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Biophysica
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Biomedical Optics
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Biomedical Optics

A special issue of Biophysica (ISSN 2673-4125).

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 8838

Special Issue Editor

Prof. Dr. Herbert Schneckenburger

E-Mail Website
Guest Editor
Institute of Applied Research, Aalen University, Beethovenstr. 1, 73430 Aalen, Germany
Interests: biomedical optics; laser; microscopy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biomedical optics play an increasing role in the diagnosis and treatment of patients, as well as in advanced studies of biology. Novel methods of 3D microscopy based on various kinds of illumination patterns (wide field, focused laser beam, structured, or light sheet) are adapted for investigations of 3-dimensional cell cultures, tissues or whole organs. In addition, laser-assisted micromanipulation, e.g., optical tweezers or optoporation techniques, have been revealed as helpful tools for the diagnosis or treatment of single cells. In vitro diagnostics often requires methods of (super-resolution) microscopy, hyperspectral imaging or fluorescence lifetime imaging as well as the application of opto-acoustic methods, high-content reader systems or optical biosensors. Deconvolution, automated image processing and machine learning have become valuable tools for the evaluation of large data sets. Contributions on all these and related techniques, as well as their applications in various fields of biology, are welcome in this Special Issue.

Prof. Dr. Herbert Schneckenburger
Guest Editor

Manuscript Submission Information

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Published Papers (6 papers)

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Research

11 pages, 6238 KiB  
Article
Inactivating Host Bacteria for Characterization and Use of Phages
by James P. Chambers, Elena T. Wright, Barbara Hunter and Philip Serwer
Biophysica 2023, 3(4), 558-568; https://doi.org/10.3390/biophysica3040038 - 27 Sep 2023
Viewed by 2446
Abstract
Phage characterization for research and therapy can involve newly isolated phages propagated in pathogenic bacteria. If so, characterization requires safety-managing the bacteria. In the current study, we adapt a common and inexpensive reagent, PrimeStore (Longhorn Vaccines and Diagnostics, San Antonio, TX, USA), to [...] Read more.
Phage characterization for research and therapy can involve newly isolated phages propagated in pathogenic bacteria. If so, characterization requires safety-managing the bacteria. In the current study, we adapt a common and inexpensive reagent, PrimeStore (Longhorn Vaccines and Diagnostics, San Antonio, TX, USA), to safety-manage bacteria in 20 min by selectively inactivating the bacteria. No bacterial survivors are observed among >109 bacteria per ml for a representative of both Gram-negative bacteria (Escherichia coli) and Gram-positive bacteria (Bacillus thuringiensis). This procedure causes no detected inactivation of podophage T3, myophage T4 and siphophage 0105phi7-2. Margins of safety for PrimeStore concentration exist for bacterial inactivation and phage non-inactivation. Thus, general applicability is expected. Subsequent dialysis is used to block long-term effects on phages. Nonetheless, comparable tests should be performed for each pathogenic bacterial strain/phage. Electron microscopy of thin sections reveals inactivation-altered bacterial cytoplasm and a non-disintegrated bacterial envelope (ghosts). Ghosting of E. coli includes re-arrangement of the cytoplasm and the release of endotoxin. The activity of the released endotoxin is >99% reduced after subsequent dialysis, which also removes PrimeStore components. Ghosting of B. thuringiensis includes apparent phase separation within the cytoplasm. The primary application envisaged is biophysical and other screening of phages for therapy of infectious disease. Full article
(This article belongs to the Special Issue Biomedical Optics)
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10 pages, 4660 KiB  
Article
A Dynamic Representation of mRNA Nucleotides Clarifies the Conundrum of Codon Redundancy
by Daniele Funaro
Biophysica 2023, 3(3), 548-557; https://doi.org/10.3390/biophysica3030037 - 11 Sep 2023
Viewed by 948
Abstract
The deciphering of the genetic code takes place through the reading of the nitrogenous bases, which are four in number. In most cases, the bases are taken three by three, thus generating 64 possible combinations with repetition. Each combination (codon) allows for the [...] Read more.
The deciphering of the genetic code takes place through the reading of the nitrogenous bases, which are four in number. In most cases, the bases are taken three by three, thus generating 64 possible combinations with repetition. Each combination (codon) allows for the synthesis of a specific amino acid. Since the latter are only 21 in number, the codon-amino acid conversion table shows a strong redundancy. Countless efforts have been made to understand the true encryption mechanism. Here, we want to add our version, which consists of associating a periodic sound based on three notes to each codon. RNA now becomes a dynamic object and not just a list of static instructions. In addition to a different interpretation of the genetic code, there is also a considerable reduction in redundancy, given that the number of periodic sounds that can be produced with three notes drops to 20 (with the addition of four pure frequencies). Finally, we discuss the possibility of how these sounds can be generated and travel inside the double helix, and possibly emitted as biophotons. Full article
(This article belongs to the Special Issue Biomedical Optics)
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15 pages, 5470 KiB  
Article
Probing Biochemical Differences in Lipid Components of Human Cells by Means of ATR-FTIR Spectroscopy
by Marianna Portaccio, Bahar Faramarzi and Maria Lepore
Biophysica 2023, 3(3), 524-538; https://doi.org/10.3390/biophysica3030035 - 01 Sep 2023
Cited by 5 | Viewed by 1634
Abstract
Infrared spectroscopy has emerged as a promising technique for studying the composition of biological samples like lipids that play important roles in cellular functions and are involved in various diseases. For this reason, lipids are a target of interest in many biomedical studies. [...] Read more.
Infrared spectroscopy has emerged as a promising technique for studying the composition of biological samples like lipids that play important roles in cellular functions and are involved in various diseases. For this reason, lipids are a target of interest in many biomedical studies. The objective of the present study is to utilize Fourier-Transform Infrared (FT-IR) spectroscopy to examine the main lipid components of human cells (phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, C18 ceramide, sphingosine-1-phosphate, ceramide-1-phosphate, sphingomyelin, cholesterol, and triolein). FT-IR analysis on the previously mentioned lipid samples was performed in Attenuated Total Reflection (ATR) mode. The obtained spectra clearly evidence the contributions of the different functional groups that are present in the examined samples. Detailed assignments of spectral features were carried out in agreement with the literature. Similarities and differences among the different types of commercial lipid samples are evidenced and discussed, with particular attention to phospholipid and sphingolipid components. A quantitative analysis of phosphatidylinositol and sphingomyelin spectra using a ratiometric approach is reported. Moreover, a reconstruction procedure of FT-IR spectra of complex lipids useful for chemometrics applications is described. These representative examples of the potential use of the results of the present study can certainly contribute to a larger use of FT-IR spectroscopy in lipidomics. Full article
(This article belongs to the Special Issue Biomedical Optics)
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11 pages, 1846 KiB  
Article
Experimental Determination of the Stability of the «Flamena» Gel Pharmacological Structure under the Influence of Low-Intensity Laser Radiation
by Diana V. Prikule, Vladislav F. Prikuls, Aleksejs Potrivailo and Anna K. Kamavosyan
Biophysica 2023, 3(3), 513-523; https://doi.org/10.3390/biophysica3030034 - 30 Aug 2023
Viewed by 730
Abstract
In modern dentistry, the problem of the prevention and treatment of peri-implantitis is relevant. Proposed methods of treating patients with peri-implantitis do not stop the pathological process with the possibility of achieving long-term remission. Liposomal complexes with dihydroquercetin make it possible to influence [...] Read more.
In modern dentistry, the problem of the prevention and treatment of peri-implantitis is relevant. Proposed methods of treating patients with peri-implantitis do not stop the pathological process with the possibility of achieving long-term remission. Liposomal complexes with dihydroquercetin make it possible to influence the pathogenetic links of the inflammatory process in periodontal tissues with the prospect of normalizing blood circulation and regeneration processes in the affected area. It has been established that the complex simultaneous effect of low-intensity laser radiation and a pharmaceutical (laserophoresis) provides the possibility of more significant penetration of the drug components into periodontal tissues. The study of the laserophoresis of the liposomal complex with dihydroquercetin in the treatment of patients with peri-implantitis is relevant. However, in the modern literature, there is a lack of studies on the effect of low-intensity laser radiation on the pharmaceutical structure of drugs based on the above-mentioned basis. Full article
(This article belongs to the Special Issue Biomedical Optics)
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12 pages, 2456 KiB  
Article
Beta-Caryophyllene Induces Significant Changes in the Lipid Bilayer at Room and Physiological Temperatures: ATR-FTIR Spectroscopy Studies
by Ivan D. Yakimov, Ilya M. Kolmogorov and Irina M. Le-Deygen
Biophysica 2023, 3(3), 501-512; https://doi.org/10.3390/biophysica3030033 - 30 Aug 2023
Viewed by 854
Abstract
Beta-caryophyllene (BCP) is a natural bicyclic sesquiterpene with high biological activity. Potentially, it can be used in the treatment of a wide range of neurological diseases. However, to date, there are practically no data on the interaction of BCP with biological membranes. In [...] Read more.
Beta-caryophyllene (BCP) is a natural bicyclic sesquiterpene with high biological activity. Potentially, it can be used in the treatment of a wide range of neurological diseases. However, to date, there are practically no data on the interaction of BCP with biological membranes. In the present work, we studied for the first time the interaction of BCP with model membranes—liposomes based on egg yolk phosphatidylcholine (Egg PC) with a variable cholesterol content (from 0 to 25 w.%). Using ATR-FTIR spectroscopy, we have shown that the membrane rigidity and cholesterol content dramatically affect the nature of the interaction of BCP with the bilayer both at room temperature and at physiological temperatures. The incorporation of BCP into the thickness of the bilayer leads to changes in the subpolar region of the bilayer, and at a high cholesterol content, it can provoke the formation of defects in the membrane. Full article
(This article belongs to the Special Issue Biomedical Optics)
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11 pages, 2213 KiB  
Article
Comparative Investigation of XPS Spectra of Oxidated Carbon Nanotubes and Graphene
by Viktor P. Afanas’ev, Grigorii S. Bocharov, Alexander V. Eletskii, Lidiya G. Lobanova, Konstantin I. Maslakov and Serguei V. Savilov
Biophysica 2023, 3(2), 307-317; https://doi.org/10.3390/biophysica3020020 - 13 Apr 2023
Cited by 2 | Viewed by 1611
Abstract
X-ray photoelectron emission spectra of thermally reduced graphene oxide samples and carbon nanotubes (CNTs) with various oxidation degrees are presented in this paper. A method for the reconstruction of differential electron inelastic scattering cross sections from the energy loss spectra of photoelectrons is [...] Read more.
X-ray photoelectron emission spectra of thermally reduced graphene oxide samples and carbon nanotubes (CNTs) with various oxidation degrees are presented in this paper. A method for the reconstruction of differential electron inelastic scattering cross sections from the energy loss spectra of photoelectrons is described and discussed. The analysis of the part of the characteristic photoelectron energy loss spectrum adjacent to the C1 peak indicated a considerable influence of the thermal reduction of graphene oxide on the electron properties of the samples obtained. On the contrary, the oxidation of CNTs by refluxing in a concentrated HNO3 solution does not change the free electron excitation spectrum. Full article
(This article belongs to the Special Issue Biomedical Optics)
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