Biophysical reviewsPub Date : 2024-09-27eCollection Date: 2025-02-01DOI: 10.1007/s12551-024-01230-5
Shruti Biyani, Amol Patil, Vinit Swami
{"title":"The influence of SDF-1 (CXCL12) gene in health and disease: a review of literature.","authors":"Shruti Biyani, Amol Patil, Vinit Swami","doi":"10.1007/s12551-024-01230-5","DOIUrl":"10.1007/s12551-024-01230-5","url":null,"abstract":"<p><p>C-X-C motif chemokine ligand 12 (CXCL12), often referred to as stromal cell-derived factor 1 (SDF-1), is a crucial factor for musculoskeletal biology. SDF-1 is a powerful chemokine that has been shown to have a significant impact on a variety of physiological functions, including tissue repair, homeostasis maintenance, and embryonic development. SDF-1 plays a dominant role in bone and cartilage metabolism. It directs mesenchymal stem cell migration, controls osteogenesis and chondrogenesis, promotes angiogenesis, and modifies the inflammatory environment. SDF-1 also acts as an inflammatory chemokine during joint inflammation, recruiting inflammatory mediators to act and cause bone and cartilage degradation, thus causing osteoarthritis. Age-related bone loss and osteoporosis is exacerbated by SDF-1, which is elevated in the peripheral circulation due to a phenomenon known as \"senescence associated secretory phenotype\" of SDF-1. SDF-1 is also implicated in cancer metastasis causing the spread of secondary malignancies. Thus, the aim of this review is to explore the complex methods by which SDF-1 affects the fine equilibrium of bone and cartilage metabolism, providing insight into its importance in both healthy and diseased conditions.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 1","pages":"127-138"},"PeriodicalIF":4.9,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11885715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584727","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}
Biophysical reviewsPub Date : 2024-09-26eCollection Date: 2024-10-01DOI: 10.1007/s12551-024-01237-y
Manuel Prieto
{"title":"A commentary on the 21st IUPAB/62ND BSJ Congress at Kyoto June 24-28, 2024.","authors":"Manuel Prieto","doi":"10.1007/s12551-024-01237-y","DOIUrl":"https://doi.org/10.1007/s12551-024-01237-y","url":null,"abstract":"","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 5","pages":"501"},"PeriodicalIF":4.9,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766103","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}
Biophysical reviewsPub Date : 2024-09-26eCollection Date: 2024-10-01DOI: 10.1007/s12551-024-01234-1
Yutong Zou, Constance B Bailey
{"title":"Cofactor recycling strategies for secondary metabolite production in cell-free protein expression systems.","authors":"Yutong Zou, Constance B Bailey","doi":"10.1007/s12551-024-01234-1","DOIUrl":"https://doi.org/10.1007/s12551-024-01234-1","url":null,"abstract":"<p><p>Cell-free protein synthesis (CFPS) has emerged as an attractive platform for biotechnology and synthetic biology due to its numerous advantages to cell-based technologies for specific applications. CFPS can be faster, less sensitive to metabolite toxicity, and amenable to systems that are not easily genetically manipulated. Due to these advantages, a promising application of CFPS is to characterize biosynthetic gene clusters, particularly those harbored within the genomes of microorganisms that generate secondary metabolites, otherwise known as natural products. In the postgenomic era, genome sequencing has revealed an incredible wealth of metabolic diversity. However, far more of these pathways are termed \"cryptic,\" i.e., unable to be produced under standard laboratory conditions than have been characterized. A major barrier to characterizing these cryptic natural products using CFPS is that many of these pathways require utilization of complex cofactors, many of which to date are not recycled efficiently or in an economically viable fashion. In this perspective, we outline strategies to regenerate cofactors relevant to secondary metabolite production in CFPS. This includes adenosine 5'-triphosphate, coenzyme A, redox cofactors (iron-sulfur clusters, nicotinamide adenine dinucleotide phosphate, flavin adenine dinucleotide), all of which play a crucial role in important biosynthetic enzymes. Such advances in cofactor recycling enable continuous production of complex metabolites in CFPS and expand the utility of this emergent platform.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 5","pages":"591-603"},"PeriodicalIF":4.9,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766264","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}
Biophysical reviewsPub Date : 2024-09-26eCollection Date: 2024-10-01DOI: 10.1007/s12551-024-01227-0
Satoshi Takahashi
{"title":"Efforts for younger generations: the Biophysical Society of Japan and IUPAB2024.","authors":"Satoshi Takahashi","doi":"10.1007/s12551-024-01227-0","DOIUrl":"10.1007/s12551-024-01227-0","url":null,"abstract":"<p><p>A personal note from the 2023-2024 President of the Biophysical Society of Japan (BSJ) on the role and activities of the BSJ in preparation for the 2024 IUPAB Congress in Kyoto.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 5","pages":"503-504"},"PeriodicalIF":4.9,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765855","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}
Biophysical reviewsPub Date : 2024-09-26eCollection Date: 2024-10-01DOI: 10.1007/s12551-024-01223-4
Navaniswaran Tharumen, Mahendran Sithamparam, Tony Z Jia, Kuhan Chandru
{"title":"Prebiotic chemistry and protocells during the faint young sun event.","authors":"Navaniswaran Tharumen, Mahendran Sithamparam, Tony Z Jia, Kuhan Chandru","doi":"10.1007/s12551-024-01223-4","DOIUrl":"10.1007/s12551-024-01223-4","url":null,"abstract":"<p><p>The sun generates light and heat for life on Earth to flourish. However, during the late Hadean-early Archean epoch on Earth, the \"faint young sun\" (FYS) was less luminous, influencing prebiotic chemistry and, by extension, the origins of life (OoL). However, higher levels of ultraviolet (UV) radiation from the FYS, especially UV-C, due to the lack of an ozone layer, would likely have impacted the assembly, stability, persistence, and functions of prebiotic cellular precursors, i.e., protocells. Consequently, it is essential to study how such UV-C radiation would have affected the synthesis and stability of prebiotically relevant molecules and protocells to better understand the plausibility of the OoL during the FYS period. In this letter, we introduce unanswered questions surrounding the structure and stability of protocells under UV-C radiation. Such a perspective may be vital to exoplanetary systems orbiting other stars, enhancing our understanding of life's potential beyond our solar system.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 5","pages":"651-654"},"PeriodicalIF":4.9,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766066","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}
Biophysical reviewsPub Date : 2024-09-24eCollection Date: 2024-10-01DOI: 10.1007/s12551-024-01228-z
Takanobu A Katoh, Elizabeth Hinde
{"title":"Overview of the super-resolution and advanced microscopy imaging session at the 21st IUPAB and the 62nd Biophysics Society of Japan joint congress.","authors":"Takanobu A Katoh, Elizabeth Hinde","doi":"10.1007/s12551-024-01228-z","DOIUrl":"10.1007/s12551-024-01228-z","url":null,"abstract":"<p><p>Recent advancements in microscopic techniques have significantly progressed, with improvements in fundamental parameters such as resolution, as well as the emergence of novel imaging techniques for measuring cellular information. In this session, six invited speakers introduced recent advancements in super-resolution and advanced microscopy imaging, covering both the development of novel microscopy techniques and their biological applications.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 5","pages":"547-550"},"PeriodicalIF":4.9,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766007","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}
Biophysical reviewsPub Date : 2024-09-20eCollection Date: 2024-10-01DOI: 10.1007/s12551-024-01225-2
Haruki Nakamura
{"title":"Commentary: <i>Biophysics and Physicobiology</i>, the official international journal of the Biophysical Society of Japan.","authors":"Haruki Nakamura","doi":"10.1007/s12551-024-01225-2","DOIUrl":"10.1007/s12551-024-01225-2","url":null,"abstract":"<p><p>This Commentary outlines recent advances of <i>Biophysics and Physicobiology</i> (<i>BPPB</i>), the official international peer-reviewed journal published by the Biophysical Society of Japan (BSJ), a member of the International Union of Pure and Applied Biophysics (IUPAB). In June 2024, BSJ hosted the 21st IUPAB Congress in Kyoto, which was attended by over 1900 participants from 52 countries and regions. The role of <i>BPPB</i> as an open-access (OA) journal within the framework of the future Japanese governmental OA policy is also discussed.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 5","pages":"505-507"},"PeriodicalIF":4.9,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766195","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}
Biophysical reviewsPub Date : 2024-09-19eCollection Date: 2024-10-01DOI: 10.1007/s12551-024-01224-3
C E Hatton, P Mehrabi
{"title":"Exploring the dynamics of allostery through multi-dimensional crystallography.","authors":"C E Hatton, P Mehrabi","doi":"10.1007/s12551-024-01224-3","DOIUrl":"https://doi.org/10.1007/s12551-024-01224-3","url":null,"abstract":"<p><p>By delving into the applications, methodologies, and case studies of multi-dimensional crystallography, whereby time and temperature are varied in the context of allostery, this review aims to elucidate the intricate interplay between structure, dynamics, and function in allosteric proteins. As the field of structural biology continues to advance, integrating multi-dimensional approaches promises to unlock new frontiers in our quest to decipher the molecular mechanisms governing life.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 5","pages":"563-570"},"PeriodicalIF":4.9,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765856","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}
Biophysical reviewsPub Date : 2024-09-02eCollection Date: 2024-10-01DOI: 10.1007/s12551-024-01222-5
Florence Tama, Jianhan Chen
{"title":"Data Science for Integrated Dynamic Structural Biology-the 21st IUPAB Congress session summary commentary.","authors":"Florence Tama, Jianhan Chen","doi":"10.1007/s12551-024-01222-5","DOIUrl":"10.1007/s12551-024-01222-5","url":null,"abstract":"<p><p>The session \"Data Science for Integrated Dynamic Structural Biology\" was a notable success at the joint congress of the 21st IUPAB and the 62nd BSJ (Biophysics Society of Japan). This session included four invited talks and one contributed talk, which together delved into recent advancements in computational methods integrating physics, experimental data, and bioinformatics to study the structure and dynamic properties of molecular assemblies and their interactions.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 5","pages":"529-531"},"PeriodicalIF":4.9,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766198","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}
Biophysical reviewsPub Date : 2024-08-31eCollection Date: 2024-12-01DOI: 10.1007/s12551-024-01221-6
Ariana Bujan, Silvia Del Valle Alonso, Nadia S Chiaramoni
{"title":"Photopolymerizable robust lipids towards reliability and their applications.","authors":"Ariana Bujan, Silvia Del Valle Alonso, Nadia S Chiaramoni","doi":"10.1007/s12551-024-01221-6","DOIUrl":"10.1007/s12551-024-01221-6","url":null,"abstract":"<p><p>Synthetic lipids have been studied as components in membrane models and drug delivery systems. Polymerizable phospholipids, especially photosensitive ones, can form new bilayer bonds when UV light irradiates. These phospholipids have been known since the 1980s, but in the last few years, new applications have been highlighted. Its use in drug delivery systems is interesting since the photopolymerization reaction produces highly stable vesicles. Additionally, the rearrangement of the acyl chains during the photopolymerization process can be applied in the generation of pores, resulting in systems that serve for drug-controlled release. In this article, our goal was to envision earlier photopolymers' publications towards the implications of these versatile phospholipids that led to proposed systems for drug delivery and controlled release of drugs at specific sites. This review offers a broad background towards a simple, reliable, and robust platform to make its application available.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 6","pages":"773-782"},"PeriodicalIF":4.9,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11735817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142999973","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}