Pub Date : 2024-12-15DOI: 10.1016/j.plrev.2024.12.006
Sergiy O. Garbuzynskiy, Victor V. Marchenkov, Natalia Y. Marchenko, Gennady V. Semisotnov, Alexei V. Finkelstein
This review presents the current understanding of (i) spontaneous self-organization of spatial structures of protein molecules, and (ii) possible ways of chaperones’ assistance to this process. Specifically, we overview the most important features of spontaneous folding of proteins (mostly, of the single-domain water-soluble globular proteins): the choice of the unique protein structure among zillions of alternatives, the nucleation of the folding process, and phase transitions within protein molecules. We consider the main experimental facts on protein folding, both in vivo and in vitro, of both kinetic and thermodynamic nature. We discuss the famous Levinthal's paradox of protein folding and its solution, theoretical models of protein folding and unfolding, and the dependence of the rates of these processes on the protein chain length. Special attention is paid to relatively small, single-domain, and water-soluble globular proteins whose structure and folding are much better studied and understood than those of large proteins, especially membrane or fibrous proteins. Lastly, we describe the chaperone-assisted protein folding with an emphasis on the chaperones’ ability to prevent proteins from their irreversible aggregation. Since the possible assistance mechanisms connected with chaperones are still debatable, experimental data useful in selecting the most likely mechanisms of chaperone-assisted protein folding are presented.
{"title":"How proteins manage to fold and how chaperones manage to assist the folding","authors":"Sergiy O. Garbuzynskiy, Victor V. Marchenkov, Natalia Y. Marchenko, Gennady V. Semisotnov, Alexei V. Finkelstein","doi":"10.1016/j.plrev.2024.12.006","DOIUrl":"10.1016/j.plrev.2024.12.006","url":null,"abstract":"<div><div>This review presents the current understanding of (i) spontaneous self-organization of spatial structures of protein molecules, and (ii) possible ways of chaperones’ assistance to this process. Specifically, we overview the most important features of spontaneous folding of proteins (mostly, of the single-domain water-soluble globular proteins): the choice of the unique protein structure among zillions of alternatives, the nucleation of the folding process, and phase transitions within protein molecules. We consider the main experimental facts on protein folding, both in vivo and in vitro, of both kinetic and thermodynamic nature. We discuss the famous Levinthal's paradox of protein folding and its solution, theoretical models of protein folding and unfolding, and the dependence of the rates of these processes on the protein chain length. Special attention is paid to relatively small, single-domain, and water-soluble globular proteins whose structure and folding are much better studied and understood than those of large proteins, especially membrane or fibrous proteins. Lastly, we describe the chaperone-assisted protein folding with an emphasis on the chaperones’ ability to prevent proteins from their irreversible aggregation. Since the possible assistance mechanisms connected with chaperones are still debatable, experimental data useful in selecting the most likely mechanisms of chaperone-assisted protein folding are presented.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"52 ","pages":"Pages 66-79"},"PeriodicalIF":13.7,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-13DOI: 10.1016/j.plrev.2024.12.007
Richard Parncutt
{"title":"The emotional connotations of major and minor: The role of harmonicity and pitch height","authors":"Richard Parncutt","doi":"10.1016/j.plrev.2024.12.007","DOIUrl":"10.1016/j.plrev.2024.12.007","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"52 ","pages":"Pages 129-131"},"PeriodicalIF":13.7,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142891179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-07DOI: 10.1016/j.plrev.2024.12.003
Salikoko S. Mufwene
{"title":"Languages are cultural artifacts and align with cultural evolution: Comment on “Language follows a distinct mode of extra-genomic evolution” by Balthasar Bickel, Anne-Lise Giraud, Klaus Zuberbühler, Carel P. van Schaik (this issue)","authors":"Salikoko S. Mufwene","doi":"10.1016/j.plrev.2024.12.003","DOIUrl":"10.1016/j.plrev.2024.12.003","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"52 ","pages":"Pages 57-60"},"PeriodicalIF":13.7,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-06DOI: 10.1016/j.plrev.2024.12.004
Matthew Pelowski , Katherine N. Cotter , Stephanie Miller , Helmut Leder
In this brief contribution—happily afforded by the 20th anniversary of Physics of Life Reviews—we take the opportunity to reflect on our earlier published paper, which had introduced a theoretical framework, the VIMAP (Vienna Integrated Model of (Top-Down and Bottom-up processes in) Art Perception; (Pelowski et al., [1])) that has come to represent a major basis for organizing, anticipating, and empirically investigating the nuanced, multivariate visual art experience. We look back at the original model and its hypotheses, especially as these regard distinct "outcomes," which we had argued may provide a superstructure of supraordinate, shared varieties of art experience detected across individual meetings of viewer, context, and artworks. In the present paper we consider whether these outcomes could also be a useful tool for approaching new demands across multiple art-related areas that have strengthened in the years since the original publication regarding applying the arts to wellbeing, societal challenges, and health. All of which require a framework for better understanding and testing the nuanced features of individual-centered art experience. We briefly—and admitedly very speculatively—consider how these new topics could be fit to the VIMAP [2]. Guided also by new evidence from our team that has provided a bottom-up verification of the specified outcome types and their implications, we provide a working set of suggestions whereby we might connect wellbeing- or attitude/behavioral change-related targets to the specific VIMAP outcomes, which we argue may provide a powerful mechanistic structure for future research.
在这篇简短的文章中——很高兴由《生命物理学评论》20周年提供——我们借此机会反思我们早期发表的论文，该论文介绍了一个理论框架，VIMAP(维也纳综合模型（自上而下和自下而上的过程）艺术感知；（Pelowski et al.,[1]）)，这已经成为组织、预测和实证调查微妙、多元视觉艺术体验的主要基础。我们回顾了最初的模型和它的假设，特别是当它们考虑到不同的“结果”时，我们认为这些结果可能提供了一种超越的、共享的艺术体验的上层建筑，这种艺术体验贯穿了观众、环境和艺术品的个人会议。在本论文中，我们考虑这些结果是否也可以成为一种有用的工具，用于满足多个艺术相关领域的新需求，这些领域自最初发表以来一直在加强，将艺术应用于福祉、社会挑战和健康。所有这些都需要一个框架来更好地理解和测试以个人为中心的艺术体验的细微特征。我们简要地考虑了这些新主题如何适用于VIMAP[2]。在我们团队提供的新证据的指导下，对特定的结果类型及其含义进行了自下而上的验证，我们提供了一套工作建议，据此我们可以将幸福感或态度/行为变化相关目标与特定的VIMAP结果联系起来，我们认为这可能为未来的研究提供强大的机制结构。
{"title":"Framing wellbeing and societal challenge mechanisms via distinct outcomes of art experience? A brief revisit to the VIMAP","authors":"Matthew Pelowski , Katherine N. Cotter , Stephanie Miller , Helmut Leder","doi":"10.1016/j.plrev.2024.12.004","DOIUrl":"10.1016/j.plrev.2024.12.004","url":null,"abstract":"<div><div>In this brief contribution—happily afforded by the 20th anniversary of Physics of Life Reviews—we take the opportunity to reflect on our earlier published paper, which had introduced a theoretical framework, the VIMAP (Vienna Integrated Model of (Top-Down and Bottom-up processes in) Art Perception; (Pelowski et al., <span><span>[1]</span></span>)) that has come to represent a major basis for organizing, anticipating, and empirically investigating the nuanced, multivariate visual art experience. We look back at the original model and its hypotheses, especially as these regard distinct \"outcomes,\" which we had argued may provide a superstructure of supraordinate, shared varieties of art experience detected across individual meetings of viewer, context, and artworks. In the present paper we consider whether these outcomes could also be a useful tool for approaching new demands across multiple art-related areas that have strengthened in the years since the original publication regarding applying the arts to wellbeing, societal challenges, and health. All of which require a framework for better understanding and testing the nuanced features of individual-centered art experience. We briefly—and admitedly very speculatively—consider how these new topics could be fit to the VIMAP <span><span>[2]</span></span>. Guided also by new evidence from our team that has provided a bottom-up verification of the specified outcome types and their implications, we provide a working set of suggestions whereby we might connect wellbeing- or attitude/behavioral change-related targets to the specific VIMAP outcomes, which we argue may provide a powerful mechanistic structure for future research.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"52 ","pages":"Pages 132-143"},"PeriodicalIF":13.7,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142913479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-06DOI: 10.1016/j.plrev.2024.12.002
E. Fanchon, A. Stéphanou
{"title":"The role of mathematical models in epidemic prediction and the challenges of COVID-19. Comment on ‘data-driven mathematical modeling approaches for COVID-19: A survey’ by J. Demongeot, P. Magal","authors":"E. Fanchon, A. Stéphanou","doi":"10.1016/j.plrev.2024.12.002","DOIUrl":"10.1016/j.plrev.2024.12.002","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"52 ","pages":"Pages 55-56"},"PeriodicalIF":13.7,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-06DOI: 10.1016/j.plrev.2024.11.019
Francesco Pappalardo, Giulia Russo
{"title":"Comment on “A decade of thermostatted kinetic theory models for complex active matter living systems” by Carlo Bianca","authors":"Francesco Pappalardo, Giulia Russo","doi":"10.1016/j.plrev.2024.11.019","DOIUrl":"10.1016/j.plrev.2024.11.019","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"52 ","pages":"Pages 61-62"},"PeriodicalIF":13.7,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-06DOI: 10.1016/j.plrev.2024.12.005
François Osiurak , Nicolas Claidière
{"title":"Language is a unique form of communication that transformed human evolution but how unique is linguistic evolution?","authors":"François Osiurak , Nicolas Claidière","doi":"10.1016/j.plrev.2024.12.005","DOIUrl":"10.1016/j.plrev.2024.12.005","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"52 ","pages":"Pages 63-64"},"PeriodicalIF":13.7,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142821653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-05DOI: 10.1016/j.plrev.2024.12.001
R. Eftimie
{"title":"Multi-scale phenomena behind the transmission of infectious disease","authors":"R. Eftimie","doi":"10.1016/j.plrev.2024.12.001","DOIUrl":"10.1016/j.plrev.2024.12.001","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"52 ","pages":"Pages 53-54"},"PeriodicalIF":13.7,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-05DOI: 10.1016/j.plrev.2024.11.017
Giulio Carraturo , Victor Pando-Naude , Marco Costa , Peter Vuust , Leonardo Bonetti , Elvira Brattico
In Western tonal music, major and minor modes are recognized as the primary musical features in eliciting emotional responses. The underlying correlates of this dichotomy in music perception have been extensively investigated through decades of psychological and neuroscientific research, yielding plentiful yet often discordant results that highlight the complexity and individual differences in how these modes are perceived. This variability suggests that a deeper understanding of major-minor mode perception in music is still needed. We present the first comprehensive systematic review and meta-analysis, providing both qualitative and quantitative syntheses of major-minor mode perception and its behavioural and neural correlates. The qualitative synthesis includes 70 studies, revealing significant diversity in how the major-minor dichotomy has been empirically investigated. Most studies focused on adults, considered participants' expertise, used real-life musical stimuli, conducted behavioural evaluations, and were predominantly performed with Western listeners. Meta-analyses of behavioural, electroencephalography, and neuroimaging data (37 studies) consistently show that major and minor modes elicit distinct neural and emotional responses, though these differences are heavily influenced by subjective perception. Based on our findings, we propose a framework to describe a Major-Minor Mode(l) of music perception and its correlates, incorporating individual factors such as age, expertise, cultural background, and emotional disorders. Moreover, this work explores the cultural and historical implications of the major-minor dichotomy in music, examining its origins, universality, and emotional associations across both Western and non-Western contexts. By considering individual differences and acoustic characteristics, we contribute to a broader understanding of how musical frameworks develop across cultures. Limitations, implications, and suggestions for future research are discussed, including potential clinical applications for mood regulation and emotional disorders, alongside recommendations for experimental paradigms in investigating major-minor modes.
{"title":"The major-minor mode dichotomy in music perception","authors":"Giulio Carraturo , Victor Pando-Naude , Marco Costa , Peter Vuust , Leonardo Bonetti , Elvira Brattico","doi":"10.1016/j.plrev.2024.11.017","DOIUrl":"10.1016/j.plrev.2024.11.017","url":null,"abstract":"<div><div>In Western tonal music, major and minor modes are recognized as the primary musical features in eliciting emotional responses. The underlying correlates of this dichotomy in music perception have been extensively investigated through decades of psychological and neuroscientific research, yielding plentiful yet often discordant results that highlight the complexity and individual differences in how these modes are perceived. This variability suggests that a deeper understanding of major-minor mode perception in music is still needed. We present the first comprehensive systematic review and meta-analysis, providing both qualitative and quantitative syntheses of major-minor mode perception and its behavioural and neural correlates. The qualitative synthesis includes 70 studies, revealing significant diversity in how the major-minor dichotomy has been empirically investigated. Most studies focused on adults, considered participants' expertise, used real-life musical stimuli, conducted behavioural evaluations, and were predominantly performed with Western listeners. Meta-analyses of behavioural, electroencephalography, and neuroimaging data (37 studies) consistently show that major and minor modes elicit distinct neural and emotional responses, though these differences are heavily influenced by subjective perception. Based on our findings, we propose a framework to describe a Major-Minor Mode(l) of music perception and its correlates, incorporating individual factors such as age, expertise, cultural background, and emotional disorders. Moreover, this work explores the cultural and historical implications of the major-minor dichotomy in music, examining its origins, universality, and emotional associations across both Western and non-Western contexts. By considering individual differences and acoustic characteristics, we contribute to a broader understanding of how musical frameworks develop across cultures. Limitations, implications, and suggestions for future research are discussed, including potential clinical applications for mood regulation and emotional disorders, alongside recommendations for experimental paradigms in investigating major-minor modes.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"52 ","pages":"Pages 80-106"},"PeriodicalIF":13.7,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142891180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-04DOI: 10.1016/j.plrev.2024.11.018
V. Volpert
{"title":"From SIR to delay models in epidemiology","authors":"V. Volpert","doi":"10.1016/j.plrev.2024.11.018","DOIUrl":"10.1016/j.plrev.2024.11.018","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"52 ","pages":"Pages 49-52"},"PeriodicalIF":13.7,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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