Journal Description
Biophysica
Biophysica
is an international, peer-reviewed, open access journal on applying the methods of physics, chemistry, and math to study biological systems, published quarterly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within ESCI (Web of Science), Scopus, EBSCO, and other databases.
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 16.7 days after submission; acceptance to publication is undertaken in 3.7 days (median values for papers published in this journal in the second half of 2023).
- Recognition of reviewers: APC discount vouchers, optional signed peer review and reviewer names are published annually in the journal.
- Biophysica is a companion journal of IJMS.
Latest Articles
Competitive Distribution of Public Goods: The Role of Quorum Sensing in the Development of Bacteria Colonies
Biophysica 2024, 4(3), 327-339; https://doi.org/10.3390/biophysica4030023 - 21 Jun 2024
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The production of public goods is a necessary condition for the survival of the species, but it comes at the expense of individual growth. In a prototype bacterial colony, we model the role of quorum sensing as a resource redistribution mechanism. Two types
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The production of public goods is a necessary condition for the survival of the species, but it comes at the expense of individual growth. In a prototype bacterial colony, we model the role of quorum sensing as a resource redistribution mechanism. Two types of bacterial colonies are analyzed, one made up of a single strain and one made up of two different strains. Based on a recent series of experimental data present in the literature, we analyze two types of strains with different extinction times: strains that consume available resources very quickly, therefore becoming extinct quickly, and strains that consume resources slowly and die due to aging. We show that the proposed quorum sensing model describes the main experimental result that coexistence may favor the survival of both strains. Furthermore, the production of public goods is maximized when both types of individuals have the maximum proliferation output. Finally, we highlight the role played by so-called dormant cells in the duration of survival time. These cells are of particular interest because their ability to counteract different types of stress (e.g., the use of antibiotics) still constitutes a challenge.
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Open AccessArticle
Interaction between Vitamins C and E When Scavenging the Superoxide Radical Shown by Hydrodynamic Voltammetry and DFT
by
Francesco Caruso, Jens Z. Pedersen, Sandra Incerpi, Stuart Belli, Raiyan Sakib and Miriam Rossi
Biophysica 2024, 4(2), 310-326; https://doi.org/10.3390/biophysica4020022 - 18 Jun 2024
Abstract
In this study, we examine the cooperative effect between vitamins C and E that mitigates oxidative stress by using experimental and computational methods. We performed superoxide scavenging experiments on each vitamin individually and their combination using rotating ring–disk electrode voltammetry. The results indicate
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In this study, we examine the cooperative effect between vitamins C and E that mitigates oxidative stress by using experimental and computational methods. We performed superoxide scavenging experiments on each vitamin individually and their combination using rotating ring–disk electrode voltammetry. The results indicate that vitamins E and C together produce more effective scavenging of superoxide as evaluated by a steeper slope in the efficiency graph, −7.2 × 104, compared to that of vitamin E alone, −1.8 × 103, or vitamin C alone, −1.3 × 104. Density Functional Theory calculations agree with our experimental results, and we describe a mechanism for the antioxidant action of individual vitamins E and C, plus the synergistic action when both vitamins interact. This process involves the restoration of vitamin E by vitamin C and includes π-π interactions between superoxide and scavengers. The overall result produces an increase in scavenging superoxide radicals when both vitamins act together.
Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System 2.0)
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Open AccessArticle
Gibbs Free Energy and Enthalpy–Entropy Compensation in Protein–Ligand Interactions
by
Juan S. Jiménez and María J. Benítez
Biophysica 2024, 4(2), 298-309; https://doi.org/10.3390/biophysica4020021 - 14 Jun 2024
Abstract
The thermodynamics of protein–ligand interactions seems to be associated with a narrow range of Gibbs free energy. As a consequence, a linear enthalpy–entropy relationship showing an apparent enthalpy–entropy compensation (EEC) is frequently associated with protein–ligand interactions. When looking for the most negative values
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The thermodynamics of protein–ligand interactions seems to be associated with a narrow range of Gibbs free energy. As a consequence, a linear enthalpy–entropy relationship showing an apparent enthalpy–entropy compensation (EEC) is frequently associated with protein–ligand interactions. When looking for the most negative values of ∆H to gain affinity, the entropy compensation gives rise to a barely noticeable increase in affinity, therefore negatively affecting the design and discovery of new and more efficient drugs capable of binding protein targets with a higher affinity. Originally attributed to experimental errors, compensation between ∆H and T∆S values is an observable fact, although its molecular origin has remained obscure and controversial. The thermodynamic parameters of a protein–ligand interaction can be interpreted in terms of the changes in molecular weak interactions as well as in vibrational, rotational, and translational energy levels. However, a molecular explanation to an EEC rendering a linear enthalpy–entropy relationship is still lacking. Herein, we show the results of a data search of ∆G values of 3025 protein–ligand interactions and 2558 “in vivo” ligand concentrations from the Protein Data Bank database and the Metabolome Database (2020). These results suggest that the EEC may be plausibly explained as a consequence of the narrow range of ∆G associated with protein–ligand interactions. The Gaussian distribution of the ∆G values matches very well with that of ligands. These results suggest the hypothesis that the set of ∆G values for the protein–ligand interactions is the result of the evolution of proteins. The conformation versatility of present proteins and the exchange of thousands (even millions) of minute amounts of energy with the environment may have functioned as a homeostatic mechanism to make the ∆G of proteins adaptive to changes in the availability of ligands and therefore achieve the maximum regulatory capacity of the protein function. Finally, plausible strategies to avoid the EEC consequences are suggested.
Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain 2.0)
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Open AccessArticle
Emergence of Diverse Epidermal Patterns via the Integration of the Turing Pattern Model with the Majority Voting Model
by
Takeshi Ishida
Biophysica 2024, 4(2), 283-297; https://doi.org/10.3390/biophysica4020020 - 28 May 2024
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Animal skin patterns are increasingly explained using the Turing pattern model proposed by Alan Turing. The Turing model, a self-organizing model, can produce spotted or striped patterns. However, several animal patterns exist that do not correspond to these patterns. For example, the body
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Animal skin patterns are increasingly explained using the Turing pattern model proposed by Alan Turing. The Turing model, a self-organizing model, can produce spotted or striped patterns. However, several animal patterns exist that do not correspond to these patterns. For example, the body patterns of the ornamental carp Nishiki goi produced in Japan vary randomly among individuals. Therefore, predicting the pattern of offspring is difficult based on the parent fish. Such a randomly formed pattern could be explained using a majority voting model. This model is a type of cellular automaton model that counts the surrounding states and transitions to high-number states. Nevertheless, the utility of these two models in explaining fish patterns remains unclear. Interestingly, the patterns generated by these two models can be detected among very closely related species. It is difficult to think that completely different epidermal formation mechanisms are used among species of the same family. Therefore, there may be a basic model that can produce both patterns. Herein, the Turing pattern and majority voting method are represented using cellular automata, and the possibility of integrating these two methods is examined. This integrated model is equivalent to both models when the parameters are adjusted. Although this integrated model is extremely simple, it can produce more varied patterns than either one of the individual models. However, further research is warranted to determine whether this model is consistent with the mechanisms involved in the formation of animal fish patterns from a biological perspective.
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Open AccessReview
Mathematical Models of the Arabidopsis Circadian Oscillator
by
Lucas Henao, Saúl Ares and Pablo Catalán
Biophysica 2024, 4(2), 267-282; https://doi.org/10.3390/biophysica4020019 - 28 May 2024
Abstract
We review the construction and evolution of mathematical models of the Arabidopsis circadian clock, structuring the discussion into two distinct historical phases of modeling strategies: extension and reduction. The extension phase explores the bottom-up assembly of regulatory networks, introducing as many components and
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We review the construction and evolution of mathematical models of the Arabidopsis circadian clock, structuring the discussion into two distinct historical phases of modeling strategies: extension and reduction. The extension phase explores the bottom-up assembly of regulatory networks, introducing as many components and interactions as possible to capture the oscillatory nature of the clock. The reduction phase deals with functional decomposition, distilling complex models to their essential dynamical repertoire. Current challenges in this field, including the integration of spatial considerations and environmental influences like light and temperature, are also discussed. The review emphasizes the ongoing need for models that balance molecular detail with practical simplicity.
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(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain 2.0)
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Open AccessArticle
Enhanced Adsorption of Cage-Shaped Proteins on Carbon Surfaces by Carbon Nanotube (CNT)-Binding Peptide Aptamers
by
Narangerel Ganbaatar, Ting-Chieh Chu, Naofumi Okamoto, Kenji Iwahori, Masakazu Nakamura and Ichiro Yamashita
Biophysica 2024, 4(2), 256-266; https://doi.org/10.3390/biophysica4020018 - 24 May 2024
Abstract
The adsorption behavior of recombinant cage-shaped proteins with carbon nanotube (CNT)-binding peptides on carbon surfaces was quantitatively and dynamically analyzed using a highly stable quartz crystal microbalance (QCM). Two types of CNT-binding peptide aptamers obtained by the phage display method were attached to
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The adsorption behavior of recombinant cage-shaped proteins with carbon nanotube (CNT)-binding peptides on carbon surfaces was quantitatively and dynamically analyzed using a highly stable quartz crystal microbalance (QCM). Two types of CNT-binding peptide aptamers obtained by the phage display method were attached to the N- and C-termini of the Dps (DNA-binding protein derived from starved cells) to produce carbonaceous material-binding Dps. The carbon adsorption ability of the mutant Dps was studied by QCM measurement using a carbon-coated QCM sensor. The produced peptide aptamer-modified Dps showed higher affinity than a wild Dps and also showed higher adsorption capacity than a previously used Dps with carbon nanohorn-binding peptides. The newly obtained peptide aptamers were proven to provide Dps with high adsorption affinity on carbon surfaces. Furthermore, the aptamer modified to the N-terminus of the Dps subunit showed more efficient adsorption than the aptamers attached to the C-terminus of the Dp, and the linker was found to improve the adsorption ability.
Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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Open AccessArticle
Bay Laurel of Northern Morocco: A Comprehensive Analysis of Its Phytochemical Profile, Mineralogical Composition, and Antioxidant Potential
by
Amena Mrabet, Bahia Abdelfattah, Fouad El Mansouri, Ayoub Simou and Mohamed Khaddor
Biophysica 2024, 4(2), 238-255; https://doi.org/10.3390/biophysica4020017 - 15 May 2024
Abstract
Laurus nobilis, sometimes referred to as laurel, has been used for medicinal and culinary purposes for a very long time. The main subjects of this study are the phytochemical composition, mineralogical profile, and potential antioxidant properties of Laurus nobilis in Tangier, Northern
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Laurus nobilis, sometimes referred to as laurel, has been used for medicinal and culinary purposes for a very long time. The main subjects of this study are the phytochemical composition, mineralogical profile, and potential antioxidant properties of Laurus nobilis in Tangier, Northern Morocco. For phytochemical analysis of methanolic extracts, high-performance liquid chromatography (HPLC-UV-MS) was used, and Fourier transformation infrared spectroscopy (FT-IR) was used to identify each individual component. Minerals were studied by inductively coupled plasma atomic emission spectroscopy (ICP-AES) and wavelength dispersive X-ray fluorescence (WD-XRF). Total tannin, flavonoid, and phenolic amounts were quantified using aqueous and methanolic extracts. The antioxidant properties were assessed using 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis (3ethylbenzothiazoline-6-sulfonic acid) (ABTS), ferric reducing antioxidant power (FRAP), and oxygen radical absorbance capacity (ORAC) assays. Research has revealed a complex array of phytochemicals, including tannins, flavonoids, and phenolic acids. Mineral analysis has revealed the existence of vital components that are beneficial to health. Comparing the methanolic extract to the water extract, it demonstrated higher levels of phenols, flavonoids, and tannins as well as stronger antioxidant activity, indicating greater health benefits. This comprehensive study highlights the importance of Laurus nobilis from Northern Morocco as a reliable botanic resource with potential pharmaceutical, nutritional, and cosmetic uses.
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(This article belongs to the Special Issue Biomedical Optics 2.0)
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Open AccessArticle
Differential Scanning Calorimetry of Proteins and the Two-State Model: Comparison of Two Formulas
by
Knarik Yeritsyan and Artem Badasyan
Biophysica 2024, 4(2), 227-237; https://doi.org/10.3390/biophysica4020016 - 13 May 2024
Abstract
Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. In order to connect the measured profile to the properties of a particular protein, a model is required to fit. We discuss here the
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Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. In order to connect the measured profile to the properties of a particular protein, a model is required to fit. We discuss here the application of an exact two-state formula with its approximation and process the DSC experimental data on protein folding in water. The approximate formula relies on the smallness of the transition interval, which is different for each protein. With an example of the set of 33 different proteins, we show the practical validity of the approximation and the equivalence of exact and approximate two-state formulas for processing DSC data.
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(This article belongs to the Collection Feature Papers in Biophysics)
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Open AccessArticle
Benefits of Combined Fluorescence Lifetime Imaging Microscopy and Fluorescence Correlation Spectroscopy for Biomedical Studies Demonstrated by Using a Liposome Model System
by
Kristina Bruun, Hans-Gerd Löhmannsröben and Carsten Hille
Biophysica 2024, 4(2), 207-226; https://doi.org/10.3390/biophysica4020015 - 25 Apr 2024
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Drug delivery systems play a pivotal role in targeted pharmaceutical transport and controlled release at specific sites. Liposomes, commonly used as drug carriers, constitute a fundamental part of these systems. Moreover, the drug–liposome model serves as a robust platform for investigating interaction processes
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Drug delivery systems play a pivotal role in targeted pharmaceutical transport and controlled release at specific sites. Liposomes, commonly used as drug carriers, constitute a fundamental part of these systems. Moreover, the drug–liposome model serves as a robust platform for investigating interaction processes at both cellular and molecular levels. To advance our understanding of drug carrier uptake mechanisms, we employed fluorescence lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS), leveraging the unique benefits of two-photon (2P) excitation. Our approach utilized giant unilamellar vesicles (GUVs) as a simplified model system for cell membranes, labelled with the amphiphilic fluorescent dye 3,3′-dioctadecyloxa-carbocyanine (DiOC18(3)). Additionally, large unilamellar vesicles (LUVs) functioned as a drug carrier system, incorporating the spectrally distinct fluorescent sulforhodamine 101 (SRh101) as a surrogate drug. The investigation emphasized the diverse interactions between GUVs and LUVs based on the charged lipids employed. We examined the exchange kinetics and structural alterations of liposome carriers during the uptake process. Our study underscores the significance of employing 2P excitation in conjunction with FLIM and FCS. This powerful combination offers a valuable methodological approach for studying liposome interactions, positioning them as an exceptionally versatile model system with a distinct technical advantage.
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Open AccessOpinion
Biophysical Breakthroughs Projected for the Phage Therapy of Bacterial Disease
by
James P. Chambers, Miranda Aldis, Julie A. Thomas, Cara B. Gonzales, Richard Allen White III and Philip Serwer
Biophysica 2024, 4(2), 195-206; https://doi.org/10.3390/biophysica4020014 - 12 Apr 2024
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Past anti-bacterial use of bacteriophages (phage therapy) is already well reviewed as a potential therapeutic response to the emergence of multidrug-resistant, pathogenic bacteria. Phage therapy has been limited by the following. (1) The success rate is too low for routine use and Food
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Past anti-bacterial use of bacteriophages (phage therapy) is already well reviewed as a potential therapeutic response to the emergence of multidrug-resistant, pathogenic bacteria. Phage therapy has been limited by the following. (1) The success rate is too low for routine use and Food and Drug Administration (FDA) approval. (2) Current strategies of routine phage characterization do not sufficiently improve the success rate of phage therapy. (3) The stability of many phages at ambient temperature is not high enough to routinely store and transport phages at ambient temperature. In the present communication, we present new and previous data that we interpret as introductory to biophysically and efficiently transforming phage therapy to the needed level of effectiveness. Included are (1) procedure and preliminary data for the use of native gel electrophoresis (a low-cost procedure) for projecting the therapy effectiveness of a newly isolated phage, (2) data that suggest a way to achieve stabilizing of dried, ambient-temperature phages via polymer embedding, and (3) data that suggest means to increase the blood persistence, and therefore the therapy effectiveness, of what would otherwise be a relatively low-persistence phage.
Full article
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Open AccessArticle
Deciphering the Molecular Interaction Process of Gallium Maltolate on SARS-CoV-2 Main and Papain-Like Proteases: A Theoretical Study
by
Kevin Taype-Huanca, Manuel I. Osorio, Diego Inostroza, Luis Leyva-Parra, Lina Ruíz, Ana Valderrama-Negrón, Jesús Alvarado-Huayhuaz, Osvaldo Yañez and William Tiznado
Biophysica 2024, 4(2), 182-194; https://doi.org/10.3390/biophysica4020013 - 10 Apr 2024
Abstract
This study explored the inhibitory potential of gallium maltolate against severe acute respiratory syndrome coronavirus 2 and main and papain-like proteases. Computational methods, including density functional theory and molecular docking, were used to assess gallium maltolate reactivity and binding interactions. Density functional theory
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This study explored the inhibitory potential of gallium maltolate against severe acute respiratory syndrome coronavirus 2 and main and papain-like proteases. Computational methods, including density functional theory and molecular docking, were used to assess gallium maltolate reactivity and binding interactions. Density functional theory calculations revealed gallium maltolate’s high electron-capturing capacity, particularly around the gallium metal atom, which may contribute to their activity. Molecular docking demonstrated that gallium maltolate can form strong hydrogen bonds with key amino acid residues like glutamate-166 and cysteine-145, tightly binding to main and papain-like proteases. The binding energy and interactions of gallium maltolate were comparable to known SARS-CoV-2 inhibitors like N-[(5-methyl-1,2-oxazol-3-yl)carbonyl]-L-alanyl-L-valyl-N-{(2S,3E)-5-(benzyloxy)-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pent-3-en-2-yl}-L-leucinamide, indicating its potential as an antiviral agent. However, further experimental validation is required to confirm its effectiveness in inhibiting SARS-CoV-2 replication and treating COVID-19.
Full article
(This article belongs to the Special Issue The Structure and Function of Proteins, Lipids, and Nucleic Acids)
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Open AccessArticle
Search for Entanglement between Spatially Separated Living Systems: Experiment Design, Results, and Lessons Learned
by
Chris Fields, Lorenzo Cohen, Andrew Cusimano, Sharmistha Chakraborty, Phuong Nguyen, Defeng Deng, Shafaqmuhammad Iqbal, Monica Nelson, Daoyan Wei, Arnaud Delorme and Peiying Yang
Biophysica 2024, 4(2), 168-181; https://doi.org/10.3390/biophysica4020012 - 30 Mar 2024
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Statistically significant violations of the Clauser–Horne–Shimony–Holt (CHSH) inequality are the “gold standard” test for quantum entanglement between spatially separated systems. Here, we report an experimental design that implements a CHSH test between bioelectric state variables for a human subject and bioelectric and/or biochemical
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Statistically significant violations of the Clauser–Horne–Shimony–Holt (CHSH) inequality are the “gold standard” test for quantum entanglement between spatially separated systems. Here, we report an experimental design that implements a CHSH test between bioelectric state variables for a human subject and bioelectric and/or biochemical state variables for cultured human cells in vitro. While we were unable to obtain evidence for entanglement with this design, observing only classical correlation, we report lessons learned and suggest possible avenues for future studies.
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Open AccessPerspective
Never Fold to Fold Continuously: A Conundrum in Ubiquitin–Proteasome System (UPS)-Mediated Protein Quality Control (PQC)
by
Stefano Magnati and Enrico Bracco
Biophysica 2024, 4(2), 158-167; https://doi.org/10.3390/biophysica4020011 - 30 Mar 2024
Abstract
In the last few decades, the traditional paradigm of teleonomy, in which the amino acid sequence of a protein is tightly associated with its structure and, in turn, with its function, has been partially undermined. The idea of a protein as a two-state
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In the last few decades, the traditional paradigm of teleonomy, in which the amino acid sequence of a protein is tightly associated with its structure and, in turn, with its function, has been partially undermined. The idea of a protein as a two-state object has been superseded by that of understanding it as a multistate object. Indeed, some proteins, or portions of a protein, display intrinsically disordered regions (IDRs), which means that they lack stable secondary or tertiary structures. While we are aware that IDRs are present in almost half of the total human proteins, we are still quite far away from understanding their contextual-specific functions and figuring out how they mechanistically work. In the present perspective article, we will attempt to summarize the role/s of IDRs in ubiquitin–proteasome system (UPS)-mediated protein quality control (PQC) at different levels, ranging from ubiquitination to protein degradation through the proteasome machinery up to their role in decoding the complex ubiquitin code. Ultimately, we will critically discuss the future challenges we are facing to gain insights into the role of IDRs in regulating UPS-mediated PQC.
Full article
(This article belongs to the Special Issue Protein Disorder)
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Open AccessReview
Axial Tomography in Live Cell Microscopy
by
Herbert Schneckenburger and Christoph Cremer
Biophysica 2024, 4(2), 142-157; https://doi.org/10.3390/biophysica4020010 - 29 Mar 2024
Abstract
For many biomedical applications, laser-assisted methods are essential to enhance the three-dimensional (3D) resolution of a light microscope. In this report, we review possibilities to improve the 3D imaging potential by axial tomography. This method allows us to rotate the object in a
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For many biomedical applications, laser-assisted methods are essential to enhance the three-dimensional (3D) resolution of a light microscope. In this report, we review possibilities to improve the 3D imaging potential by axial tomography. This method allows us to rotate the object in a microscope into the best perspective required for imaging. Furthermore, images recorded under variable angles can be combined to one image with isotropic resolution. After a brief review of the technical state of the art, we show some biomedical applications, and discuss future perspectives for Deep View Microscopy and Molecular Imaging.
Full article
(This article belongs to the Special Issue Biomedical Optics 2.0)
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Open AccessReview
Assessing the Impact of Agents with Antiviral Activities on Transmembrane Ionic Currents: Exploring Possible Unintended Actions
by
Geng-Bai Lin, Chia-Lung Shih, Rasa Liutkevičienė, Vita Rovite, Edmund Cheung So, Chao-Liang Wu and Sheng-Nan Wu
Biophysica 2024, 4(2), 128-141; https://doi.org/10.3390/biophysica4020009 - 27 Mar 2024
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As the need for effective antiviral treatment intensifies, such as with the coronavirus disease 19 (COVID-19) infection, it is crucial to understand that while the mechanisms of action of these drugs or compounds seem apparent, they might also interact with unexplored targets, such
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As the need for effective antiviral treatment intensifies, such as with the coronavirus disease 19 (COVID-19) infection, it is crucial to understand that while the mechanisms of action of these drugs or compounds seem apparent, they might also interact with unexplored targets, such as cell membrane ion channels in diverse cell types. In this review paper, we demonstrate that many different drugs or compounds, in addition to their known interference with viral infections, may also directly influence various types of ionic currents on the surface membrane of the host cell. These agents include artemisinin, cannabidiol, memantine, mitoxantrone, molnupiravir, remdesivir, SM-102, and sorafenib. If achievable at low concentrations, these regulatory effects on ion channels are highly likely to synergize with the identified initial mechanisms of viral replication interference. Additionally, the immediate regulatory impact of these agents on the ion-channel function may potentially result in unintended adverse effects, including changes in cardiac electrical activity and the prolongation of the QTc interval. Therefore, it is essential for patients receiving these related agents to exercise additional caution to prevent unnecessary complications.
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Open AccessArticle
Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers
by
David Naranjo, Pablo M. Blanco, Josep L. Garcés, Sergio Madurga and Francesc Mas
Biophysica 2024, 4(1), 107-127; https://doi.org/10.3390/biophysica4010008 - 28 Feb 2024
Abstract
A coarse-grained model of linear polyfunctional weak charged biopolymers was implemented, formed of different proportions of acid-base groups resembling the composition of humic substances. These substances are mainly present in dissolved organic matter in natural water. The influence of electrostatic interactions computing methods,
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A coarse-grained model of linear polyfunctional weak charged biopolymers was implemented, formed of different proportions of acid-base groups resembling the composition of humic substances. These substances are mainly present in dissolved organic matter in natural water. The influence of electrostatic interactions computing methods, factors concerning the structure of the chain, different functional groups, and the ionic strength on polyelectrolytes were studied. Langevin dynamics with constant pH simulations were performed using the ESPResSO package and the Python-based Molecule Builder for ESPResSo (pyMBE) library. The coverage was fitted to a polyfunctional Frumkin isotherm, with a mean-field interaction between charged beads. The composition of the chain affects the charge while ionic strength affects both the charge and the radius of gyration. Additionally, the parameters intrinsic to the polyelectrolyte model were well reproduced by fitting the polyfunctional Frumkin isotherm. In contrast, the non-intrinsic parameters depended on the ionic strength. The method developed and applied to a polyfunctional polypeptide model, that resembles a humic acid, will be very useful for characterizing biopolymers with several acid-base functional groups, where their structure, the composition of the different functional groups, and the determination of the main intrinsic proton binding constants and their proportion are not exactly known.
Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System 2.0)
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Open AccessArticle
The Signature of Fluctuations of the Hydrogen Bond Network Formed by Water Molecules in the Interfacial Layer of Anionic Lipids
by
Ana-Marija Pavlek, Barbara Pem and Danijela Bakarić
Biophysica 2024, 4(1), 92-106; https://doi.org/10.3390/biophysica4010007 - 21 Feb 2024
Abstract
As the water molecules found at the interface of lipid bilayers exhibit distinct structural and reorientation dynamics compared to water molecules found in bulk, the fluctuations in their hydrogen bond (HB) network are expected to be different from those generated by the bulk
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As the water molecules found at the interface of lipid bilayers exhibit distinct structural and reorientation dynamics compared to water molecules found in bulk, the fluctuations in their hydrogen bond (HB) network are expected to be different from those generated by the bulk water molecules. The research presented here aims to gain an insight into temperature-dependent fluctuations of a HB network of water molecules found in an interfacial layer of multilamellar liposomes (MLVs) composed of anionic 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine (DMPS) lipids. Besides suspending DMPS lipids in phosphate buffer saline (PBS) of different pH values (6.0, 7.4, and 8.0), the changes in HB network fluctuations were altered by the incorporation of a non-polar flavonoid molecule myricetin (MCE) within the hydrocarbon chain region. By performing a multivariate analysis on the water combination band observed in temperature-dependent FTIR spectra, the results of which were further mathematically analyzed, the temperature-dependent fluctuations of interfacial water molecules were captured; the latter were the greatest for DMPS in PBS with a pH value of 7.4 and in general were greater for DMPS multibilayers in the absence of MCE. The presence of MCE made DMPS lipids more separated, allowing deeper penetration of water molecules towards the non-polar region and their restricted motion that resulted in decreased fluctuations. The experimentally observed results were supported by MD simulations of DMPS (+MCE) lipid bilayers.
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(This article belongs to the Collection Feature Papers in Biophysics)
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Open AccessCommunication
Direct Interaction of Zirconia Nanoparticles with Human Immune Cells
by
Anna M. Barbasz and Barbara Dyba
Biophysica 2024, 4(1), 83-91; https://doi.org/10.3390/biophysica4010006 - 14 Feb 2024
Abstract
Nanomaterials play a crucial role in various aspects of modern life. Zirconia nanoparticles, extensively employed in medicine for fortifying and stabilizing implants in reconstructive medicine, exhibit unique electrical, thermal, catalytic, sensory, optical, and mechanical properties. While these nanoparticles have shown antibacterial activity, they
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Nanomaterials play a crucial role in various aspects of modern life. Zirconia nanoparticles, extensively employed in medicine for fortifying and stabilizing implants in reconstructive medicine, exhibit unique electrical, thermal, catalytic, sensory, optical, and mechanical properties. While these nanoparticles have shown antibacterial activity, they also exhibit cytotoxic effects on human cells. Our research focuses on understanding how the cells of the human immune system (both the innate response, namely HL-60 and U-937, and the acquired response, namely HUT-78 and COLO-720L) respond to the presence of zirconium (IV) oxide nanoparticles (ZrO2-NPs). Viability tests indicate that ZrO2-NPs exert the highest cytotoxicity on HL-60 > U-937 > HUT-78 > COLO 720L cell lines. Notably, concentrations exceeding 100 μg mL−1 of ZrO2-NPs result in significant cytotoxicity. These nanoparticles readily penetrate the cell membrane, causing mitochondrial damage, and their cytotoxicity is associated with heightened oxidative stress in cells. The use of ZrO2-NP-based materials may pose a risk to immune system cells, the first responders to foreign entities in the body. Biofunctionalizing the surface of ZrO2-NPs could serve as an effective strategy to mitigate cytotoxicity and introduce new properties for biomedical applications.
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(This article belongs to the Special Issue Functional Application of Nanoparticles in Molecular Biology)
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Open AccessCommunication
Neurite Growth and Electrical Activity in PC-12 Cells: Effects of H3 Receptor-Inspired Electromagnetic Fields and Inherent Schumann Frequencies
by
Landon M. Lefebvre, Adam D. Plourde-Kelly, Kevin S. Saroka and Blake T. Dotta
Biophysica 2024, 4(1), 74-82; https://doi.org/10.3390/biophysica4010005 - 7 Feb 2024
Abstract
Cells are continually exposed to a range of electromagnetic fields (EMFs), including those from the Schumann resonance to radio waves. The effects of EMFs on cells are diverse and vary based on the specific EMF type. Recent research suggests potential therapeutic applications of
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Cells are continually exposed to a range of electromagnetic fields (EMFs), including those from the Schumann resonance to radio waves. The effects of EMFs on cells are diverse and vary based on the specific EMF type. Recent research suggests potential therapeutic applications of EMFs for various diseases. In this study, we explored the impact of a physiologically patterned EMF, inspired by the H3 receptor associated with wakefulness, on PC-12 cells in vitro. Our hypothesis posited that the application of this EMF to differentiated PC-12 cells could enhance firing patterns at specific frequencies. Cell electrophysiology was assessed using a novel device, allowing the computation of spectral power density (SPD) scores for frequencies between 1 Hz and 128 Hz. T-tests comparing SPD at certain frequencies (e.g., 29 Hz, 30 Hz, and 79 Hz) between the H3-EMF and control groups showed a significantly higher SPD in the H3 group (p < 0.050). Moreover, at 7.8 Hz and 71 Hz, a significant correlation was observed between predicted and percentages of cells with neurites (R = 0.542). Key findings indicate the efficacy of the new electrophysiology measure for assessing PC-12 cell activity, a significant increase in cellular activity with the H3-receptor-inspired EMF at specific frequencies, and the influence of 7.8 Hz and 71 Hz frequencies on neurite growth. The overall findings support the idea that the electrical frequency profiles of developing cell systems can serve as an indicator of their progression and eventual cellular outcomes.
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(This article belongs to the Special Issue Biological Effects of Ionizing Radiation)
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Open AccessReview
Bioprinting of Hydrogel-Based Drug Delivery Systems for Nerve Tissue Regeneration
by
Eliza Marie Steele, Zacheus L. Carr and Emily Dosmar
Biophysica 2024, 4(1), 58-73; https://doi.org/10.3390/biophysica4010004 - 31 Jan 2024
Abstract
Globally, thousands of people are affected by severe nerve injuries or neurodegenerative disorders. These conditions cannot always be cured because nerve tissue either does not regenerate or does so at a slow rate. Therefore, tissue engineering has emerged as a potential treatment approach.
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Globally, thousands of people are affected by severe nerve injuries or neurodegenerative disorders. These conditions cannot always be cured because nerve tissue either does not regenerate or does so at a slow rate. Therefore, tissue engineering has emerged as a potential treatment approach. This review discusses 3D bioprinting for scaffold manufacturing, highlights the advantages and disadvantages of common bioprinting techniques, describes important considerations for bioinks, biomaterial inks, and scaffolds, and discusses some drug delivery systems. The primary goal of this review is to bring attention to recent advances in nerve tissue engineering and its possible clinical applications in peripheral nerve, spinal cord, and cerebral nerve regeneration. Only studies that use 3D bioprinting or 3D printing to manufacture hydrogel scaffolds and incorporate the sustained release of a drug or growth factor for nerve regeneration are included. This review indicates that 3D printing is a fast and precise scaffold manufacturing technique but requires printing materials with specific properties to be effective in nervous tissue applications. The results indicate that the sustained release of certain drugs and growth factors from scaffolds can significantly improve post-printing cell viability, cell proliferation, adhesion, and differentiation, as well as functional recovery compared with scaffolds alone. However, more in vivo research needs to be conducted before this approach can be used in clinical applications.
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(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System 2.0)
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