State-of-the-Art Biophysics in Spain

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

Deadline for manuscript submissions: closed (30 September 2022) | Viewed by 28731

Special Issue Editor


E-Mail Website
Guest Editor
1. Departament de Física de la Matèria Condensada, Universitat de Barcelona, 08028 Barcelona, Spain
2. Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 Barcelona, Spain
Interests: molecular motors; cell motility; collective cell migration; tissue mechanics; morphogenesis; development; active matter; hydrodynamics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biophysics is one of the most promising and innovative areas of multidisciplinary research. Spain has actively participated in its development during the last decades, from the original concept of biophysics as a branch of biology that involved physical concepts and instruments, to the current status as a consolidated area of research where Biology and Physics meet and cross-fertilize. Many Spanish groups have pioneered a physical approach to biological systems, both contributing to a deeper understanding of the physical mechanisms that underlay biological phenomena and to the pursuit of new physics in living matter. This Special Issue aims to provide a comprehensive overview of the state-of-the-art of Biophysics in Spain, ranging from the more traditional and established areas to the most innovative approaches. We invite researchers in the Spanish research system to submit full research articles or comprehensive reviews. Potential topics include but are not limited to the following research areas:

  • Structure and Dynamics of Biomolecules and Their Assemblies Biomolecular Machines;
  • Biomembranes;
  • Genetics and Gene Expression Mechanisms;
  • Cell Biophysics;
  • Tissue Biophysics;
  • Developmental Biophysics;
  • Biophysical Techniques and Instrumentation;
  • Theory and Modeling of Biological Systems;
  • Systems Biology;
  • Neuronal networks;
  • Synthetic Biology;
  • Physics of Evolution;

Prof. Dr. Jaume Casademunt
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. 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

  • self-assembly
  • self-organization
  • living matter
  • molecular biophysics
  • protein folding
  • protein aggregation
  • single-molecule physics
  • molecular motors
  • ion channels
  • membrane dynamics
  • signaling
  • gene expression
  • cell biophysics
  • cell mechanics
  • tissue mechanics
  • mechanobiology
  • cell motility
  • cell migration
  • development
  • embryogenesis
  • morphogenesis
  • pattern formation
  • neuron physics
  • neuronal networks
  • systems biology
  • synthetic biology
  • evolution
  • computational biology

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (8 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

22 pages, 8519 KiB  
Article
Neuronal Cultures: Exploring Biophysics, Complex Systems, and Medicine in a Dish
by Jordi Soriano
Biophysica 2023, 3(1), 181-202; https://doi.org/10.3390/biophysica3010012 - 10 Mar 2023
Cited by 9 | Viewed by 3596
Abstract
Neuronal cultures are one of the most important experimental models in modern interdisciplinary neuroscience, allowing to investigate in a control environment the emergence of complex behavior from an ensemble of interconnected neurons. Here, I review the research that we have conducted at the [...] Read more.
Neuronal cultures are one of the most important experimental models in modern interdisciplinary neuroscience, allowing to investigate in a control environment the emergence of complex behavior from an ensemble of interconnected neurons. Here, I review the research that we have conducted at the neurophysics laboratory at the University of Barcelona over the last 15 years, describing first the neuronal cultures that we prepare and the associated tools to acquire and analyze data, to next delve into the different research projects in which we actively participated to progress in the understanding of open questions, extend neuroscience research on new paradigms, and advance the treatment of neurological disorders. I finish the review by discussing the drawbacks and limitations of neuronal cultures, particularly in the context of brain-like models and biomedicine. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain)
Show Figures

Figure 1

19 pages, 23226 KiB  
Article
Genotype-to-Protein Map and Collective Adaptation in a Viral Population
by Ariadna Villanueva, Henry Secaira-Morocho, Luis F. Seoane, Ester Lázaro and Susanna Manrubia
Biophysica 2022, 2(4), 381-399; https://doi.org/10.3390/biophysica2040034 - 27 Oct 2022
Cited by 2 | Viewed by 2303
Abstract
Viral populations are large and highly heterogeneous. Despite the evolutionary relevance of such heterogeneity, statistical approaches to quantifying the extent to which viruses maintain a high genotypic and/or phenotypic diversity have been rarely pursued. Here, we address this issue by analyzing a nucleotide-to-protein [...] Read more.
Viral populations are large and highly heterogeneous. Despite the evolutionary relevance of such heterogeneity, statistical approaches to quantifying the extent to which viruses maintain a high genotypic and/or phenotypic diversity have been rarely pursued. Here, we address this issue by analyzing a nucleotide-to-protein sequence map through deep sequencing of populations of the Qβ phage adapted to high temperatures. Tens of thousands of different sequences corresponding to two fragments of the gene coding for the viral replicase were recovered. A diversity analysis of two independent populations consistently revealed that about 40% of the mutations identified caused changes in protein amino acids, leading to an almost complete exploration of the protein neighborhood of (non-silent) mutants at a distance of one. The functional form of the empirical distribution of phenotype abundance agreed with analytical calculations that assumed random mutations in the nucleotide sequence. Our results concur with the idea that viral populations maintain a high diversity as an efficient adaptive mechanism and support the hypothesis of universality for a lognormal distribution of phenotype abundances in biologically meaningful genotype–phenotype maps, highlighting the relevance of entropic effects in molecular evolution. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain)
Show Figures

Figure 1

Review

Jump to: Research

14 pages, 2020 KiB  
Review
Biological Calorimetry: Old Friend, New Insights
by Olga Abian, Sonia Vega and Adrian Velazquez-Campoy
Biophysica 2023, 3(1), 21-34; https://doi.org/10.3390/biophysica3010002 - 20 Jan 2023
Cited by 3 | Viewed by 2650
Abstract
Calorimetry is an old experimental technique (first instrument developed in S. XVIII), but it is broadly used and still provides key information for understanding biological processes at the molecular level, particularly, cooperative phenomena in protein interactions. Here, we review and highlight some key [...] Read more.
Calorimetry is an old experimental technique (first instrument developed in S. XVIII), but it is broadly used and still provides key information for understanding biological processes at the molecular level, particularly, cooperative phenomena in protein interactions. Here, we review and highlight some key aspects of biological calorimetry. Several biological systems will be described in which calorimetry was instrumental for modeling the behavior of the protein and obtaining further biological insight. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain)
Show Figures

Figure 1

20 pages, 3772 KiB  
Review
A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation
by Carlos Pintado-Grima, Oriol Bárcenas, Andrea Bartolomé-Nafría, Marc Fornt-Suñé, Valentín Iglesias, Javier Garcia-Pardo and Salvador Ventura
Biophysica 2023, 3(1), 1-20; https://doi.org/10.3390/biophysica3010001 - 18 Jan 2023
Cited by 5 | Viewed by 4007
Abstract
The presence of insoluble protein deposits in tissues and organs is a hallmark of many human pathologies. In addition, the formation of protein aggregates is considered one of the main bottlenecks to producing protein-based therapeutics. Thus, there is a high interest in rationalizing [...] Read more.
The presence of insoluble protein deposits in tissues and organs is a hallmark of many human pathologies. In addition, the formation of protein aggregates is considered one of the main bottlenecks to producing protein-based therapeutics. Thus, there is a high interest in rationalizing and predicting protein aggregation. For almost two decades, our laboratory has been working to provide solutions for these needs. We have traditionally combined the core tenets of both bioinformatics and wet lab biophysics to develop algorithms and databases to study protein aggregation and its functional implications. Here, we review the computational toolbox developed by our lab, including programs for identifying sequential or structural aggregation-prone regions at the individual protein and proteome levels, engineering protein solubility, finding and evaluating prion-like domains, studying disorder-to-order protein transitions, or categorizing non-conventional amyloid regions of polar nature, among others. In perspective, the succession of the tools we describe illustrates how our understanding of the protein aggregation phenomenon has evolved over the last fifteen years. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain)
Show Figures

Figure 1

17 pages, 2815 KiB  
Review
Optical Tweezers to Force Information out of Biological and Synthetic Systems One Molecule at a Time
by Rebeca Bocanegra, María Ortiz-Rodríguez, Ismael Plaza Garcia-Abadillo, Carlos R-Pulido and Borja Ibarra
Biophysica 2022, 2(4), 564-580; https://doi.org/10.3390/biophysica2040047 - 9 Dec 2022
Viewed by 2943
Abstract
Over the last few decades, in vitro single-molecule manipulation techniques have enabled the use of force and displacement as controlled variables in biochemistry. Measuring the effect of mechanical force on the real-time kinetics of a biological process gives us access to the rates, [...] Read more.
Over the last few decades, in vitro single-molecule manipulation techniques have enabled the use of force and displacement as controlled variables in biochemistry. Measuring the effect of mechanical force on the real-time kinetics of a biological process gives us access to the rates, equilibrium constants and free-energy landscapes of the mechanical steps of the reaction; this information is not accessible by ensemble assays. Optical tweezers are the current method of choice in single-molecule manipulation due to their versatility, high force and spatial and temporal resolutions. The aim of this review is to describe the contributions of our lab in the single-molecule manipulation field. We present here several optical tweezers assays refined in our laboratory to probe the dynamics and mechano-chemical properties of biological molecular motors and synthetic molecular devices at the single-molecule level. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain)
Show Figures

Figure 1

16 pages, 1743 KiB  
Review
The Forces behind Directed Cell Migration
by Isabela C. Fortunato and Raimon Sunyer
Biophysica 2022, 2(4), 548-563; https://doi.org/10.3390/biophysica2040046 - 1 Dec 2022
Cited by 5 | Viewed by 5687
Abstract
Directed cell migration is an essential building block of life, present when an embryo develops, a dendritic cell migrates toward a lymphatic vessel, or a fibrotic organ fails to restore its normal parenchyma. Directed cell migration is often guided by spatial gradients in [...] Read more.
Directed cell migration is an essential building block of life, present when an embryo develops, a dendritic cell migrates toward a lymphatic vessel, or a fibrotic organ fails to restore its normal parenchyma. Directed cell migration is often guided by spatial gradients in a physicochemical property of the cell microenvironment, such as a gradient in chemical factors dissolved in the medium or a gradient in the mechanical properties of the substrate. Single cells and tissues sense these gradients, establish a back-to-front polarity, and coordinate the migration machinery accordingly. Central to these steps we find physical forces. In some cases, these forces are integrated into the gradient sensing mechanism. Other times, they transmit information through cells and tissues to coordinate a collective response. At any time, they participate in the cellular migratory system. In this review, we explore the role of physical forces in gradient sensing, polarization, and coordinating movement from single cells to multicellular collectives. We use the framework proposed by the molecular clutch model and explore to what extent asymmetries in the different elements of the clutch can lead to directional migration. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain)
Show Figures

Figure 1

19 pages, 2374 KiB  
Review
Characterisation of Amyloid Aggregation and Inhibition by Diffusion-Based Single-Molecule Fluorescence Techniques
by David Polanco, Alejandra Carrancho, Pablo Gracia and Nunilo Cremades
Biophysica 2022, 2(4), 506-524; https://doi.org/10.3390/biophysica2040043 - 21 Nov 2022
Viewed by 4701
Abstract
Protein amyloid aggregation has been associated with more than 50 human disorders, including the most common neurodegenerative disorders Alzheimer’s and Parkinson’s disease. Interfering with this process is considered as a promising therapeutic strategy for these diseases. Our understanding of the process of amyloid [...] Read more.
Protein amyloid aggregation has been associated with more than 50 human disorders, including the most common neurodegenerative disorders Alzheimer’s and Parkinson’s disease. Interfering with this process is considered as a promising therapeutic strategy for these diseases. Our understanding of the process of amyloid aggregation and its role in disease has typically been limited by the use of ensemble-based biochemical and biophysical techniques, owing to the intrinsic heterogeneity and complexity of the process. Single-molecule techniques, and particularly diffusion-based single-molecule fluorescence approaches, have been instrumental to obtain meaningful information on the dynamic nature of the fibril-forming process, as well as the characterisation of the heterogeneity of the amyloid aggregates and the understanding of the molecular basis of inhibition of a number of molecules with therapeutic interest. In this article, we reviewed some recent contributions on the characterisation of the amyloid aggregation process, the identification of distinct structural groups of aggregates in homotypic or heterotypic aggregation, as well as on the study of the interaction of amyloid aggregates with other molecules, allowing the estimation of the binding sites, affinities, and avidities as examples of the type of relevant information we can obtain about these processes using these techniques. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain)
Show Figures

Figure 1

8 pages, 907 KiB  
Review
Birth and Early Steps of the Organization of Biophysics in Spain
by Félix M. Goñi
Biophysica 2022, 2(4), 498-505; https://doi.org/10.3390/biophysica2040042 - 19 Nov 2022
Viewed by 1370
Abstract
In the 1960s, Biophysics was an unheard of scientific field in Spain, and even outside Spain, the distinction between Biophysics and Molecular Biology was not clear at the time. This paper describes briefly the developments that led to the foundation of the Spanish [...] Read more.
In the 1960s, Biophysics was an unheard of scientific field in Spain, and even outside Spain, the distinction between Biophysics and Molecular Biology was not clear at the time. This paper describes briefly the developments that led to the foundation of the Spanish National Committee for Biophysics (1981) and of the Spanish Biophysical Society (1987), the incorporation of Spain into IUPAB and EBSA, and the normalized presence of Biophysics as a compulsory subject in undergraduate curricula in Spain. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain)
Show Figures

Figure 1

Back to TopTop