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DNA damage and repair in the nucleosome: insights from computational methods. 核小体中的 DNA 损伤和修复：计算方法的启示。
IF 4.9
Biophysical reviews Pub Date : 2024-03-12 eCollection Date: 2024-06-01 DOI: 10.1007/s12551-024-01183-9
Natacha Gillet, Elise Dumont, Emmanuelle Bignon
{"title":"DNA damage and repair in the nucleosome: insights from computational methods.","authors":"Natacha Gillet, Elise Dumont, Emmanuelle Bignon","doi":"10.1007/s12551-024-01183-9","DOIUrl":"10.1007/s12551-024-01183-9","url":null,"abstract":"<p><p>Cellular DNA is constantly exposed to endogenous or exogenous factors that can induce lesions. Several types of lesions have been described that can result from UV/ionizing irradiations, oxidative stress, or free radicals, among others. In order to overcome the deleterious effects of such damages, i.e., mutagenicity or cytotoxicity, cells possess a highly complex DNA repair machinery, involving repair enzymes targeting specific types of lesions through dedicated cellular pathways. In addition, DNA is highly compacted in the nucleus, the first level of compaction consisting of ~ 147 DNA base pairs wrapped around a core of histones, the so-called nucleosome core particle. In this complex environment, the DNA structure is highly constrained, and fine-tuned mechanisms involving remodeling processes are required to expose the DNA to repair enzymes and to facilitate the damage removal. However, these nucleosome-specific mechanisms remain poorly understood, and computational methods emerged only recently as powerful tools to investigate DNA damages in such complex systems as the nucleosome. In this mini-review, we summarize the latest advances brought out by computational approaches in the field, opening new exciting perspectives for the study of DNA damage and repair in the nucleosome context.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 3","pages":"345-356"},"PeriodicalIF":4.9,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11297232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Biophysical Reviews: peering into 2024. 生物物理评论》：展望 2024 年。
IF 4.9
Biophysical reviews Pub Date : 2024-02-20 eCollection Date: 2024-02-01 DOI: 10.1007/s12551-024-01182-w
Damien Hall
{"title":"Biophysical Reviews: peering into 2024.","authors":"Damien Hall","doi":"10.1007/s12551-024-01182-w","DOIUrl":"10.1007/s12551-024-01182-w","url":null,"abstract":"<p><p>After introducing the winner of this year's Michèle Auger Award for Young Scientists' Independent Research, this Editorial for Volume 16 Issue 1 then describes the Issue contents. The Editorial concludes by providing a look into what lies ahead for 2024.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 1","pages":"1-7"},"PeriodicalIF":4.9,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10937855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140142761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Biophysical reviews Special issue call: The 21st IUPAB Congress 2024 Kyoto Japan. 生物物理评论特刊征集：第 21 届 IUPAB 大会 2024 日本京都。
Biophysical reviews Pub Date : 2024-02-19 eCollection Date: 2024-02-01 DOI: 10.1007/s12551-024-01181-x
Wilma K Olson, Damien Hall
{"title":"<i>Biophysical reviews</i> Special issue call: The 21st IUPAB Congress 2024 Kyoto Japan.","authors":"Wilma K Olson, Damien Hall","doi":"10.1007/s12551-024-01181-x","DOIUrl":"https://doi.org/10.1007/s12551-024-01181-x","url":null,"abstract":"<p><p>This commentary describes an open call for submissions to the upcoming <i>Biophysical Reviews</i>' Special Issue: The 21st IUPAB Congress 2024 Kyoto Japan. The submission deadline is July 1st of 2024. Interested parties are requested to make contact with the Special Issue editors prior to submission.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 1","pages":"9-10"},"PeriodicalIF":0.0,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10937856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140142759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Special Mini-Issue: Quantitative methods to decipher cellular heterogeneity - from single-cell to spatial omic methods. 小型特刊：解读细胞异质性的定量方法--从单细胞到空间 omic 方法。
IF 4.9
Biophysical reviews Pub Date : 2024-01-30 eCollection Date: 2024-02-01 DOI: 10.1007/s12551-024-01180-y
Xi Chen, Angela Ruohao Wu
{"title":"<i>Special Mini-Issue</i>: Quantitative methods to decipher cellular heterogeneity - from single-cell to spatial omic methods.","authors":"Xi Chen, Angela Ruohao Wu","doi":"10.1007/s12551-024-01180-y","DOIUrl":"10.1007/s12551-024-01180-y","url":null,"abstract":"<p><p>In this mini-issue, we have a collection of eight reviews that discuss various advanced topics on the investigation of cellular heterogeneity. These reviews highlight the latest developments in technologies that capture and assess biology at single cell resolution, as well as approaches for cellular measurements with spatial information. Challenges and opportunities to develop future innovations and approaches are also presented.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 1","pages":"11-12"},"PeriodicalIF":4.9,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10937863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140142760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Emerging tools for uncovering genetic and transcriptomic heterogeneities in bacteria 揭示细菌遗传和转录组异质性的新兴工具
Biophysical reviews Pub Date : 2024-01-02 DOI: 10.1007/s12551-023-01178-y
Yi Liao
{"title":"Emerging tools for uncovering genetic and transcriptomic heterogeneities in bacteria","authors":"Yi Liao","doi":"10.1007/s12551-023-01178-y","DOIUrl":"https://doi.org/10.1007/s12551-023-01178-y","url":null,"abstract":"","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"51 7","pages":"1-16"},"PeriodicalIF":0.0,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139390199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Ionic liquids meet lipid bilayers: a state-of-the-art review. 离子液体与脂质双分子层：最新进展综述。
IF 4.9
Biophysical reviews Pub Date : 2024-01-02 eCollection Date: 2023-12-01 DOI: 10.1007/s12551-023-01173-3
Antonio Benedetto
{"title":"Ionic liquids meet lipid bilayers: a state-of-the-art review.","authors":"Antonio Benedetto","doi":"10.1007/s12551-023-01173-3","DOIUrl":"10.1007/s12551-023-01173-3","url":null,"abstract":"<p><p>In the past 25 years, a vast family of complex organic salts known as room-temperature ionic liquids (ILs) has received increasing attention due to their potential applications. ILs are composed by an organic cation and either an organic or inorganic anion, and possess several intriguing properties such as low vapor pressure and being liquid around room temperature. Several biological studies flagged their moderate-to-high (cyto)-toxicity. Toxicity is, however, also a synonym of affinity, and this boosted a series of biophysical and chemical-physical investigations aimed at exploiting ILs in bio-nanomedicine, drug-delivery, pharmacology, and bio-nanotechnology. Several of these investigations focused on the interaction between ILs and lipid membranes, aimed at determining the microscopic mechanisms behind their interaction. This is the focus of this review work. These studies have been carried out on a variety of different lipid bilayer systems ranging from 1-lipid to 5-lipids systems, and also on cell-extracted membranes. They have been carried out at different chemical-physical conditions and by the use of a number of different approaches, including atomic force microscopy, neutron and X-ray scattering, dynamic light scattering, differential scanning calorimetry, surface quartz microbalance, nuclear magnetic resonance, confocal fluorescence microscopy, and molecular dynamics simulations. The aim of this \"2023 Michèle Auger Award\" review work is to provide the reader with an <i>up-to-date</i> overview of this fascinating research field where \"ILs meet lipid bilayers (aka biomembranes),\" with the aim to boost it further and expand its cross-disciplinary edges towards novel high-impact ideas/applications in pharmacology, drug delivery, biomedicine, and bio-nanotechnology.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"15 6","pages":"1909-1939"},"PeriodicalIF":4.9,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10771448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139401823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Biophysical Reviews: A goodbye to 2023 生物物理评论》：告别 2023 年
Biophysical reviews Pub Date : 2023-12-26 DOI: 10.1007/s12551-023-01177-z
Damien Hall
{"title":"Biophysical Reviews: A goodbye to 2023","authors":"Damien Hall","doi":"10.1007/s12551-023-01177-z","DOIUrl":"https://doi.org/10.1007/s12551-023-01177-z","url":null,"abstract":"","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"8 16","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139155517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Simulating biological surface dynamics in high-speed atomic force microscopy experiments 在高速原子力显微镜实验中模拟生物表面动力学
Biophysical reviews Pub Date : 2023-12-23 DOI: 10.1007/s12551-023-01169-z
Damien Hall
{"title":"Simulating biological surface dynamics in high-speed atomic force microscopy experiments","authors":"Damien Hall","doi":"10.1007/s12551-023-01169-z","DOIUrl":"https://doi.org/10.1007/s12551-023-01169-z","url":null,"abstract":"","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"25 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139162695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Biophysical Reviews’ “Meet the Editors Series”: a profile of Damien Hall 生物物理评论》"编辑见面系列"：达米恩-霍尔简介
Biophysical reviews Pub Date : 2023-12-22 DOI: 10.1007/s12551-023-01176-0
Damien Hall
{"title":"Biophysical Reviews’ “Meet the Editors Series”: a profile of Damien Hall","authors":"Damien Hall","doi":"10.1007/s12551-023-01176-0","DOIUrl":"https://doi.org/10.1007/s12551-023-01176-0","url":null,"abstract":"","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"18 26","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138946975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Computational biophysics of atomic force microscopy—an IUPAB-sponsored workshop 原子力显微镜的计算生物物理学--IUPAB 主办的研讨会
Biophysical reviews Pub Date : 2023-12-22 DOI: 10.1007/s12551-023-01170-6
Damien Hall, Holger Flechsig, Takashi Sumikama
{"title":"Computational biophysics of atomic force microscopy—an IUPAB-sponsored workshop","authors":"Damien Hall, Holger Flechsig, Takashi Sumikama","doi":"10.1007/s12551-023-01170-6","DOIUrl":"https://doi.org/10.1007/s12551-023-01170-6","url":null,"abstract":"","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"2 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138944917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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