Lisi Wei, Xin Wang, Min Sun, Wonchul Shin, Kevin D Gillis, Ling-Gang Wu
{"title":"Sub-quantal release is not dominant during prolonged depolarization in adrenal chromaffin cells.","authors":"Lisi Wei, Xin Wang, Min Sun, Wonchul Shin, Kevin D Gillis, Ling-Gang Wu","doi":"10.1016/j.bpr.2025.100212","DOIUrl":"https://doi.org/10.1016/j.bpr.2025.100212","url":null,"abstract":"<p><p>Exocytosis, which mediates important functions like synaptic transmission and stress responses, has been postulated to release all transmitter molecules in the vesicle in the \"all-or-none\" quantal hypothesis. Challenging this hypothesis, amperometric current recordings of catecholamine release propose that sub-quantal or partial transmitter release is dominant in various cell types, particularly chromaffin cells. The sub-quantal hypothesis predicts that fusion pore closure (kiss-and-run fusion), the cause of sub-quantal release, is dominant, and blocking pore closure increases quantal size. We tested these predictions by imaging fusion pore closure and amperometric recording of catecholamine release in chromaffin cells during high potassium application, the most used stimulation protocol for sub-quantal release study. We found that fusion pore closure is not predominant, and inhibition of the fusion pore closure does not increase the quantal size calculated from the amperometric current charge when a sufficiently long integration time is used. These results suggest that sub-quantal release is not prevalent during high potassium application in adrenal chromaffin cells.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100212"},"PeriodicalIF":2.4,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jakob Vorlaufer, Nikolai Semenov, Caroline Kreuzinger, Manjunath G Javoor, Bettina Zens, Nathalie Agudelo Dueñas, Mojtaba R Tavakoli, Marek Šuplata, Wiebke Jahr, Julia Lyudchik, Andreas Wartak, Florian K M Schur, Johann G Danzl
{"title":"Image-based 3D active sample stabilization on the nanometer scale for optical microscopy.","authors":"Jakob Vorlaufer, Nikolai Semenov, Caroline Kreuzinger, Manjunath G Javoor, Bettina Zens, Nathalie Agudelo Dueñas, Mojtaba R Tavakoli, Marek Šuplata, Wiebke Jahr, Julia Lyudchik, Andreas Wartak, Florian K M Schur, Johann G Danzl","doi":"10.1016/j.bpr.2025.100211","DOIUrl":"https://doi.org/10.1016/j.bpr.2025.100211","url":null,"abstract":"<p><p>Super-resolution microscopy often entails long acquisition times of minutes to hours. Since drifts during the acquisition adversely affect data quality, active sample stabilization is commonly used for some of these techniques to reach their full potential. While drifts in the lateral plane can often be corrected after acquisition, this is not always possible or may come with drawbacks. Therefore, it is appealing to stabilize sample position in three dimensions during acquisition. Various schemes for active sample stabilization have been demonstrated previously, with some reaching sub-nm stability in three dimensions. Here, we present a scheme for active drift correction that delivers the nm-scale 3D stability demanded by state-of-the-art super-resolution techniques and is straightforward to implement compared to previous schemes capable of reaching this level of stabilization precision. Using a refined algorithm that can handle various type of reference structures, without sparse signal peaks being mandatory, we stabilized sample position to ∼1 nm in 3D using objective lenses both with high and low numerical aperture. Our implementation requires only the addition of a simple widefield imaging path and we provide an open-source control software with graphical user interface to facilitate easy adoption of the module. Finally, we demonstrate how this has the potential to enhance data collection for diffraction-limited and super-resolution imaging techniques using single-molecule localization microscopy and cryo-confocal imaging as showcases.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100211"},"PeriodicalIF":2.4,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144061183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Open-source 3D active sample stabilization for fluorescence microscopy.","authors":"Sanket Patil, Giuseppe Vicidomini, Eli Slenders","doi":"10.1016/j.bpr.2025.100208","DOIUrl":"https://doi.org/10.1016/j.bpr.2025.100208","url":null,"abstract":"<p><p>Super-resolution microscopy has enabled imaging at nanometer-scale resolution. However, achieving this level of detail without introducing artifacts that could mislead data interpretation requires maintaining sample stability throughout the entire imaging acquisition. This process can range from a few seconds to several hours, particularly when combining live-cell imaging with super-resolution techniques. Here, we present a three-dimensional active sample stabilization system based on real-time tracking of fiducial markers. To ensure broad accessibility, the system is designed using readily available off-the-shelf optical and photonic components. Additionally, the accompanying software is open source and written in Python, facilitating adoption and customization by the community. We achieve a standard deviation of the sample movement within 1 nm in both the lateral and axial directions for a duration in the range of hours. Our approach allows easy integration into existing microscopes, not only making prolonged super-resolution microscopy more accessible but also allowing confocal and widefield live-cell imaging experiments spanning hours or even days.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"5 2","pages":"100208"},"PeriodicalIF":2.4,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144031484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Leandro Cruz Rodríguez, Nahuel Naum Foressi, María Soledad Celej
{"title":"Tracking protein transitions through fluorescence spectral phasor analysis with ACDAN.","authors":"Leandro Cruz Rodríguez, Nahuel Naum Foressi, María Soledad Celej","doi":"10.1016/j.bpr.2025.100209","DOIUrl":"https://doi.org/10.1016/j.bpr.2025.100209","url":null,"abstract":"<p><p>This study investigates the use of spectral phasor analysis, hyperspectral imaging, and 6-acetyl-2-dimethylaminonaphthalene (ACDAN) fluorescence to explore key protein transitions: unfolding, amyloid aggregation, and liquid-liquid phase separation. We show that ACDAN fluorescence can sensitively detect subtle conformational changes before the complete protein unfolds, revealing early microenvironmental shifts. During amyloid formation, ACDAN identifies solvent dipolar relaxation events undetectable by conventional thioflavin T, providing critical insight into early aggregation events. Additionally, we map the physicochemical properties of protein biocondensates and highlight distinct microenvironments within these condensates, emphasizing the significance of dipolar relaxation in phase-separated systems. The approach provides a flexible and user-friendly toolkit for studying protein transitions, which can be easily implemented in commercial spectrofluorometers and microscopes.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"5 2","pages":"100209"},"PeriodicalIF":2.4,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144012383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mechanical properties of mandibular and maxillary bone collagen fibrils based on nonlocal elasticity theory.","authors":"Elaheh Alibeigi Beni, Alireza Shahidi, Behnaz Ebadian","doi":"10.1016/j.bpr.2025.100210","DOIUrl":"https://doi.org/10.1016/j.bpr.2025.100210","url":null,"abstract":"<p><p>In this paper, the mechanical properties of collagen fibrils in the cortical bone and cortical-trabecular bone interface of the human mandible and maxilla have been investigated. Force-indentation curves on wet collagen fibrils are taken by applying the atomic force microscopy nanoindentation technique, and the elastic modulus is measured. The distribution of stress and strain is determined by considering an elastic medium when it is deformed by a rigid cone. Afterward, by applying the nonlocal elasticity theory and the indentation parameters, the nonlocal parameter of the collagen fibrils is calculated at the nanoscale. Finally, the elastic modulus and nonlocal modulus of the collagen fibrils are compared. According to the results, the highest and lowest values of the elastic modulus of the collagen fibrils are determined in the maxillary cortical-trabecular bone interface (4.16 ± 0.18 MPa) and mandibular cortical bone (2.03 ± 0.14 MPa), respectively. In general, in collagen fibrils, this parameter is higher in the maxillary bone than in the mandibular one. In the upper and lower jaws, the elastic modulus of collagen fibrils in the cortical-trabecular bone interface is higher than that of the cortical bone. In mandibular and maxillary bone collagen fibrils, the range of nonlocal parameter and scaling parameter e<sub>0</sub> are computed as (0.430 ± 0.013-0.483 ± 0.011 nm) and (0.269 ± 0.006-0.302 ± 0.006), respectively. Also, the highest value of this parameter is recorded in the maxillary cortical-trabecular bone interface. The difference between the nanoscale modulus of collagen fibrils and the elastic modulus at large length scales is significant.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"5 2","pages":"100210"},"PeriodicalIF":2.4,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144059209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Myra Awan, Maya Papez, Ankita P Walvekar, Sang-Joon J Lee, Kinjal Dasbiswas, Anand K Ramasubramanian
{"title":"Surface-bound FXIII enhances deposition and straightness of fibrin fibers.","authors":"Myra Awan, Maya Papez, Ankita P Walvekar, Sang-Joon J Lee, Kinjal Dasbiswas, Anand K Ramasubramanian","doi":"10.1016/j.bpr.2025.100207","DOIUrl":"10.1016/j.bpr.2025.100207","url":null,"abstract":"<p><p>Cross-linked fibrous networks are central to maintaining the structural integrity and functional relevance of many biological and engineered materials. Fibrin networks are the building blocks of blood clots, mediators of tissue injury and repair, and synthetic wound sealants. Cross-linking of fibrin fibers is catalyzed by the activated form of transglutaminase enzyme FXIIIa, which becomes available in plasma but is also readily presented on the surface of activated platelets and macrophages. The contribution of surface-bound FXIIIa to fibrin structure has not been well understood. In this work, we investigated the role of surface-bound FXIIIa on the formation and structure of fibrin fibers from FXIII-deficient plasma by confining the cross-linking reactions to the surface of microspheres. Quantitative microscopy revealed that cross-linking on FXIIIa-coated surfaces facilitates fibrin deposition following a sigmoidal kinetics, and that these fibers were straighter, longer, and more numerous compared with uncross-linked fibers bound to surfaces coated with anti-fibrin antibody. Our results suggest that, by modifying local fibrin density and structure, surface-bound FXIIIa may play a significant role in the mechanobiology of hemostasis and inflammation.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100207"},"PeriodicalIF":2.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12002612/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kerri Kukovetz, Matea Cartolano, Manuela Gebhardt, Lars E Schumann, Stefan M Kast, Anna Moroni, Gerhard Thiel, Oliver Rauh
{"title":"Yeast complementation assays provide limited information on functional features of K<sup>+</sup> channels.","authors":"Kerri Kukovetz, Matea Cartolano, Manuela Gebhardt, Lars E Schumann, Stefan M Kast, Anna Moroni, Gerhard Thiel, Oliver Rauh","doi":"10.1016/j.bpr.2025.100206","DOIUrl":"10.1016/j.bpr.2025.100206","url":null,"abstract":"<p><p>We investigate to what extent yeast complementation assays, which in principle can provide large amounts of training data for machine-learning models, yield quantitative correlations between growth rescue and single-channel recordings. If this were the case, yeast complementation results could be used as surrogate data for machine-learning-based channel design. Therefore, we mutated position L94 at the cavity entry of the model K<sup>+</sup> channel Kcv<sub>PBCV1</sub> to all proteinogenic amino acids. The function of the wild-type channel and its mutants was investigated by reconstituting them in planar lipid bilayers and by their ability to rescue the growth of a yeast strain deficient in K<sup>+</sup> uptake. The single-channel data show a distinct effect of mutations in this critical position on unitary conductance and open probability, with no apparent causal relationship between the two functional parameters. We also found that even conservative amino acid replacements can alter the unitary conductance and/or open probability and that most functional changes show no systematic relationship with the physicochemical nature of the amino acids. This emphasizes that the functional influence of an amino acid on channel function cannot be reduced to a single chemical property. Mutual comparison of single-channel data and yeast complementation results exhibit only a partial correlation between their electrical parameters and their potency of rescuing growth. Hence, complementation data alone are not sufficient for enabling functional channel design; they need to be complemented by additional parameters such as the number of channels in the plasma membrane.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100206"},"PeriodicalIF":2.4,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11985088/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143631097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biophysical reportsPub Date : 2025-03-12Epub Date: 2025-01-28DOI: 10.1016/j.bpr.2025.100197
Anupam Mondal, Anatoly B Kolomeisky
{"title":"Microscopic origin of the spatial and temporal precision in biological systems.","authors":"Anupam Mondal, Anatoly B Kolomeisky","doi":"10.1016/j.bpr.2025.100197","DOIUrl":"10.1016/j.bpr.2025.100197","url":null,"abstract":"<p><p>All living systems display remarkable spatial and temporal precision, despite operating in intrinsically fluctuating environments. It is even more surprising given that biological phenomena are regulated by multiple chemical reactions that are also random. Although the underlying molecular mechanisms of surprisingly high precision in biology remain not well understood, a novel theoretical picture that relies on the coupling of relevant stochastic processes has recently been proposed and applied to explain different phenomena. To illustrate this approach, in this review, we discuss two systems that exhibit precision control: spatial regulation in bacterial cell size and temporal regulation in the timing of cell lysis by λ bacteriophage. In cell-size regulation, it is argued that a balance between stochastic cell growth and cell division processes leads to a narrow distribution of cell sizes. In cell lysis, it is shown that precise timing is due to the coupling of holin protein accumulation and the breakage of the cellular membrane. The stochastic coupling framework also allows us to explicitly evaluate dynamic properties for both biological systems, eliminating the need to utilize the phenomenological concept of thresholds. Excellent agreement with experimental observations is observed, supporting the proposed theoretical ideas. These observations also suggest that the stochastic coupling method captures the important aspects of molecular mechanisms of precise cellular regulation, providing a powerful new tool for more advanced investigations of complex biological phenomena.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100197"},"PeriodicalIF":2.4,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11867269/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biophysical reportsPub Date : 2025-03-12Epub Date: 2024-11-27DOI: 10.1016/j.bpr.2024.100187
Levi Diggins, Daniel Ross, Sundeep Bhanot, Rebecca Corallo, Rachel Daley, Krishna Patel, Olivia Lewis, Shane Donahue, Jacob Thaddeus, Lauren Hiers, Christopher Syed, David Eagerton, Bidyut K Mohanty
{"title":"CD spectra reveal the state of G-quadruplexes and i-motifs in repeated and other DNA sequences.","authors":"Levi Diggins, Daniel Ross, Sundeep Bhanot, Rebecca Corallo, Rachel Daley, Krishna Patel, Olivia Lewis, Shane Donahue, Jacob Thaddeus, Lauren Hiers, Christopher Syed, David Eagerton, Bidyut K Mohanty","doi":"10.1016/j.bpr.2024.100187","DOIUrl":"10.1016/j.bpr.2024.100187","url":null,"abstract":"<p><p>The B-DNA of the genome contains numerous sequences that can form various noncanonical structures including G-quadruplex (G4), formed by two or more stacks of four guanine residues in a plane, and intercalating motif (i-motif [iM]) formed by alternately arranged C-C<sup>+</sup> pairs. One of the easy yet sensitive methods to study G4s and iMs is circular dichroism (CD) spectroscopy, which generates characteristic G4 and iM peaks. We have analyzed and compared the effects of various environmental factors including pH, buffer composition, temperature, flanking sequences, complimentary DNA strands, and single-stranded DNA binding protein (SSB) on the CD patterns of G4s and iMs generated by two groups of DNA molecules, one containing tandem repeats of GGGGCC and CCCCGG from the C9ORF72 gene associated with amyotrophic lateral sclerosis and frontotemporal dementia, and the second containing polyG/polyC clusters from oncogene promoter-proximal regions without such tandem repeats. Changes in pH caused drastic changes in CCCCGG-iM and GGGGCC-G4 and the changes were dependent on repeat numbers and G-C basepairing. In contrast, with the DNA sequences from the promoter-proximal regions of oncogenes, iMs disassembled upon pH changes with the peak slowly shifting to lower wavelength but the G4s did not show significant change. Complementary DNA strands and flanking DNA sequences also regulate G4 and iM formation. The SSB disassembled both G4s and iMs formed by almost all sequences suggesting an in vivo role for SSBs in the disassembly of G4s and iMs during DNA replication and other DNA transactions.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100187"},"PeriodicalIF":2.4,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11699388/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142752552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biophysical reportsPub Date : 2025-03-12Epub Date: 2025-01-29DOI: 10.1016/j.bpr.2025.100198
Phuc Phan, Jason Hoang, Thallapuranam Krishnaswamy Suresh Kumar
{"title":"Overexpression and biophysical and functional characterization of a recombinant FGF21.","authors":"Phuc Phan, Jason Hoang, Thallapuranam Krishnaswamy Suresh Kumar","doi":"10.1016/j.bpr.2025.100198","DOIUrl":"10.1016/j.bpr.2025.100198","url":null,"abstract":"<p><p>Fibroblast growth factor 21 (FGF21) is an endocrine FGF that plays a vital role in regulating essential metabolic pathways. FGF21 increases glucose uptake by cells, promotes fatty acid oxidation, reduces blood glucose levels, and alleviates metabolic diseases. However, detailed studies on its stability and biophysical characteristics have not been reported. Herein, we present the overexpression, biophysical characterization, and metabolic activity of a soluble recombinant FGF21 (rFGF21). The far-UV circular dichroism spectra of rFGF21 show a negative trough at 215 nm, indicating that the protein's backbone predominantly adopts a β sheet conformation. rFGF21 shows intrinsic tyrosine fluorescence at 305 nm. Thermal denaturation using differential scanning calorimetry reveals that rFGF21 is relatively thermally unstable, with a melting temperature of 46.8°C (±0.1°C). The urea-induced unfolding of rFGF21 is rapid, with a chemical transition midpoint of 0.4 M. rFGF21 is readily cleaved by trypsin in limited trypsin digestion assays. Isothermal titration calorimetry experiments show that rFGF21 does not bind to heparin. Interestingly, rFGF21 demonstrates proliferative activity in NIH/3T3 fibroblasts and enhances mitochondrial oxidative phosphorylation and fatty acid oxidation in 3T3-L1 adipocytes. These findings provide a crucial framework for the engineering of novel structure-based variants of FGF21 with improved stability and biological activity to treat metabolic disorders.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100198"},"PeriodicalIF":2.4,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11869967/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}