Annual Review of Biophysics最新文献_第10页

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 DOI: 10.1146/annurev-biophys-062920-063657

Sen-Fang Sui

引用次数: 22

Recent Developments in the Field of Intrinsically Disordered Proteins: Intrinsic Disorder-Based Emergence in Cellular Biology in Light of the Physiological and Pathological Liquid-Liquid Phase Transitions. 内在无序蛋白领域的新进展:从生理和病理的液-液相变看细胞生物学中基于内在无序的出现

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-01-27 DOI: 10.1146/annurev-biophys-062920-063704

Vladimir N Uversky

引用次数: 41

The Phasor Plot: A Universal Circle to Advance Fluorescence Lifetime Analysis and Interpretation. 相量图:推进荧光寿命分析和解释的通用循环。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 DOI: 10.1146/annurev-biophys-062920-063631

Leonel Malacrida, Suman Ranjit, David M Jameson, Enrico Gratton

{"title":"The Phasor Plot: A Universal Circle to Advance Fluorescence Lifetime Analysis and Interpretation.","authors":"Leonel Malacrida, Suman Ranjit, David M Jameson, Enrico Gratton","doi":"10.1146/annurev-biophys-062920-063631","DOIUrl":"https://doi.org/10.1146/annurev-biophys-062920-063631","url":null,"abstract":"The phasor approach to fluorescence lifetime imaging has become a common method to analyze complicated fluorescence signals from biological samples. The appeal of the phasor representation of complex fluorescence decays in biological systems is that a visual representation of the decay of entire cells or tissues can be used to easily interpret fundamental biological states related to metabolism and oxidative stress. Phenotyping based on autofluorescence provides new avenues for disease characterization and diagnostics. The phasor approach is a transformation of complex fluorescence decays that does not use fits to model decays and therefore has the same information content as the original data. The phasor plot is unique for a given system, is highly reproducible, and provides a robust method to evaluate the existence of molecular interactions such as Förster resonance energy transfer or the response of ion indicators. Recent advances permitquantification of multiple components from phasor plots in fluorescence lifetime imaging microscopy, which is not presently possible using data fitting methods, especially in biological systems.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"50 ","pages":"575-593"},"PeriodicalIF":12.4,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38956583","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}

引用次数: 46

Directed Evolution of Microbial Communities. 微生物群落的定向进化。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2020-07-28 DOI: 10.32942/osf.io/gsz7j

Álvaro Sánchez, Jean C. C. Vila, Chang-Yu Chang, Juan Díaz-Colunga, Sylvie Estrela, María Rebolleda-Gómez

{"title":"Directed Evolution of Microbial Communities.","authors":"Álvaro Sánchez, Jean C. C. Vila, Chang-Yu Chang, Juan Díaz-Colunga, Sylvie Estrela, María Rebolleda-Gómez","doi":"10.32942/osf.io/gsz7j","DOIUrl":"https://doi.org/10.32942/osf.io/gsz7j","url":null,"abstract":"Directed evolution is a form of artificial selection that has been used for decades to find biomolecules and organisms with new or enhanced functional traits. Directed evolution can be conceptualized as a guided exploration of the genotype-phenotype map, where genetic variants with desirable phenotypes are first selected and then mutagenized to search the genotype space for an even better mutant. In recent years, the idea of applying artificial selection to microbial communities has gained momentum. In this article, we review the main limitations of artificial selection when applied to large and diverse collectives of asexually dividing microbes and discuss how the tools of directed evolution may be deployed to engineer communities from the top down. We conceptualize directed evolution of microbial communities as a guided exploration of an ecological structure-function landscape and propose practical guidelines for navigating these ecological landscapes. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"1 1","pages":""},"PeriodicalIF":12.4,"publicationDate":"2020-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44829334","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}

引用次数: 43

Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions. 细胞内相变复杂生物学的物理原理。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2020-05-06 Epub Date: 2020-01-31 DOI: 10.1146/annurev-biophys-121219-081629

Jeong-Mo Choi, Alex S Holehouse, Rohit V Pappu

引用次数: 438

Light Microscopy of Mitochondria at the Nanoscale. 纳米尺度下线粒体的光学显微镜。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2020-05-06 DOI: 10.1146/annurev-biophys-121219-081550

Stefan Jakobs, Till Stephan, Peter Ilgen, Christian Brüser

{"title":"Light Microscopy of Mitochondria at the Nanoscale.","authors":"Stefan Jakobs, Till Stephan, Peter Ilgen, Christian Brüser","doi":"10.1146/annurev-biophys-121219-081550","DOIUrl":"https://doi.org/10.1146/annurev-biophys-121219-081550","url":null,"abstract":"Mitochondria are essential for eukaryotic life. These double-membrane organelles often form highly dynamic tubular networks interacting with many cellular structures. Their highly convoluted contiguous inner membrane compartmentalizes the organelle, which is crucial for mitochondrial function. Since the diameter of the mitochondrial tubules is generally close to the diffraction limit of light microscopy, it is often challenging, if not impossible, to visualize submitochondrial structures or protein distributions using conventional light microscopy. This renders super-resolution microscopy particularly valuable, and attractive, for studying mitochondria. Super-resolution microscopy encompasses a diverse set of approaches that extend resolution, as well as nanoscopy techniques that can even overcome the diffraction limit. In this review, we provide an overview of recent studies using super-resolution microscopy to investigate mitochondria, discuss the strengths and opportunities of the various methods in addressing specific questions in mitochondrial biology, and highlight potential future developments.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"49 ","pages":"289-308"},"PeriodicalIF":12.4,"publicationDate":"2020-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biophys-121219-081550","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10654948","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}

引用次数: 40

Temperature, Dynamics, and Enzyme-Catalyzed Reaction Rates. 温度、动力学和酶催化反应速率。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2020-05-06 DOI: 10.1146/annurev-biophys-121219-081520

Vickery L Arcus, Adrian J Mulholland

{"title":"Temperature, Dynamics, and Enzyme-Catalyzed Reaction Rates.","authors":"Vickery L Arcus, Adrian J Mulholland","doi":"10.1146/annurev-biophys-121219-081520","DOIUrl":"https://doi.org/10.1146/annurev-biophys-121219-081520","url":null,"abstract":"We review the adaptations of enzyme activity to different temperatures. Psychrophilic (cold-adapted) enzymes show significantly different activation parameters (lower activation enthalpies and entropies) than their mesophilic counterparts. Furthermore, there is increasing evidence that the temperature dependence of many enzyme-catalyzed reactions is more complex than is widely believed. Many enzymes show curvature in plots of activity versus temperature that is not accounted for by denaturation or unfolding. This is explained by macromolecular rate theory: A negative activation heat capacity for the rate-limiting chemical step leads directly to predictions of temperature optima; both entropy and enthalpy are temperature dependent. Fluctuations in the transition state ensemble are reduced compared to the ground state. We show how investigations combining experiment with molecular simulation are revealing fundamental details of enzyme thermoadaptation that are relevant for understanding aspects of enzyme evolution. Simulations can calculate relevant thermodynamic properties (such as activation enthalpies, entropies, and heat capacities) and reveal the molecular mechanisms underlying experimentally observed behavior. Expected final online publication date for the Annual Review of Biophysics, Volume 49 is May 6, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"49 ","pages":"163-180"},"PeriodicalIF":12.4,"publicationDate":"2020-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biophys-121219-081520","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9146131","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}

引用次数: 44

RNA-Mediated Virus Assembly: Mechanisms and Consequences for Viral Evolution and Therapy. rna介导的病毒组装:病毒进化和治疗的机制和后果。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2019-05-06 DOI: 10.1146/annurev-biophys-052118-115611

Reidun Twarock, Peter G Stockley

{"title":"RNA-Mediated Virus Assembly: Mechanisms and Consequences for Viral Evolution and Therapy.","authors":"Reidun Twarock, Peter G Stockley","doi":"10.1146/annurev-biophys-052118-115611","DOIUrl":"https://doi.org/10.1146/annurev-biophys-052118-115611","url":null,"abstract":"Viruses, entities composed of nucleic acids, proteins, and in some cases lipids lack the ability to replicate outside their target cells. Their components self-assemble at the nanoscale with exquisite precision-a key to their biological success in infection. Recent advances in structure determination and the development of biophysical tools such as single-molecule spectroscopy and noncovalent mass spectrometry allow unprecedented access to the detailed assembly mechanisms of simple virions. Coupling these techniques with mathematical modeling and bioinformatics has uncovered a previously unsuspected role for genomic RNA in regulating formation of viral capsids, revealing multiple, dispersed RNA sequence/structure motifs [packaging signals (PSs)] that bind cognate coat proteins cooperatively. The PS ensemble controls assembly efficiency and accounts for the packaging specificity seen in vivo. The precise modes of action of the PSs vary between viral families, but this common principle applies across many viral families, including major human pathogens. These insights open up the opportunity to block or repurpose PS function in assembly for both novel antiviral therapy and gene/drug/vaccine applications.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"48 ","pages":"495-514"},"PeriodicalIF":12.4,"publicationDate":"2019-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biophys-052118-115611","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9103478","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}

引用次数: 50

Hydrogel-Tissue Chemistry: Principles and Applications. 水凝胶-组织化学:原理和应用。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2018-05-20 DOI: 10.1146/annurev-biophys-070317-032905

Viviana Gradinaru, Jennifer Treweek, Kristin Overton, Karl Deisseroth

{"title":"Hydrogel-Tissue Chemistry: Principles and Applications.","authors":"Viviana Gradinaru, Jennifer Treweek, Kristin Overton, Karl Deisseroth","doi":"10.1146/annurev-biophys-070317-032905","DOIUrl":"https://doi.org/10.1146/annurev-biophys-070317-032905","url":null,"abstract":"Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial phenotypic information regarding constituent cells and molecules (and their joint interrelationships) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons-even within vertebrate brains. This new approach and its variants, as applied to neuroscience, are beginning to illuminate the fundamental cellular and chemical representations of sensation, cognition, and action. More generally, reimagining metazoans as metareactants-or positionally defined three-dimensional graphs of constituent chemicals made available for ongoing functionalization, transformation, and readout-is stimulating innovation across biology and medicine.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"47 ","pages":"355-376"},"PeriodicalIF":12.4,"publicationDate":"2018-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biophys-070317-032905","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9340255","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}

引用次数: 90

The Biophysics of 3D Cell Migration 三维细胞迁移的生物物理学

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2018-05-20 DOI: 10.1146/ANNUREV-BIOPHYS-070816-033854

Pei-Hsun Wu, Daniele M. Gilkes, D. Wirtz

引用次数: 34