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Applications of Spectroscopy in Biophysical Research
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Applications of Spectroscopy in Biophysical Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (15 April 2023) | Viewed by 7478

Special Issue Editor

Dr. Maria Teresa Caccamo

E-Mail Website
Guest Editor
Department of Mathematical and Computer Sciences, Physical and Earth Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy
Interests: complementary spectroscopic techniques; infrared spectroscopy; Raman spectroscopic; neutron scattering; polymers; peo; peg; disaccharides; trehalose; maltose; sucrose
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is well known that the integrated use of experimental investigation techniques for the characterization of space–time correlations of systems of biophysical interest represents a powerful tool to characterize such types of systems. Biophysical research deals with the physical phenomena within living things, on scales that span molecules, cells, tissues and organisms. In particular, such systems are provided by a dynamic structure that can be parameterized by means of suitable space–time scales. In studying such phenomena in such a way, the principles and methods of physics are used to understand biological systems, so biophysical research can be considered an interdisciplinary science, being closely related to quantitative and systems biology. The Special Issue “Application of Spectroscopy in Biophysical Research” is an opportunity to collect and share papers that deal with different systems of biophysical interest by means of spectroscopy techniques.

Dr. Maria Teresa Caccamo
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (4 papers)

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Research

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13 pages, 2971 KiB  
Article
Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy
by Annalisa D’Arco, Marta Di Fabrizio, Tiziana Mancini, Rosanna Mosetti, Salvatore Macis, Giovanna Tranfo, Giancarlo Della Ventura, Augusto Marcelli, Massimo Petrarca and Stefano Lupi
Int. J. Mol. Sci. 2023, 24(11), 9550; https://doi.org/10.3390/ijms24119550 - 31 May 2023
Viewed by 1917
Abstract
All coronaviruses are characterized by spike glycoproteins whose S1 subunits contain the receptor binding domain (RBD). The RBD anchors the virus to the host cellular membrane to regulate the virus transmissibility and infectious process. Although the protein/receptor interaction mainly depends on the spike’s [...] Read more.
All coronaviruses are characterized by spike glycoproteins whose S1 subunits contain the receptor binding domain (RBD). The RBD anchors the virus to the host cellular membrane to regulate the virus transmissibility and infectious process. Although the protein/receptor interaction mainly depends on the spike’s conformation, particularly on its S1 unit, their secondary structures are poorly known. In this paper, the S1 conformation was investigated for MERS-CoV, SARS-CoV, and SARS-CoV-2 at serological pH by measuring their Amide I infrared absorption bands. The SARS-CoV-2 S1 secondary structure revealed a strong difference compared to those of MERS-CoV and SARS-CoV, with a significant presence of extended β-sheets. Furthermore, the conformation of the SARS-CoV-2 S1 showed a significant change by moving from serological pH to mild acidic and alkaline pH conditions. Both results suggest the capability of infrared spectroscopy to follow the secondary structure adaptation of the SARS-CoV-2 S1 to different environments. Full article
(This article belongs to the Special Issue Applications of Spectroscopy in Biophysical Research)
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13 pages, 3464 KiB  
Article
Fluorescence Analysis of Biocide Efficiency in Antifouling Coatings against Cyanobacteria
by Aleksandra Orzechowska, Anna Czaderna-Lekka, Martin Trtílek and Piotr Rusiniak
Int. J. Mol. Sci. 2023, 24(5), 4972; https://doi.org/10.3390/ijms24054972 - 04 Mar 2023
Cited by 1 | Viewed by 1238
Abstract
This study focused on the antifouling effect of copper oxide (Cu2O)- and zineb-based coatings against Cyanothece sp. ATCC 51142 by analysing photosynthetic activity using chlorophyll fluorescence. The photoautotrophically grown cyanobacterium was exposed to toxic coatings over a short-term period of 32 [...] Read more.
This study focused on the antifouling effect of copper oxide (Cu2O)- and zineb-based coatings against Cyanothece sp. ATCC 51142 by analysing photosynthetic activity using chlorophyll fluorescence. The photoautotrophically grown cyanobacterium was exposed to toxic coatings over a short-term period of 32 h. The study showed that Cyanothece cultures are particularly sensitive to biocides (i) released from antifouling paints and (ii) exhibited by contact with the coated surfaces. Changes in the maximum quantum yield of photosystem II (FV/FM) were observed within the first 12 h of exposure to the coatings. Partial recovery of FV/FM in Cyanothece was revealed 24 h post exposure to a copper- and zineb-free coating. In this research, we proposed an analysis of the evaluation of fluorescence data to study the initial response of cyanobacterial cells to copper- and non-copper-based antifouling coatings formulated with zineb. We evaluated the dynamics of coating toxicity by determining the characteristic time constants of changes in the FV/FM. Within the most toxic paints studied, those formulated with the highest concentration of Cu2O and zineb, the estimated time constants were 3.9 times lower compared to the copper- and zineb-free paint. The use of zineb in copper-based antifouling coatings enhanced the toxic effect of paints and contributed to a faster decline in photosystem II activity in Cyanothece cells. The analysis we proposed, along with the fluorescence screening results, may be useful in evaluating the initial antifouling dynamic action against photosynthetic aquacultures. Full article
(This article belongs to the Special Issue Applications of Spectroscopy in Biophysical Research)
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21 pages, 5110 KiB  
Article
Cellular Lactate Spectroscopy Using 1.5 Tesla Clinical Apparatus
by Adrian Truszkiewicz, Dorota Bartusik-Aebisher, Jolanta Zalejska-Fiolka, Aleksandra Kawczyk-Krupka and David Aebisher
Int. J. Mol. Sci. 2022, 23(19), 11355; https://doi.org/10.3390/ijms231911355 - 26 Sep 2022
Cited by 2 | Viewed by 1361
Abstract
Cellular lactate is a key cellular metabolite and marker of anaerobic glycolysis. Cellular lactate uptake, release, production from glucose and glycogen, and interconversion with pyruvate are important determinants of cellular energy. It is known that lactate is present in the spectrum of neoplasms [...] Read more.
Cellular lactate is a key cellular metabolite and marker of anaerobic glycolysis. Cellular lactate uptake, release, production from glucose and glycogen, and interconversion with pyruvate are important determinants of cellular energy. It is known that lactate is present in the spectrum of neoplasms and low malignancy (without necrotic lesions). Also, the appearance of lactate signals is associated with anaerobic glucose, mitochondrial dysfunction, and other inflammatory responses. The aim of this study was the detection of lactate in cell cultures with the use of proton magnetic resonance (1H MRS) and a 1.5 Tesla clinical apparatus (MR OPTIMA 360), characterized as a medium-field system. In this study, selected metabolites, together with cellular lactate, were identified with the use of an appropriate protocol and management algorithm. This paper describes the results obtained for cancer cell cultures. This medium-field system has proven the possibility of detecting small molecules, such as lactate, with clinical instruments. 1H MRS performed using clinical MR apparatus is a useful tool for clinical analysis. Full article
(This article belongs to the Special Issue Applications of Spectroscopy in Biophysical Research)
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Review

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14 pages, 2382 KiB  
Review
Synchrotron Infrared Microspectroscopy for Stem Cell Research
by Jiang Qian, Xue Gao, Ya-Di Wang, Xue-Ling Li, Jun Hu and Jun-Hong Lü
Int. J. Mol. Sci. 2022, 23(17), 9878; https://doi.org/10.3390/ijms23179878 - 30 Aug 2022
Cited by 3 | Viewed by 1815
Abstract
Stem cells have shown great potential functions for tissue regeneration and repair because of their unlimited self-renewal and differentiation. Stem cells reside in their niches, making them a hotspot for the development and diagnosis of diseases. Complex interactions between niches and stem cells [...] Read more.
Stem cells have shown great potential functions for tissue regeneration and repair because of their unlimited self-renewal and differentiation. Stem cells reside in their niches, making them a hotspot for the development and diagnosis of diseases. Complex interactions between niches and stem cells create the balance between differentiation, self-renewal, maturation, and proliferation. However, the multi-facet applications of stem cells have been challenged since the complicated responses of stem cells to biological processes were explored along with the limitations of current systems or methods. Emerging evidence highlights that synchrotron infrared microspectroscopy, known as synchrotron radiation-based Fourier transform infrared microspectroscopy, has been investigated as a potentially attractive technology with its non-invasive and non-biological probes in stem cell research. With their unique vibration bands, the quantitative mapping of the content and distribution of biomolecules can be detected and characterized in cells or tissues. In this review, we focus on the potential applications of synchrotron infrared microspectroscopy for investigating the differentiation and fate determination of stem cells. Full article
(This article belongs to the Special Issue Applications of Spectroscopy in Biophysical Research)
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