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Biophysica
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State-of-the-Art Biophysics in Italy
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State-of-the-Art Biophysics in Italy

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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 9554

Special Issue Editors

Dr. Danilo Milardi

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Guest Editor
Institute of Crystallography, National Research Council, 95126 Catania, Italy
Interests: protein folding; protein aggregation; calorimetry; model membranes; lipid bilayer; amyloid; metal dyshomeostasis; proteasome
Prof. Dr. Gianluca Lattanzi

E-Mail Website
Guest Editor
Department of Physics, University of Trento, 38123 Trento, Italy
Interests: statistical mechanics; molecular dynamics simulations; membrane proteins modelling; protein model; computational biophysics
Prof. Dr. Giuseppe Maulucci

E-Mail Website
Guest Editor
1. Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
2. Institute of Physics, Catholic University of Rome, Largo F. Vito 1, 00168 Rome, Italy
Interests: metabolic imaging; fluorescence microscopy; membrane biophysics; artificial intelligence; biophysical methods; instrumentation
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Morten Gram Pedersen

E-Mail Website
Guest Editor
Department of Information Engineering, University of Padova, 35131 Padova, Italy
Interests: mathematical modeling; electrical activity; calcium dynamics; exocytosis; hormone secretion

Special Issue Information

Dear Colleagues,

This Special Issue aims to provide a comprehensive overview of the state of the art of biophysics in Italy. We invite full research articles and comprehensive reviews that showcase current efforts and ongoing projects involving biophysics in Italy. Potential topics include but are not limited to the following research areas: cellular biophysics, biophysics of disease, ion channels, live-cell imaging, mathematical modeling, cellular signaling, medical physics, and application of biophysics in medicine.

Dr. Danilo Milardi
Prof. Dr. Gianluca Lattanzi
Prof. Dr. Giuseppe Maulucci
Prof. Dr. Morten Gram Pedersen
Guest Editors

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. Biophysica is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). 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.

Keywords

  • biophysics
  • statistical mechanics
  • computer simulations
  • mathematical modelling
  • stochastic modeling
  • molecular dynamics
  • membrane dynamics
  • ion channels
  • fluorescence imaging
  • single-molecule microscopy
  • exocytosis
  • cell-to-cell communication
  • calcium dynamics
  • systems biology
  • protein folding
  • amyloid aggregation
  • nucleotide assembly

Published Papers (5 papers)

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Research

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15 pages, 2328 KiB  
Article
Microgravity as an Anti-Metastatic Agent in an In Vitro Glioma Model
by Maurizio Sabbatini, Valentina Bonetto, Valeria Magnelli, Candida Lorusso, Francesco Dondero and Maria Angela Masini
Biophysica 2023, 3(4), 636-650; https://doi.org/10.3390/biophysica3040043 - 25 Nov 2023
Viewed by 755
Abstract
Gravity is a primary physical force that has a profound influence on the stability of the cell cytoskeleton. In our research, we investigated the influence of microgravity on altering the cytoskeletal pathways of glioblastoma cells. The highly infiltrative behavior of glioblastoma is supported [...] Read more.
Gravity is a primary physical force that has a profound influence on the stability of the cell cytoskeleton. In our research, we investigated the influence of microgravity on altering the cytoskeletal pathways of glioblastoma cells. The highly infiltrative behavior of glioblastoma is supported by cytoskeletal dynamics and surface proteins that allow glioblastoma cells to avoid stable connections with the tissue environment and other cells. Glioblastoma cell line C6 was exposed to a microgravity environment for 24, 48, and 72 h by 3D-RPM, a laboratory instrument recognized to reproduce the effect of microgravity in cell cultures. The immunofluorescence for GFAP, vinculin, and Connexin-43 was investigated as signals related to cytoskeleton dynamics. The polymerization of GFAP and the expression of focal contact structured by vinculin were found to be altered, especially after 48 and 72 h of microgravity. Connexin-43, involved in several intracellular pathways that critically promote cell motility and invasion of glioma cells, was found to be largely reduced following microgravity exposure. In conclusion, microgravity, by reducing the expression of Connexin-43, alters the architecture of specific cytoskeletal elements such as GFAP and increases the focal contact, which can induce a reduction in glioma cell mobility, thereby inhibiting their aggressive metastatic behavior. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Italy)
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11 pages, 1654 KiB  
Article
Did Maxwell Dream of Electrical Bacteria?
by Eleonora Alfinito, Maura Cesaria and Matteo Beccaria
Biophysica 2022, 2(3), 281-291; https://doi.org/10.3390/biophysica2030026 - 13 Sep 2022
Cited by 1 | Viewed by 1162
Abstract
We propose a model for bacterial Quorum Sensing based on an auxiliary electrostatic-like interaction originating from a fictitious electrical charge that represents bacteria activity. A cooperative mechanism for charge/activity exchange is introduced to implement chemotaxis and replication. The bacteria system is thus represented [...] Read more.
We propose a model for bacterial Quorum Sensing based on an auxiliary electrostatic-like interaction originating from a fictitious electrical charge that represents bacteria activity. A cooperative mechanism for charge/activity exchange is introduced to implement chemotaxis and replication. The bacteria system is thus represented by means of a complex resistor network where link resistances take into account the allowed activity-flow among individuals. By explicit spatial stochastic simulations, we show that the model exhibits different quasi-realistic behaviors from colony formation to biofilm aggregation. The electrical signal associated with Quorum Sensing is analyzed in space and time and provides useful information about the colony dynamics. In particular, we analyze the transition between the planktonic and colony phases as the intensity of Quorum Sensing is varied. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Italy)
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Review

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23 pages, 4140 KiB  
Review
A Brief Review of FT-IR Spectroscopy Studies of Sphingolipids in Human Cells
by Bahar Faramarzi, Martina Moggio, Nadia Diano, Marianna Portaccio and Maria Lepore
Biophysica 2023, 3(1), 158-180; https://doi.org/10.3390/biophysica3010011 - 02 Mar 2023
Cited by 4 | Viewed by 3777
Abstract
In recent years, sphingolipids have attracted significant attention due to their pivotal role in cellular functions and physiological diseases. A valuable tool for investigating the characteristics of sphingolipids can be represented via FT-IR spectroscopy, generally recognized as a very powerful technique that provides [...] Read more.
In recent years, sphingolipids have attracted significant attention due to their pivotal role in cellular functions and physiological diseases. A valuable tool for investigating the characteristics of sphingolipids can be represented via FT-IR spectroscopy, generally recognized as a very powerful technique that provides detailed biochemical information on the examined sample with the unique properties of sensitivity and accuracy. In the present paper, some fundamental aspects of sphingolipid components of human cells are summarized, and the most relevant articles devoted to the FT-IR spectroscopic studies of sphingolipids are revised. A short description of different FT-IR experimental approaches adopted for investigating sphingolipids is also given, with details about the most commonly used data analysis procedures. The present overview of FT-IR investigations, although not exhaustive, attests to the relevant role this vibrational technique has played in giving significant insight into many aspects of this fascinating class of lipids. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Italy)
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23 pages, 3565 KiB  
Review
A Long Journey into the Investigation of the Structure–Dynamics–Function Paradigm in Proteins through the Activities of the Palermo Biophysics Group
by Grazia Cottone, Antonio Cupane, Maurizio Leone, Valeria Vetri and Valeria Militello
Biophysica 2022, 2(4), 452-474; https://doi.org/10.3390/biophysica2040040 - 17 Nov 2022
Viewed by 1324
Abstract
An overview of the biophysics activity at the Department of Physics and Chemistry Emilio Segrè of the University of Palermo is given. For forty years, the focus of the research has been on the protein structure–dynamics–function paradigm, with the aim of understanding the [...] Read more.
An overview of the biophysics activity at the Department of Physics and Chemistry Emilio Segrè of the University of Palermo is given. For forty years, the focus of the research has been on the protein structure–dynamics–function paradigm, with the aim of understanding the molecular basis of the relevant mechanisms and the key role of solvent. At least three research lines are identified; the main results obtained in collaboration with other groups in Italy and abroad are presented. This review is dedicated to the memory of Professors Massimo Ugo Palma, Maria Beatrice Palma Vittorelli, and Lorenzo Cordone, which were the founders of the Palermo School of Biophysics. We all have been, directly or indirectly, their pupils; we miss their enthusiasm for scientific research, their deep physical insights, their suggestions, their strict but always constructive criticisms, and, most of all, their friendship. This paper is dedicated also to the memory of Prof. Hans Frauenfelder, whose pioneering works on nonexponential rebinding kinetics, protein substates, and energy landscape have inspired a large part of our work in the field of protein dynamics. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Italy)
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16 pages, 8125 KiB  
Review
Supramolecular-Covalent Peptides Self-Assembly: From Design to Regenerative Medicine and Beyond
by Raffaele Pugliese
Biophysica 2022, 2(4), 324-339; https://doi.org/10.3390/biophysica2040030 - 11 Oct 2022
Cited by 1 | Viewed by 1666
Abstract
The field of supramolecular peptides self-assembly has undergone outstanding growth since the early 1990s after the serendipitously discovery by Shuguang Zhang of an ionic self-complementary peptide as a repeating segment in a yeast protein. From then on, the field expanded at an accelerating [...] Read more.
The field of supramolecular peptides self-assembly has undergone outstanding growth since the early 1990s after the serendipitously discovery by Shuguang Zhang of an ionic self-complementary peptide as a repeating segment in a yeast protein. From then on, the field expanded at an accelerating pace and these self-assembled materials have become an integral part of a broad plethora of designer supramolecular nanomaterials useful for different applications ranging from 3D tissue cell cultures, regenerative medicine, up to optoelectronics. However, the supramolecular peptide based-nanomaterials available thus far for regenerative medicine still lack the dynamic complexity found in the biological structures that mediate regeneration. Indeed, self-assembling peptide (SAPs) suffer from poor mechanical stability, losing mechanical properties at low strains. Just like the extracellular matrix (ECM) of living systems, the chemical structure of the SAP-biomaterials should concurrently contain non-covalent and covalent bonds, bringing, respectively, infinite and finite lifetimes of interactions to obtain a reversibly dynamic matrix. In this review, will be highlighted the major advantages and current limitations of SAP-based biomaterials, and it will be discussed the most widely used strategies for precisely tune their mechanical properties (stiffness, resilience, strain-failure, stress resistance), describing recent and promising approaches in tissue engineering, regenerative medicine, and beyond. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Italy)
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