Biophysics reviews最新文献_第3页

Spatially defined microenvironment for engineering organoids. 空间限定的有机体工程微环境

IF 3.4

Biophysics reviews Pub Date : 2024-10-18 eCollection Date: 2024-12-01 DOI: 10.1063/5.0198848

Yilan Zhang, Fukang Qi, Peng Chen, Bi-Feng Liu, Yiwei Li

{"title":"Spatially defined microenvironment for engineering organoids.","authors":"Yilan Zhang, Fukang Qi, Peng Chen, Bi-Feng Liu, Yiwei Li","doi":"10.1063/5.0198848","DOIUrl":"10.1063/5.0198848","url":null,"abstract":"In the intricately defined spatial microenvironment, a single fertilized egg remarkably develops into a conserved and well-organized multicellular organism. This observation leads us to hypothesize that stem cells or other seed cell types have the potential to construct fully structured and functional tissues or organs, provided the spatial cues are appropriately configured. Current organoid technology, however, largely depends on spontaneous growth and self-organization, lacking systematic guided intervention. As a result, the structures replicated in vitro often emerge in a disordered and sparse manner during growth phases. Although existing organoids have made significant contributions in many aspects, such as advancing our understanding of development and pathogenesis, aiding personalized drug selection, as well as expediting drug development, their potential in creating large-scale implantable tissue or organ constructs, and constructing multicomponent microphysiological systems, together with functioning at metabolic levels remains underutilized. Recent discoveries have demonstrated that the spatial definition of growth factors not only induces directional growth and migration of organoids but also leads to the formation of assembloids with multiple regional identities. This opens new avenues for the innovative engineering of higher-order organoids. Concurrently, the spatial organization of other microenvironmental cues, such as physical stresses, mechanical loads, and material composition, has been minimally explored. This review delves into the burgeoning field of organoid engineering with a focus on potential spatial microenvironmental control. It offers insight into the molecular principles, expected outcomes, and potential applications, envisioning a future perspective in this domain.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 4","pages":"041302"},"PeriodicalIF":3.4,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11646138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142831118","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

Regulation of epithelial cell jamming transition by cytoskeleton and cell-cell interactions. 细胞骨架和细胞间相互作用对上皮细胞干扰转换的调控。

IF 4.5

Biophysics reviews Pub Date : 2024-10-14 eCollection Date: 2024-12-01 DOI: 10.1063/5.0220088

Zoe D Latham, Alexandra Bermudez, Jimmy K Hu, Neil Y C Lin

{"title":"Regulation of epithelial cell jamming transition by cytoskeleton and cell-cell interactions.","authors":"Zoe D Latham, Alexandra Bermudez, Jimmy K Hu, Neil Y C Lin","doi":"10.1063/5.0220088","DOIUrl":"10.1063/5.0220088","url":null,"abstract":"Multicellular systems, such as epithelial cell collectives, undergo transitions similar to those in inert physical systems like sand piles and foams. To remodel or maintain tissue organization during development or disease, these collectives transition between fluid-like and solid-like states, undergoing jamming or unjamming transitions. While these transitions share principles with physical systems, understanding their regulation and implications in cell biology is challenging. Although cell jamming and unjamming follow physics principles described by the jamming diagram, they are fundamentally biological processes. In this review, we explore how cellular processes and interactions regulate jamming and unjamming transitions. We begin with an overview of how these transitions control tissue remodeling in epithelial model systems and describe recent findings of the physical principles governing tissue solidification and fluidization. We then explore the mechanistic pathways that modulate the jamming phase diagram axes, focusing on the regulation of cell fluctuations and geometric compatibility. Drawing upon seminal works in cell biology, we discuss the roles of cytoskeleton and cell-cell adhesion in controlling cell motility and geometry. This comprehensive view illustrates the molecular control of cell jamming and unjamming, crucial for tissue remodeling in various biological contexts.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 4","pages":"041301"},"PeriodicalIF":4.5,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11479637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482225","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

Structural visualization of inhibitor binding in prolyl oligopeptidase. 脯氨酰寡肽酶抑制剂结合的结构可视化。

IF 3.4

Biophysics reviews Pub Date : 2024-08-22 eCollection Date: 2024-09-01 DOI: 10.1063/5.0226428

Katarzyna Walczewska-Szewc, Jakub Rydzewski

{"title":"Structural visualization of inhibitor binding in prolyl oligopeptidase.","authors":"Katarzyna Walczewska-Szewc, Jakub Rydzewski","doi":"10.1063/5.0226428","DOIUrl":"10.1063/5.0226428","url":null,"abstract":"The association and dissociation of proteins and ligands are crucial in biophysics for potential drug development [Baron and McCammon, Annu. Rev. Phys. Chem. 64, 151-175 (2013)]. However, identifying and characterizing the reaction pathways for these rare events has been a long-standing challenge. Molecular dynamics (MD) simulations are limited in exploring biophysical processes on experimental timescales, so ligand transport processes through complex transient tunnels formed by proteins during dynamics are often simulated using enhanced sampling MD [Rydzewski and Nowak, Phys. Life Rev. 22-23, 58-74 (2017)]. Erroneously identified ligand binding pathways can affect thermodynamic and kinetic characteristics calculated from MD trajectories. A system that has the potential to be a therapeutic target for neurodegenerative diseases is prolyl oligopeptidase (PREP). This is due to its involvement in promoting protein aggregation and disrupting cellular function through affecting protein-protein interactions (PPI). The recent discovery of a new type of PREP inhibitor that targets PPI raises important questions about the diversity of ligand binding pathways in PREP and their impact on protein dynamics [Pätsi et al., J. Med. Chem. 67, 5421-5436 (2024); Kilpeläinen et al., J. Med. Chem. 66, 7475-7496 (2023); and Walczewska-Szewc et al., Phys. Chem. Chem. Phys. 24, 4366-4373 (2022)]. In this article, using results from enhanced sampling MD, we visually present how the binding process in PREP depends on subtle changes in inhibitors, which could be crucial in treating neurodegenerative disorders.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 3","pages":"032105"},"PeriodicalIF":3.4,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11343612/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057446","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

Capturing the illusive ring-shaped intermediates in Aβ42 amyloid formation. 捕捉 Aβ42 淀粉样蛋白形成过程中虚幻的环形中间体

IF 3.4

Biophysics reviews Pub Date : 2024-08-13 eCollection Date: 2024-09-01 DOI: 10.1063/5.0222349

Yu Yuan, Xiaozhe Dong, Huan Wang, Feng Gai

引用次数: 0

Structural interspecies variability of mammals' hairs. 哺乳动物毛发的种间结构变异。

IF 3.4

Biophysics reviews Pub Date : 2024-08-08 eCollection Date: 2024-09-01 DOI: 10.1063/5.0225513

Gabriele Greco, Anna Rising

引用次数: 0

Decoding physical principles of cell migration under controlled environment using microfluidics. 利用微流体技术解码细胞在受控环境下迁移的物理原理。

IF 4.5

Biophysics reviews Pub Date : 2024-07-29 eCollection Date: 2024-09-01 DOI: 10.1063/5.0199161

Young Joon Suh, Alan T Li, Mrinal Pandey, Cassidy S Nordmann, Yu Ling Huang, Mingming Wu

{"title":"Decoding physical principles of cell migration under controlled environment using microfluidics.","authors":"Young Joon Suh, Alan T Li, Mrinal Pandey, Cassidy S Nordmann, Yu Ling Huang, Mingming Wu","doi":"10.1063/5.0199161","DOIUrl":"10.1063/5.0199161","url":null,"abstract":"Living cells can perform incredible tasks that man-made micro/nano-sized robots have not yet been able to accomplish. One example is that white blood cells can sense and move to the site of pathogen attack within minutes. The robustness and precision of cellular functions have been perfected through billions of years of evolution. In this context, we ask the question whether cells follow a set of physical principles to sense, adapt, and migrate. Microfluidics has emerged as an enabling technology for recreating well-defined cellular environment for cell migration studies, and its ability to follow single cell dynamics allows for the results to be amenable for theoretical modeling. In this review, we focus on the development of microfluidic platforms for recreating cellular biophysical (e.g., mechanical stress) and biochemical (e.g., nutrients and cytokines) environments for cell migration studies in 3D. We summarize the basic principles that cells (including bacteria, algal, and mammalian cells) use to respond to chemical gradients learned from microfluidic systems. We also discuss about novel biological insights gained from studies of cell migration under biophysical cues and the need for further quantitative studies of cell function under well-controlled biophysical environments in the future.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 3","pages":"031302"},"PeriodicalIF":4.5,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11290890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141876856","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

Recent advances and applications of artificial intelligence in 3D bioprinting. 人工智能在 3D 生物打印中的最新进展和应用。

IF 2.9

Biophysics reviews Pub Date : 2024-07-19 eCollection Date: 2024-09-01 DOI: 10.1063/5.0190208

Hongyi Chen, Bin Zhang, Jie Huang

引用次数: 0

Visualizing the degradation of fibrin fibers. 纤维蛋白纤维降解的可视化。

IF 2.9

Biophysics reviews Pub Date : 2024-07-01 eCollection Date: 2024-09-01 DOI: 10.1063/5.0220356

Rebecca A Risman, Valerie Tutwiler

{"title":"Visualizing the degradation of fibrin fibers.","authors":"Rebecca A Risman, Valerie Tutwiler","doi":"10.1063/5.0220356","DOIUrl":"10.1063/5.0220356","url":null,"abstract":"Polymeric fibrin provides the structural and mechanical stability of a blood clot. Fibrin fibers are rod-like and create a network mesh that holds blood cells. When a clot has performed its physiological function in wound healing and preventing excessive blood loss, it must be resolved by the enzymatic degradation of fibrin, otherwise known as fibrinolysis. If a blood clot forms when or where it is not needed, as occurs in ischemic strokes and myocardial infarctions, the blood clot (thrombus) can obstruct blood flow to downstream organs. Obstructive thrombi must be degraded or removed to prevent further complications. If a clot is not degraded on its own, lytic agents (i.e., tissue plasminogen activator, tPA) are given exogenously to induce fibrinolysis. Here, we fluorescently labeled both fibrin and tPA to visualize degradation at the edge of the clot. The fibers with bound tPA were looped or coiled while the fibers farther into the clot remain straight and stable displaying the diffusion of tPA and depth of lysis. This image provides (1) a new method to monitor fibrinolysis with a commercially available chamber with convenient inlets and (2) the visualization of tPA-bound fibrin and the behavior of fibers during degradation. Future work could utilize this technique to study tPA molecule and fibrin interactions, lysis front degradation, and fibrin fiber linearity to understand the mechanisms of intermolecular dynamics dependent on network structure. An enhanced insight into this process can aid in the development of optimized therapeutics to target stubborn clots.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 3","pages":"032101"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11219076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141499799","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

Engineered heart tissue: Design considerations and the state of the art. 工程心脏组织：设计考虑因素和最新技术。

IF 2.9

Biophysics reviews Pub Date : 2024-06-20 eCollection Date: 2024-06-01 DOI: 10.1063/5.0202724

Ilhan Gokhan, Thomas S Blum, Stuart G Campbell

引用次数: 0

Macrophages on the wrinkle: Exploring microscale interactions with substrate topography. 皱纹上的巨噬细胞：探索微观尺度上与基底形貌的相互作用。

Biophysics reviews Pub Date : 2024-06-11 eCollection Date: 2024-06-01 DOI: 10.1063/5.0215563

Francesca Cecilia Lauta, Luca Pellegrino, Roberto Rusconi

引用次数: 0