Biophysics reviews最新文献_第3页

Photoresponsive peptide materials: Spatiotemporal control of self-assembly and biological functions 光致多肽材料：自组装和生物功能的时空控制

Biophysics reviews Pub Date : 2023-12-01 DOI: 10.1063/5.0179171

K. Matsuura, H. Inaba

{"title":"Photoresponsive peptide materials: Spatiotemporal control of self-assembly and biological functions","authors":"K. Matsuura, H. Inaba","doi":"10.1063/5.0179171","DOIUrl":"https://doi.org/10.1063/5.0179171","url":null,"abstract":"Peptides work as both functional molecules to modulate various biological phenomena and self-assembling artificial materials. The introduction of photoresponsive units to peptides allows the spatiotemporal remote control of their structure and function upon light irradiation. This article overviews the photoresponsive peptide design, interaction with biomolecules, and applications in self-assembling materials over the last 30 years. Peptides modified with photochromic (photoisomerizable) molecules, such as azobenzene and spiropyran, reversibly photo-controlled the binding to biomolecules and nanostructure formation through self-assembly. Photocleavable molecular units irreversibly control the functions of peptides through cleavage of the main chain and deprotection by light. Photocrosslinking between peptides or between peptides and other biomolecules enhances the structural stability of peptide assemblies and complexes. These photoresponsive peptides spatiotemporally controlled the formation and dissociation of peptide assemblies, gene expressions, protein–drug interactions, protein–protein interactions, liposome deformation and motility, cytoskeleton structure and stability, and cell functions by appropriate light irradiation. These molecular systems can be applied to photo-control biological functions, molecular robots, artificial cells, and next-generation smart drug delivery materials.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"95 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139016554","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

Metalation and activation of Zn2+ enzymes via early secretory pathway-resident ZNT proteins 通过早期分泌途径驻留的 ZNT 蛋白对 Zn2+ 酶进行金属化和激活

Biophysics reviews Pub Date : 2023-12-01 DOI: 10.1063/5.0176048

T. Kambe, T. Wagatsuma

{"title":"Metalation and activation of Zn2+ enzymes via early secretory pathway-resident ZNT proteins","authors":"T. Kambe, T. Wagatsuma","doi":"10.1063/5.0176048","DOIUrl":"https://doi.org/10.1063/5.0176048","url":null,"abstract":"Zinc (Zn2+), an essential trace element, binds to various proteins, including enzymes, transcription factors, channels, and signaling molecules and their receptors, to regulate their activities in a wide range of physiological functions. Zn2+ proteome analyses have indicated that approximately 10% of the proteins encoded by the human genome have potential Zn2+ binding sites. Zn2+ binding to the functional site of a protein (for enzymes, the active site) is termed Zn2+ metalation. In eukaryotic cells, approximately one-third of proteins are targeted to the endoplasmic reticulum; therefore, a considerable number of proteins mature by Zn2+ metalation in the early secretory pathway compartments. Failure to capture Zn2+ in these compartments results in not only the inactivation of enzymes (apo-Zn2+ enzymes), but also their elimination via degradation. This process deserves attention because many Zn2+ enzymes that mature during the secretory process are associated with disease pathogenesis. However, how Zn2+ is mobilized via Zn2+ transporters, particularly ZNTs, and incorporated in enzymes has not been fully elucidated from the cellular perspective and much less from the biophysical perspective. This review focuses on Zn2+ enzymes that are activated by Zn2+ metalation via Zn2+ transporters during the secretory process. Further, we describe the importance of Zn2+ metalation from the physiopathological perspective, helping to reveal the importance of understanding Zn2+ enzymes from a biophysical perspective.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"107 45","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138608563","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

Current progress toward isogeometric modeling of the heart biophysics 心脏生物物理学等几何建模的最新进展

Biophysics reviews Pub Date : 2023-11-13 DOI: 10.1063/5.0152690

Michele Torre, Simone Morganti, Francesco S. Pasqualini, Alessandro Reali

引用次数: 0

Quantifying nonequilibrium dynamics and thermodynamics of cell fate decision making in yeast under pheromone induction 信息素诱导下酵母细胞命运决策的非平衡动力学和热力学定量研究

Biophysics reviews Pub Date : 2023-09-01 DOI: 10.1063/5.0157759

Sheng Li, Qiong Liu, Erkang Wang, Jin Wang

{"title":"Quantifying nonequilibrium dynamics and thermodynamics of cell fate decision making in yeast under pheromone induction","authors":"Sheng Li, Qiong Liu, Erkang Wang, Jin Wang","doi":"10.1063/5.0157759","DOIUrl":"https://doi.org/10.1063/5.0157759","url":null,"abstract":"Cellular responses to pheromone in yeast can range from gene expression to morphological and physiological changes. While signaling pathways are well studied, the cell fate decision-making during cellular polar growth is still unclear. Quantifying these cellular behaviors and revealing the underlying physical mechanism remain a significant challenge. Here, we employed a hidden Markov chain model to quantify the dynamics of cellular morphological systems based on our experimentally observed time series. The resulting statistics generated a stability landscape for state attractors. By quantifying rotational fluxes as the non-equilibrium driving force that tends to disrupt the current attractor state, the dynamical origin of non-equilibrium phase transition from four cell morphological fates to a single dominant fate was identified. We revealed that higher chemical voltage differences induced by a high dose of pheromone resulted in higher chemical currents, which will trigger a greater net input and, thus, more degrees of the detailed balance breaking. By quantifying the thermodynamic cost of maintaining morphological state stability, we demonstrated that the flux-related entropy production rate provides a thermodynamic origin for the phase transition in non-equilibrium morphologies. Furthermore, we confirmed that the time irreversibility in time series provides a practical way to predict the non-equilibrium phase transition.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"195 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135298387","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

Swarming of P. aeruginosa: Through the lens of biophysics. 铜绿假单胞菌的Swarming：通过生物物理学的视角。

Biophysics reviews Pub Date : 2023-09-01 Epub Date: 2023-09-28 DOI: 10.1063/5.0128140

Jean-Louis Bru, Summer J Kasallis, Quantum Zhuo, Nina Molin Høyland-Kroghsbo, Albert Siryaporn

{"title":"Swarming of P. aeruginosa: Through the lens of biophysics.","authors":"Jean-Louis Bru, Summer J Kasallis, Quantum Zhuo, Nina Molin Høyland-Kroghsbo, Albert Siryaporn","doi":"10.1063/5.0128140","DOIUrl":"10.1063/5.0128140","url":null,"abstract":"Swarming is a collective flagella-dependent movement of bacteria across a surface that is observed across many species of bacteria. Due to the prevalence and diversity of this motility modality, multiple models of swarming have been proposed, but a consensus on a general mechanism for swarming is still lacking. Here, we focus on swarming by Pseudomonas aeruginosa due to the abundance of experimental data and multiple models for this species, including interpretations that are rooted in biology and biophysics. In this review, we address three outstanding questions about P. aeruginosa swarming: what drives the outward expansion of a swarm, what causes the formation of dendritic patterns (tendrils), and what are the roles of flagella? We review models that propose biologically active mechanisms including surfactant sensing as well as fluid mechanics-based models that consider swarms as thin liquid films. Finally, we reconcile recent observations of P. aeruginosa swarms with early definitions of swarming. This analysis suggests that mechanisms associated with sliding motility have a critical role in P. aeruginosa swarm formation.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"4 3","pages":"031305"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10540860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41154961","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

Microfluidic approaches for producing lipid-based nanoparticles for drug delivery applications 用于药物递送应用的脂基纳米颗粒的微流控方法

Biophysics reviews Pub Date : 2023-09-01 DOI: 10.1063/5.0150345

Caterina Piunti, Elisa Cimetta

{"title":"Microfluidic approaches for producing lipid-based nanoparticles for drug delivery applications","authors":"Caterina Piunti, Elisa Cimetta","doi":"10.1063/5.0150345","DOIUrl":"https://doi.org/10.1063/5.0150345","url":null,"abstract":"The importance of drug delivery for disease treatment is supported by a vast literature and increasing ongoing clinical studies. Several categories of nano-based drug delivery systems have been considered in recent years, among which lipid-based nanomedicines, both artificial and cell-derived, remain the most approved. The best artificial systems in terms of biocompatibility and low toxicity are liposomes, as they are composed of phospholipids and cholesterol, the main components of cell membranes. Extracellular vesicles—biological nanoparticles released from cells—while resembling liposomes in size, shape, and structure, have a more complex composition with up to hundreds of different types of lipids, proteins, and carbohydrates in their membranes, as well as an internal cargo. Although nanoparticle technologies have revolutionized drug delivery by enabling passive and active targeting, increased stability, improved solubilization capacity, and reduced dose and adverse effects, the clinical translation remains challenging due to manufacturing limitations such as laborious and time-consuming procedures and high batch-to-batch variability. A sea change occurred when microfluidic strategies were employed, offering advantages in terms of precise particle handling, simplified workflows, higher sensitivity and specificity, and good reproducibility and stability over bulk methods. This review examines scientific advances in the microfluidics-mediated production of lipid-based nanoparticles for therapeutic applications. We will discuss the preparation of liposomes using both hydrodynamic focusing of microfluidic flow and mixing by herringbone and staggered baffle micromixers. Then, an overview on microfluidic approaches for producing extracellular vesicles and extracellular vesicles-mimetics for therapeutic applications will describe microfluidic extrusion, surface engineering, sonication, electroporation, nanoporation, and mixing. Finally, we will outline the challenges, opportunities, and future directions of microfluidic investigation of lipid-based nanoparticles in the clinic.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"98 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135349016","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

Toward next-generation endoscopes integrating biomimetic video systems, nonlinear optical microscopy, and deep learning 集成仿生视频系统、非线性光学显微镜和深度学习的下一代内窥镜

Biophysics reviews Pub Date : 2023-06-01 DOI: 10.1063/5.0133027

Stefan G. Stanciu, Karsten König, Young Min Song, Lior Wolf, Costas A. Charitidis, Paolo Bianchini, Martin Goetz

{"title":"Toward next-generation endoscopes integrating biomimetic video systems, nonlinear optical microscopy, and deep learning","authors":"Stefan G. Stanciu, Karsten König, Young Min Song, Lior Wolf, Costas A. Charitidis, Paolo Bianchini, Martin Goetz","doi":"10.1063/5.0133027","DOIUrl":"https://doi.org/10.1063/5.0133027","url":null,"abstract":"According to the World Health Organization, the proportion of the world's population over 60 years will approximately double by 2050. This progressive increase in the elderly population will lead to a dramatic growth of age-related diseases, resulting in tremendous pressure on the sustainability of healthcare systems globally. In this context, finding more efficient ways to address cancers, a set of diseases whose incidence is correlated with age, is of utmost importance. Prevention of cancers to decrease morbidity relies on the identification of precursor lesions before the onset of the disease, or at least diagnosis at an early stage. In this article, after briefly discussing some of the most prominent endoscopic approaches for gastric cancer diagnostics, we review relevant progress in three emerging technologies that have significant potential to play pivotal roles in next-generation endoscopy systems: biomimetic vision (with special focus on compound eye cameras), non-linear optical microscopies, and Deep Learning. Such systems are urgently needed to enhance the three major steps required for the successful diagnostics of gastrointestinal cancers: detection, characterization, and confirmation of suspicious lesions. In the final part, we discuss challenges that lie en route to translating these technologies to next-generation endoscopes that could enhance gastrointestinal imaging, and depict a possible configuration of a system capable of (i) biomimetic endoscopic vision enabling easier detection of lesions, (ii) label-free in vivo tissue characterization, and (iii) intelligently automated gastrointestinal cancer diagnostic.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136177392","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

Delivery challenges for CRISPR-Cas9 genome editing for Duchenne muscular dystrophy. CRISPR-Cas9基因组编辑治疗杜氏肌营养不良症的传递挑战。

IF 2.9

Biophysics reviews Pub Date : 2023-03-01 Epub Date: 2023-02-21 DOI: 10.1063/5.0131452

Made Harumi Padmaswari, Shilpi Agrawal, Mary S Jia, Allie Ivy, Daniel A Maxenberger, Landon A Burcham, Christopher E Nelson

{"title":"Delivery challenges for CRISPR-Cas9 genome editing for Duchenne muscular dystrophy.","authors":"Made Harumi Padmaswari, Shilpi Agrawal, Mary S Jia, Allie Ivy, Daniel A Maxenberger, Landon A Burcham, Christopher E Nelson","doi":"10.1063/5.0131452","DOIUrl":"10.1063/5.0131452","url":null,"abstract":"Duchene muscular dystrophy (DMD) is an X-linked neuromuscular disorder that affects about one in every 5000 live male births. DMD is caused by mutations in the gene that codes for dystrophin, which is required for muscle membrane stabilization. The loss of functional dystrophin causes muscle degradation that leads to weakness, loss of ambulation, cardiac and respiratory complications, and eventually, premature death. Therapies to treat DMD have advanced in the past decade, with treatments in clinical trials and four exon-skipping drugs receiving conditional Food and Drug Administration approval. However, to date, no treatment has provided long-term correction. Gene editing has emerged as a promising approach to treating DMD. There is a wide range of tools, including meganucleases, zinc finger nucleases, transcription activator-like effector nucleases, and, most notably, RNA-guided enzymes from the bacterial adaptive immune system clustered regularly interspaced short palindromic repeats (CRISPR). Although challenges in using CRISPR for gene therapy in humans still abound, including safety and efficiency of delivery, the future for CRISPR gene editing for DMD is promising. This review will summarize the progress in CRISPR gene editing for DMD including key summaries of current approaches, delivery methodologies, and the challenges that gene editing still faces as well as prospective solutions.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"4 1","pages":"011307"},"PeriodicalIF":2.9,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9969352/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10106795","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

Beyond CFD: Emerging methodologies for predictive simulation in cardiovascular health and disease. 超越CFD：心血管健康和疾病预测模拟的新兴方法。

Biophysics reviews Pub Date : 2023-03-01 Epub Date: 2023-01-13 DOI: 10.1063/5.0109400

Erica L Schwarz, Luca Pegolotti, Martin R Pfaller, Alison L Marsden

{"title":"Beyond CFD: Emerging methodologies for predictive simulation in cardiovascular health and disease.","authors":"Erica L Schwarz, Luca Pegolotti, Martin R Pfaller, Alison L Marsden","doi":"10.1063/5.0109400","DOIUrl":"10.1063/5.0109400","url":null,"abstract":"Physics-based computational models of the cardiovascular system are increasingly used to simulate hemodynamics, tissue mechanics, and physiology in evolving healthy and diseased states. While predictive models using computational fluid dynamics (CFD) originated primarily for use in surgical planning, their application now extends well beyond this purpose. In this review, we describe an increasingly wide range of modeling applications aimed at uncovering fundamental mechanisms of disease progression and development, performing model-guided design, and generating testable hypotheses to drive targeted experiments. Increasingly, models are incorporating multiple physical processes spanning a wide range of time and length scales in the heart and vasculature. With these expanded capabilities, clinical adoption of patient-specific modeling in congenital and acquired cardiovascular disease is also increasing, impacting clinical care and treatment decisions in complex congenital heart disease, coronary artery disease, vascular surgery, pulmonary artery disease, and medical device design. In support of these efforts, we discuss recent advances in modeling methodology, which are most impactful when driven by clinical needs. We describe pivotal recent developments in image processing, fluid-structure interaction, modeling under uncertainty, and reduced order modeling to enable simulations in clinically relevant timeframes. In all these areas, we argue that traditional CFD alone is insufficient to tackle increasingly complex clinical and biological problems across scales and systems. Rather, CFD should be coupled with appropriate multiscale biological, physical, and physiological models needed to produce comprehensive, impactful models of mechanobiological systems and complex clinical scenarios. With this perspective, we finally outline open problems and future challenges in the field.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"4 1","pages":"011301"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9846834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10641949","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

Dynamic mechanobiology of cardiac cells and tissues: Current status and future perspective. 心脏细胞和组织的动态力学生物学:现状和未来展望。

IF 2.9

Biophysics reviews Pub Date : 2023-03-01 Epub Date: 2023-03-29 DOI: 10.1063/5.0141269

Chenyan Wang, Ghiska Ramahdita, Guy Genin, Nathaniel Huebsch, Zhen Ma

{"title":"Dynamic mechanobiology of cardiac cells and tissues: Current status and future perspective.","authors":"Chenyan Wang, Ghiska Ramahdita, Guy Genin, Nathaniel Huebsch, Zhen Ma","doi":"10.1063/5.0141269","DOIUrl":"10.1063/5.0141269","url":null,"abstract":"Mechanical forces impact cardiac cells and tissues over their entire lifespan, from development to growth and eventually to pathophysiology. However, the mechanobiological pathways that drive cell and tissue responses to mechanical forces are only now beginning to be understood, due in part to the challenges in replicating the evolving dynamic microenvironments of cardiac cells and tissues in a laboratory setting. Although many in vitro cardiac models have been established to provide specific stiffness, topography, or viscoelasticity to cardiac cells and tissues via biomaterial scaffolds or external stimuli, technologies for presenting time-evolving mechanical microenvironments have only recently been developed. In this review, we summarize the range of in vitro platforms that have been used for cardiac mechanobiological studies. We provide a comprehensive review on phenotypic and molecular changes of cardiomyocytes in response to these environments, with a focus on how dynamic mechanical cues are transduced and deciphered. We conclude with our vision of how these findings will help to define the baseline of heart pathology and of how these in vitro systems will potentially serve to improve the development of therapies for heart diseases.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"4 1","pages":"011314"},"PeriodicalIF":2.9,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10062054/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9296630","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