesized thermoresponsive copolymer brushes, such as poly(N-isopropylacrylamide-co-2-hydroxyethyl methacrylate) [P(NIPAM-co-HEMA)] and poly(oligo(ethylene glycol) methacrylate-co-2-hydroxyethyl methacrylate) [P(OEGMA-co-HEMA)], which exhibit tunable lower and upper critical solution temperatures [1]. These coatings enable precise modulation of cell adhesion and spontaneous detachment without enzymatic intervention, preserving cell viability and extracellular matrix integrity. Additionally, we have explored the temperature-responsive properties of pH-sensitive poly(methacrylic acid) (PMAA) grafted brush coatings [2]. These surfaces exhibit controlled wettability, supporting fibroblast culture and highlighting their potential in tissue engineering applications. In our latest work, we have developed Cu-nanoparticle-loaded poly(4-vinylpyridine) (P4VP) brush coatings that integrate antibacterial and thermoresponsive functionalities [3]. These coatings facilitate the harvesting of retinal cell sheets while providing antibacterial properties, demonstrating their potential in ophthalmic regenerative therapies.

Altogether, these smart brush coatings offer a modular and responsive toolkit for next-generation biointerfaces - platforms that meet the growing demand for safer, smarter, and more efficient cell sheet technologies. ...

},

type = {Poster},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Platinum nanoparticles interact with idarubicin and affect its biological activity},

author = {Marcin Zakrzewski and Patrycja Bełdzińska and Grzegorz Gołuński and Dariusz Wyrzykowski and Katarzyna Bury and Jacek Piosik},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Metallic nanoparticles have attracted the scientific community’s interest since the last century, and among them, platinum nanoparticles (PtNPs) have gained significant attention recently. Due to the variety of size, shape, composition, optical properties and possibility of surface functionalization, they exhibit a broad range of features, therefore they were applied clinically as medicinal, antibacterial or anticancer agents, either alone or in conjunction with drugs, serving as drug carriers [1]. Combining them with chemotherapeutics could result in enhancing the efficacy of the drug and possibly reduce the significance of side effects. With that in mind, we assessed the effects of commercially available platinum nanoparticles on idarubicin (IDA), an antibiotic anticancer agent used in treatment of variety of leukaemias [2]....Firstly, we employed various physicochemical methods, such as dynamic light scattering (DLS) and atomic force microscopy (AFM) to assess the possibility of interactions through aggregation. As IDA is a fluorescent compound we performed spectrofluorimetric analysis to see if there are any close-distance interactions between PtNPs and IDA. Furthermore, we assessed the enthalpy changes using isothermal titration calorimetry (ITC). Finally, the biological effects of PtNPs on IDA were evaluated using Ames Mutagenicity assay with Salmonella enterica serovar Typhimurium TA98 strain. .....

},

type = {Poster},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {How do platinum nanoparticles affect the biological activity of doxorubicin?},

author = {Patrycja Bełdzińska and Marcin Zakrzewski and Inez Mruk and Natalia Derewońko and Katarzyna Bury and Grzegorz Gołuński and Michał Rychłowski and Jacek Piosik},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Nowadays, platinum nanoparticles (PtNPs) attract much attention due to their properties, such as various sizes and shapes, surface functionalization, and large surface to volume ratio. Importantly, PtNPs are proven to possess anticancer properties and may be used as drug delivery system to provide more efficient treatment [1]. Doxorubicin (DOX), an anthracycline antibiotic, is widely used in treatment of various cancers such as breast, ovarian or hematological malignances. However its usage is limited due to major side effects, particularly severe cardiotoxicity, and drug resistance [2].

Therefore, in this research we decided to investigate whether PtNPs can interact with DOX and consequently influence the biological activity of the drug. Hence, a broad range of physicochemical methods, such as Atomic Force Microscopy (AFM), Dynamic Light Scattering (DLS),  Fluorescence Spectroscopy, and biological methods including Ames mutagenicity test and cytotoxicity assay on both non-cancerous and cancerous cell lines were employed.

Firstly, the DLS and AFM results revealed that DOX triggers PtNPs aggregation. In turn, nanoparticles decreased DOX fluorescence and the effect was dilution-independent. Moreover, the Ames assay, showed that PtNPs decrease DOX mutagenicity. Importantly, the results of AlamarBlue cytotoxicity assay revealed that nanoparticles addition promoted cell viability reduction in cancerous cell line in comparison to DOX alone, while they increased the cell viability in non-cancerous cell line....

The confocal microscopy imaging further confirmed that PtNPs had completely opposite effects in the two cell lines. In case of the cancerous MelJuSo cell line, the nanoparticles addition to DOX resulted in fluorescence quenching and a dramatic change in the morphology of the cells. Most of the cells were circular with approximately 1/3 of them showing membrane blebbing which may suggest apoptosis. However, in case of non-cancerous HaCaT cell line, PtNPs improved cell morphology and density of the cell culture compared to DOX alone [3]. 

In summary, the results confirmed that interactions between PtNPs and DOX led to promising effect in cytotoxicity against cancer cells, while simultaneously providing a protective effect on healthy tissue. 

.....},

type = {Poster},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Nucleobindin-2 as a potential modulator of biomineralization},

author = {Dominika Bystranowska and Jarosław Stolarski and Andrzej Ożyhar},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Nucleobindin-2 (Nucb2) is a multifunctional calcium- and DNA-binding protein implicated in various physiological processes, including energy homeostasiss [1], stress response [2], and cancer progression [3, 4]. Structurally, Nucb2 contains EF-hand motifs that confer high affinity for divalent cations, particularly calcium (Ca²⁺), which is crucial for its conformational stability and biological activity [5]. In addition to Ca²⁺, Nucb2 can bind other metal ions such as zinc (Zn²⁺) and magnesium (Mg²⁺) [6], influencing its intracellular localization and interactions with molecular partners. Ion binding alters the  secondary structure of the protein and may modulate its function in calcium-dependent signaling pathways. Recent studies suggest that Nucb2 possesses unique structural features—especially its EF-hand motifs and a putative acidic domain—that may implicate it in biomineralization processes. Biomineralization refers to the biologically controlled deposition of minerals, such as hydroxyapatite in bone or calcium carbonate in marine organisms, which requires tightly regulated ion transport and protein-mineral interactions. The ability of Nucb2 to bind Ca²⁺, Mg²⁺, and Zn²⁺ positions it as a potential modulator of mineral nucleation and growth. Its ion-induced conformational changes may facilitate the spatial organization of ions into stable nucleation sites or influence vesicular transport of mineral precursors. Furthermore, Nucb2 has been detected in tissues undergoing active mineralization, supporting its potential physiological relevance. Although direct evidence for the involvement of Nucb2 in mineral scaffolding remains limited, its structural parallels with other mineralization-associated proteins, such as osteopontin and calmodulin, suggest a possible regulatory function. Here, we present preliminary observations indicating that Nucb2 is involved in mineral-associated cellular processes, possibly through its interaction with divalent metal ions relevant to biomineral formation, and may directly regulate the morphology of the resulting calcium carbonate biocrystals....},

type = {Poster},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Insight into the oligomeric state of the Nudt12 NUDIX protein},

author = {Maciej Zagrodzki and Anna Modrak-Wójcik and Maciej Łukaszewicz},

isbn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Nudt12 is a member of the NUDIX protein superfamily that is characterized by a highly conserved NUDIX motif (GX5EX5[UA]XREX2EEXGU, where U is hydrophobic and X any amino acid). The glutamic acid residues within the NUDIX sequence REUXEE play role in the binding of divalent metal ions required for the catalytic activity of NUDIX enzymes [1]. Nudt12 was initially identified as NADH diphosphatase [2]. It hydrolyses also structures present on 5’ end of RNA (standard m7GpppN cap, and a “metabolite” cap structures as NAD or dpCoA [3, 4]), and is active towards a set of dinucleotide analogs of the standard mRNA cap structure, differing in methylation status of the initial guanosine and the type/methylation of the adjacent nucleotide [5, 6].

Human Nudt12 and its murine homologue are both dimeric proteins with 88% amino acid identity. Resolved crystal structures of hNudt12 and mNudt12 showed the presence of two distinct N- and C-terminal domains, and bound divalent  metal ions (Mg2+ or Cd2+) in NUDIX motif [3, 7]. Dimerization of Nudt12 is essential for its catalytic activity and stability in vivo,  as was demonstrated for the human protein: a designed monomeric mutant of hNudt12 was inactive in decapping assays [3].

The dimeric form of wild-type hNudt12 was confirmed in vitro by size exclusion chromatography (SEC) and analytical ultracentrifugation (AUC) [3]. However our initial AUC experiment for the murine protein mNudt12 showed a dimer-monomer equilibrium. Here, we report SEC analysis of mNudt12 oligomeric states under different experimental conditions (e.g. the presence of divalent ions or increasing protein concentration). Preliminary results confirmed the existence in solution dimeric forms of hNudt12, and a dimer-monomer equilibrium for mNudt12 that could be shifted in the presence of magnesium ions. As mentioned earlier, the monomeric form of hNudt12 is catalytically compromised; therefore, the influence of  the oligomeric state of murine Nudt12 on its enzymatic activity and stability needs further investigation

.....},

type = {Poster},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Cooperativity between the mRNA 5’cap and 4E-BP binding sites in eIF4E explored via tryptophan mutagenesis and fluorescence lifetime analysis},

author = {Aneta Raczyńska and Joanna Żuberek and Anna Modrak-Wójcik},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Specific recognition of the mRNAs 5’ terminal cap structure by the eukaryotic initiation factor eIF4E is the first, rate-limiting, step in the cap-dependent translation [1]. Small 4E-binding proteins (4E-BP1, 4E-BP2, and 4E-BP3) inhibit the translation initiation process by competing with eIF4G initiation factor for the same binding site and by blocking the assembly of the translation machinery [1]. Although the cap and 4E-BP binding sites in eIF4E are spatially distant ( Fig. 1), they do not act independently. According to previous studies, the cap binding to eIF4E makes the affinity of eIF4E to 4E-BP1 significantly stronger, while binding of 4E-BP1 to the cap-eIF4E complex makes the cap dissociation slightly easier [2]. This finding indicates that the binding of either cap or 4E-BP1 induces conformational changes in eIF4E, not only in the region of a given binding site, but also in a distant region encompassing the binding site of the other ligand. ....},

type = {Poster},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Dependence of the fluorescence quantum yield of individual tryptophan residues in a protein on the excitation wavelength},

author = {Karolina Stachurska-Korzeniowska and Jan M. Antosiewicz},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Sodium dodecyl sulfate (SDS) is an anionic surfactant that induces changes in both the secondary and tertiary structure of proteins. When examining such changes by fluorescence detection in the protein α-chymotrypsin, it was observed that the fluorescence of the protein, both in the presence and absence of SDS, depends not only on the presence of the surfactant itself but also on the excitation wavelength[1]. In the fluorescence spectrum measurements, a 320 nm cutoff filter was used, meaning that the detected protein fluorescence originated only from tryptophan residues. 

Accordingly, a series of fluorescence spectrum measurements were carried out for both α-chymotrypsin and another protein, α-chymotrypsinogen, in the presence and absence of SDS, at four selected excitation wavelengths: 222, 260, 280, and 295 nm

We hypothesized that the fluorescence emission of individual tryptophan residues in the protein depends on the excitation wavelength. The fluorescence spectra of the proteins were analyzed according to a method found in the literature[2], where the authors presented fluorescence spectra as relative, normalized spectra: the curve for protein + SDS was subtracted from the curve for protein + buffer, and the resulting relative spectrum was then normalized at the short-wavelength minimum to –100 units. The obtained fluorescence spectra are presented in Figure 1. This way of presenting the spectra allows for the analysis of the total effect of the signal change compared to the initial value. 



....},

type = {Poster},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics},

author = {Duc Toan Truong and Kiet Ho and Pham Dinh Quoc Huy and Mateusz Chwastyk and Thai Nguyen-Minh and Minh Tho Nguyen },

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {To ensure that an external force can break the interaction between a protein and a ligand, the steered molecular dynamics simulation requires a harmonic restrained potential applied to the protein backbone. A usual practice is that all or a certain number of protein’s heavy atoms or Cα atoms are fixed, being restrained by a small force. This present study reveals that while fixing both either all heavy atoms and or all Cα atoms is not a good approach, while fixing a too small number of few atoms sometimes cannot prevent the protein from rotating under the influence of the bulk water layer, and the pulled molecule may smack into the wall of the active site. We found that restraining the Cα atoms under certain conditions is more relevant. Thus, we would propose an alternative solution in which only the Cα atoms of the protein at a distance larger than 1.2 nm from the ligand are restrained. A more flexible, but not too flexible, protein will be expected to lead to a more natural release of the ligand....},

type = {Poster},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Biophysical aspects of adipose tissues remodeling during obesity development},

author = {Piotr Deptuła and Łukasz Suprewicz and Mariusz Sawieljew and Robert Bucki},

isbn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {During the development of chronic obesity, adipose tissue undergoes significant remodeling, which can result in chronic inflammation leading to fibrosis. This may cause local tissue damage and ultimately initiate dysfunction of multiple organs [1-4].

The aim of this study was to determine the effect of extracellular hyaluronan removal using hyaluronidase on the rheological properties of 3T3-L1 cells during their differentiation process into adipocytes, as well as to perform rheological studies on a lipid-rich adipose tissue hydrogel model. A NanoWizard 4 BioScience AFM (Bruker Nano GmbH, Berlin, Germany), operating in Force Spectroscopy mode, was used to measure the stiffness of confluent cell culture. The Young’s modulus (E) was determined by analyzing force–indentation curves and fitting the data to the Hertz contact model. Rheological characteristics of hydrogels with added lipid elements were evaluated using a strain-controlled Anton Paar MCR702e rheometer (Anton Paar GmbH, Graz, Austria) with a parallel plate setup. The tests quantified the storage modulus (G′) and loss modulus (G″) by measuring the stress required to induce deformation. Two types of shear tests were performed: (1) oscillatory shear strain tests at 1 Hz frequency and 1% amplitude under compressive strain levels of ε = 0%, 10%, 20%, 30%, and 40%; and (2) strain amplitude sweep tests ranging from 0.1% to 100% at a constant frequency of 1 Hz. 

The obtained results indicate that the removal of extracellular hyaluronan affects the mechanical properties of adipocytes. The results may contribute to a better understanding of the complex mechanics of the extracellular matrix of adipose tissue, which may affect the process of cell differentiation.

.....},

type = {Poster},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{nokey,

title = {Effects of LPS and FPR2 agonist (IG4) on the mechanical properties of microglial cells},

author = {Justyna Śmiałek-Bartyzel and Jakub Frydrych and Krzysztof Łukowicz and Beata Grygier and Ewa Trojan and Agnieszka Basta-Kaim and Małgorzata Lekka},

issn = {2084-1892},

year  = {2025},

date = {2025-06-25},

urldate = {2025-06-25},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Alzheimer's disease is a common neurodegenerative disease characterized by chronic inflammation and the accumulation of beta-amyloid (Aβ) in the brain. Microglial cells, resident macrophages in the central nervous system, are thought to play a significant role in the development of this disease. These cells have both neurotoxic and neuroprotective effects. [1]

The presented studies aimed to investigate microglia's biomechanical properties (cell rigidity) in inflammatory conditions. The primary microglial cells obtained from the knock-in murine model of late-onset Alzheimer's disease (APPNLF/NLF) and wild-type mice (WT) isolated from 1- or 2-day-old mice were used in experiments. Isolated cells were cultured in the presence or absence of bacterial endotoxin (lipopolysaccharide, LPS). Moreover, the impact of an agonist of formyl peptide receptor 2 (FPR2) (IG4) in basal and LPS-stimulated conditions was investigated. The biomechanical measurements were performed using atomic force microscopy (AFM), which worked in force spectroscopy mode. Data were collected over the nucleus region, and the Hertz-Sneddon model was used to evaluate the mechanical properties of cells.

Significant changes in the morphology of LPS-treated microglial cells from WT or APPNLF/NLF mice, contrary to non-stimulated cells, were observed. In basal conditions, WT microglia's mechanical properties differed from APPNLF/NLF  microglia. LPS significantly increased the elastic modulus for microglial cells in both models. In basal condition  IG4 agonist did not affect the biomechanical properties of microglial cells from WT and APPNLF/NLF mice. However, after immunoactivation evoked by LPS stimulation, this agonist has varied effects. In microglia cultures obtained from WT mice, IG4 significantly increases the LPS-evoked increase in Young's modulus.  In the case of APPNLF/NLF  microglia, IG4 lowered Young's modulus enhancement evoked by LPS.

In summary, our results indicate that inflammation, mimicked by LPS treatment, affects the biomechanical properties of mouse microglial cells. Moreover, the FPR2 agonist compound IG4 enhances the effect of LPS in cells isolated from WT mice, while reducing the LPS effect in cells isolated from APP mice. ...

},

type = {Poster},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{PlenaryLectures2025_3,

title = {Conjugates of DNA and boron clusters as building blocks for nanoparticle carriers of therapeutic nucleic acids with gene silencing activities},

author = {Krzysztofa Śmiałkowski and Katarzyna Bednarska-Szczepaniak and Katarzyna Ebenryter-Olbińska and Katarzyna Kulik and Justyna Suwara and Gabriela Gajek and Lidia Fiedorowicz and Aleksander Foryś and Bohumir Grűner and Barbara Nawrot and Zbigniew Leśnikowski },

issn = {2084-1892},

year  = {2025},

date = {2025-06-24},

urldate = {2025-06-24},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

issue = {44},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Despite thousands of chemotherapeutic drugs approved for clinical practice, there are still many unmet needs in the prevention and treatment of many diseases. The need to fill this never-shrinking gap is driving search for new drugs, both in the traditional chemotherapeutic category and in newer generation drugs such as biotherapeutics. Still another, emerging recently drug modality are therapeutic nucleic acids (TNAs) that have the potential to address many currently unmet by chemotherapeutic and biotherapeutic drugs needs [1-3]. However, even though already there are over 20 TNAs on the market, TNAs are still a new technology that faces challenges and problems that must to be solved. They include difficulties with delivery, susceptibility to degradation by nucleases, rapid clearance from the body, off-target effects and others. In quest to find solutions to these problems, a number of technologies are tested, one of them is nanotechnology.

For several years, our laboratory has researched modifying nucleic acids with boron clusters, a molecular cages with unique and advantageous properties [4], and studied their applications as probes for molecular diagnostics, boron carriers for boron neutron capture therapy (BNCT) and therapeutic nucleic acids. Continuing involvement in the very hot research area of TNAs we are focusing now on nanoparticle carriers of TNAs based on composites of DNA-oligomers and boron clusters.....

},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{PlenaryLectures2025_4,

title = {Cell Response Driven by Surface chemistry and Charges on electrospun polymer NANOfibers},

author = {Urszula Stachewicz},

issn = {2084-1892},

year  = {2025},

date = {2025-06-24},

urldate = {2025-06-24},

booktitle = {Abstracts of the XIX Congress of the Polish Biophysical Society (PTBF)},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

issue = {44},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Surface charge is a critical determinant in cell–biomaterial interactions, influencing adhesion, proliferation, and regenerative signaling. Electrospun polymer scaffolds, known for their high surface-area-to-volume ratio, are promising candidates for biomedical applications such as tissue engineering, drug delivery, and skin regeneration [1-2]. However, precise control over surface charge during electrospinning remains underexplored.

A comprehensive investigation of distinct mechanisms to modulate surface potential in electrospun fibers was performed. We examined the influence of polymer chain orientation induced by alternating voltage polarity during electrospinning [3]. We also explored material diffusion between core and shell phases in coaxial fibers [4]. Most recently, we evaluated the impact of incorporating two-dimensional conductive nanomaterials—reduced graphene oxide (rGO) and titanium carbide MXenes (Ti₃C₂Tₓ)—on surface potential of polymer fibers [5].We demonstrate that reversing the polarity of the applied voltage during electrospinning significantly alters the surface potential of poly(L-lactic acid) (PLLA), polycaprolactone (PCL), poly(vinylidene fluoride) (PVDF) fibers, as shown by Kelvin probe force microscopy (KPFM), and this modulation directly enhances osteoblast adhesion [6]. Additionally, we explore how diffusion between core and shell materials affects fibre surface chemistry and charge distribution, shedding light on a previously unexamined factor in coaxial electrospinning. Moreover, we show that embedding rGO and MXene nanosheets within polymer matrices modifies surface potential and bioactivity, even when these nanomaterials are not surface-exposed.

Scaffolds were systematically characterized using KPFM, X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and zeta potential measurements to correlate surface properties with cellular responses. Confocal laser scanning microscopy (CLSM) with AiryScan was employed to visualize focal adhesion complexes, offering insights into how surface charge governs outside-in and inside-out signaling pathways.

In summary, our findings highlight the pivotal role of scaffold surface potential in mediating cellular responses and underscore the importance of tailored electrospun fibre design to accelerate tissue regeneration processes. ....

},

key = {4},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{PlenaryLectures2025_5,

title = {Reengineering of a Bacterial Compartment INTO Tailorable Bionanomaterials},

author = {Yusuke Azuma},

year  = {2025},

date = {2025-06-24},

urldate = {2025-06-24},

journal = {Current Topics in Biophysics},

volume = {44 (suppl.A)},

issue = {44},

publisher = {Polish Biophysical Society and Adam Mickiewicz University},

address = {ul. Uniwersytetu Poznanskiego 2, 61-614 Poznan},

abstract = {Self-assembling protein cages are naturally occurring hollow nanostructures with inherent capabilities for compartmentalizing and organizing biomolecules, making them promising candidates for a wide range of bioengineering applications. A key challenge in this field is precisely controlling their assembly and morphology to tailor function for specific applications. Understanding the molecular mechanisms underlying the polymorphic protein assemblies provides a basis for designing ones with the desired morphology.

Our recent work elucidates fundamental principles governing the self-assembly of a model cage-forming protein, Aquifex aeolicus lumazine synthase (AaLS) [1,2]. An engineered,  circularly permuted variant of AaLS exhibits remarkable structural plasticity, assembling into diverse, hollow spherical and cylindrical structures in response to subtle changes in ionic strength (Fig. 1). Cryogenic electron microscopy (cryo-EM) reveals that these structures are composed entirely of pentameric subunits, and the dramatic cage-to-tube transformation is mediated by an α-helix domain that is untethered from its native position by circular permutation, a key structural determinant for controlling assembly [3]. The utility of this controlled assembly is demonstrated by the stabilization of labile biomolecules produced in host cells and their efficient retrieval outside biological contexts, showcasing cpAaLS as a versatile platform for nanoscale manipulation and cargo delivery [4].

Our results highlight the potential for broad advancements across biotechnological applications, ranging from bioproduction to nanomedicine. Furthermore, the structural insights gained into the assembly mechanisms and the role of circular permutation in dictating morphology provide a valuable framework for the rational design of novel nanomaterials with tailored properties....

},

key = {5},

type = {Plenar lecture},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}