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Biophysica, Volume 4, Issue 2 (June 2024) – 12 articles

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15 pages, 5225 KiB  
Article
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
Viewed by 149
Abstract
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 [...] Read more.
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. Full article
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16 pages, 1971 KiB  
Review
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
Viewed by 201
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain 2.0)
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11 pages, 1188 KiB  
Article
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
Viewed by 96
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 [...] Read more.
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)
18 pages, 1110 KiB  
Article
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
Viewed by 296
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Biomedical Optics 2.0)
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11 pages, 364 KiB  
Article
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
Viewed by 273
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 [...] Read more.
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. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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21 pages, 4551 KiB  
Article
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
Viewed by 449
Abstract
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 [...] Read more.
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. Full article
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12 pages, 707 KiB  
Opinion
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
Viewed by 726
Abstract
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 [...] Read more.
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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13 pages, 3453 KiB  
Article
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
Viewed by 601
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 [...] Read more.
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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14 pages, 558 KiB  
Article
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
Viewed by 622
Abstract
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 [...] Read more.
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. Full article
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10 pages, 869 KiB  
Perspective
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
Viewed by 515
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 [...] Read more.
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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16 pages, 3618 KiB  
Review
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
Viewed by 492
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 [...] Read more.
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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14 pages, 2140 KiB  
Review
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
Viewed by 569
Abstract
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 [...] Read more.
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. Full article
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