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Modeling Normal and Abnormal Circuit Development with Recurrent Neural Networks. 用递归神经网络模拟正常和异常电路发展
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-07-15 DOI: 10.1101/cshperspect.a041507
Daniel Zavitz, ShiNung Ching, Geoffrey Goodhill
{"title":"Modeling Normal and Abnormal Circuit Development with Recurrent Neural Networks.","authors":"Daniel Zavitz, ShiNung Ching, Geoffrey Goodhill","doi":"10.1101/cshperspect.a041507","DOIUrl":"https://doi.org/10.1101/cshperspect.a041507","url":null,"abstract":"<p><p>Neural development must construct neural circuits that can perform the computations necessary for survival. However, many theoretical models of development do not explicitly address the computational goals of the resulting networks, or computations that evolve in time. Recurrent neural networks (RNNs) have recently come to prominence as both models of neural circuit computation and building blocks of powerful artificial intelligence systems. Here, we review progress in using RNNs for understanding how developmental processes lead to effective computations, and how abnormal development disrupts these computations.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":6.9,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141619507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 0
Direct Methane Removal from Air by Aerobic Methanotrophs. 好氧脱甲烷菌直接去除空气中的甲烷。
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-07-01 DOI: 10.1101/cshperspect.a041671
Mary E Lidstrom
{"title":"Direct Methane Removal from Air by Aerobic Methanotrophs.","authors":"Mary E Lidstrom","doi":"10.1101/cshperspect.a041671","DOIUrl":"10.1101/cshperspect.a041671","url":null,"abstract":"<p><p>The rapid pace of climate change has created great urgency for short-term mitigation strategies. Appropriately, the long-term target for intervening in global warming is CO<sub>2</sub>, but experts suggest that methane should be a key short-term target. Methane has a warming impact 34 times greater than CO<sub>2</sub> on a 100-year timescale, and 86 times greater on a 20-year timescale, and its short half-life in the atmosphere provides the opportunity for near-term positive climate impacts. One approach to removing methane is the use of bacteria for which methane is their sole carbon and energy source (methanotrophs). Such bacteria convert methane to CO<sub>2</sub> and biomass, a potentially value-added product and co-benefit. If air above emissions sites with elevated methane is targeted, technology harnessing the aerobic methanotrophs has the potential to become economically viable and environmentally sound. This article discusses challenges and opportunities for using aerobic methanotrophs for methane removal from air, including the avoidance of increased N<sub>2</sub>O emissions.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":6.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11216182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71478932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 0
The Blood-Brain Barrier: Composition, Properties, and Roles in Brain Health. 血脑屏障：血脑屏障：组成、特性和在大脑健康中的作用。
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-07-01 DOI: 10.1101/cshperspect.a041422
Baptiste Lacoste, Alexandre Prat, Moises Freitas-Andrade, Chenghua Gu
{"title":"The Blood-Brain Barrier: Composition, Properties, and Roles in Brain Health.","authors":"Baptiste Lacoste, Alexandre Prat, Moises Freitas-Andrade, Chenghua Gu","doi":"10.1101/cshperspect.a041422","DOIUrl":"https://doi.org/10.1101/cshperspect.a041422","url":null,"abstract":"<p><p>Blood vessels are critical to deliver oxygen and nutrients to tissues and organs throughout the body. The blood vessels that vascularize the central nervous system (CNS) possess unique properties, termed the blood-brain barrier (BBB), which allow these vessels to tightly regulate the movement of ions, molecules, and cells between the blood and the brain. This precise control of CNS homeostasis allows for proper neuronal function and protects the neural tissue from toxins and pathogens, and alterations of this barrier are important components of the pathogenesis and progression of various neurological diseases. The physiological barrier is coordinated by a series of physical, transport, and metabolic properties possessed by the brain endothelial cells (ECs) that form the walls of the blood vessels. These properties are regulated by interactions between different vascular, perivascular, immune, and neural cells. Understanding how these cell populations interact to regulate barrier properties is essential for understanding how the brain functions in both health and disease contexts.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":6.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141476126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 0
Reactive Astrocytes and Emerging Roles in Central Nervous System (CNS) Disorders. 反应性星形胶质细胞和在中枢神经系统 (CNS) 疾病中的新作用。
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-07-01 DOI: 10.1101/cshperspect.a041356
Shane A Liddelow, Michelle L Olsen, Michael V Sofroniew
{"title":"Reactive Astrocytes and Emerging Roles in Central Nervous System (CNS) Disorders.","authors":"Shane A Liddelow, Michelle L Olsen, Michael V Sofroniew","doi":"10.1101/cshperspect.a041356","DOIUrl":"10.1101/cshperspect.a041356","url":null,"abstract":"<p><p>In addition to their many functions in the healthy central nervous system (CNS), astrocytes respond to CNS damage and disease through a process called \"reactivity.\" Recent evidence reveals that astrocyte reactivity is a heterogeneous spectrum of potential changes that occur in a context-specific manner. These changes are determined by diverse signaling events and vary not only with the nature and severity of different CNS insults but also with location in the CNS, genetic predispositions, age, and potentially also with \"molecular memory\" of previous reactivity events. Astrocyte reactivity can be associated with both essential beneficial functions as well as with harmful effects. The available information is rapidly expanding and much has been learned about molecular diversity of astrocyte reactivity. Emerging functional associations point toward central roles for astrocyte reactivity in determining the outcome in CNS disorders.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":6.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11216178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 0
Neuronal Circuit Evolution: From Development to Structure and Adaptive Significance. 神经元回路进化：从发育到结构和适应意义。
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-07-01 DOI: 10.1101/cshperspect.a041493
Nikolaos Konstantinides, Claude Desplan
{"title":"Neuronal Circuit Evolution: From Development to Structure and Adaptive Significance.","authors":"Nikolaos Konstantinides, Claude Desplan","doi":"10.1101/cshperspect.a041493","DOIUrl":"10.1101/cshperspect.a041493","url":null,"abstract":"<p><p>Neuronal circuits represent the functional units of the brain. Understanding how the circuits are generated to perform computations will help us understand how the brain functions. Nevertheless, neuronal circuits are not engineered, but have formed through millions of years of animal evolution. We posit that it is necessary to study neuronal circuit evolution to comprehensively understand circuit function. Here, we review our current knowledge regarding the mechanisms that underlie circuit evolution. First, we describe the possible genetic and developmental mechanisms that have contributed to circuit evolution. Then, we discuss the structural changes of circuits during evolution and how these changes affected circuit function. Finally, we try to put circuit evolution in an ecological context and assess the adaptive significance of specific examples. We argue that, thanks to the advent of new tools and technologies, evolutionary neurobiology now allows us to address questions regarding the evolution of circuitry and behavior that were unimaginable until very recently.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":6.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141476125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 0
Enteric Glia. 肠胶质细胞
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-07-01 DOI: 10.1101/cshperspect.a041368
Meenakshi Rao, Brian D Gulbransen
{"title":"Enteric Glia.","authors":"Meenakshi Rao, Brian D Gulbransen","doi":"10.1101/cshperspect.a041368","DOIUrl":"https://doi.org/10.1101/cshperspect.a041368","url":null,"abstract":"<p><p>Enteric glia are a unique type of peripheral neuroglia that accompany neurons in the enteric nervous system (ENS) of the digestive tract. The ENS displays integrative neural circuits that are capable of governing moment-to-moment gut functions independent of input from the central nervous system. Enteric glia are interspersed with neurons throughout these intrinsic gut neural circuits and are thought to fulfill complex roles directed at maintaining homeostasis in the neuronal microenvironment and at neuroeffector junctions in the gut. Changes to glial functions contribute to a wide range of gastrointestinal diseases, but the precise roles of enteric glia in gut physiology and pathophysiology are still under examination. This review summarizes current concepts regarding enteric glial development, diversity, and functions in health and disease.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":6.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141476123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 0
Membrane Epilipidome-Lipid Modifications, Their Dynamics, and Functional Significance. 膜表脂体-脂质修饰、其动态变化和功能意义
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-07-01 DOI: 10.1101/cshperspect.a041417
Sider Penkov, Maria Fedorova
{"title":"Membrane Epilipidome-Lipid Modifications, Their Dynamics, and Functional Significance.","authors":"Sider Penkov, Maria Fedorova","doi":"10.1101/cshperspect.a041417","DOIUrl":"10.1101/cshperspect.a041417","url":null,"abstract":"<p><p>Lipids are characterized by extremely high structural diversity translated into a wide range of physicochemical properties. As such, lipids are vital for many different functions including organization of cellular and organelle membranes, control of cellular and organismal energy metabolism, as well as mediating multiple signaling pathways. To maintain the lipid chemical diversity and to achieve rapid lipid remodeling required for the responsiveness and adaptability of cellular membranes, living systems make use of a network of chemical modifications of already existing lipids that complement the rather slow biosynthetic pathways. Similarly to biopolymers, which can be modified epigenetically and posttranscriptionally (for nucleic acids) or posttranslationally (for proteins), lipids can also undergo chemical alterations through oxygenation, nitration, phosphorylation, glycosylation, etc. In this way, an expanded collective of modified lipids that we term the \"epilipidome,\" provides the ultimate level of complexity to biological membranes and delivers a battery of active small-molecule compounds for numerous regulatory processes. As many lipid modifications are tightly controlled and often occur in response to extra- and intracellular stimuli at defined locations, the emergence of the epilipidome greatly contributes to the spatial and temporal compartmentalization of diverse cellular processes. Accordingly, epilipid modifications are observed in all living organisms and are among the most consistent prerequisites for complex life.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":6.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11216179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 0
Forces Shaping the Blastocyst. 塑造囊胚的力量
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-07-01 DOI: 10.1101/cshperspect.a041519
David Rozema, Jean-Léon Maître
{"title":"Forces Shaping the Blastocyst.","authors":"David Rozema, Jean-Léon Maître","doi":"10.1101/cshperspect.a041519","DOIUrl":"https://doi.org/10.1101/cshperspect.a041519","url":null,"abstract":"<p><p>The blastocyst forms during the first days of mammalian development. The structure of the blastocyst is conserved among placental mammals and is paramount to the establishment of the first mammalian lineages. The blastocyst is composed of an extraembryonic epithelium, the trophectoderm (TE), that envelopes a fluid-filled lumen and the inner cell mass (ICM). To shape the blastocyst, embryos transit through three stages driven by forces that have been characterized in the mouse embryo over the past decade. The morphogenetically quiescent cleavage stages mask dynamic cytoskeletal remodeling. Then, during the formation of the morula, cells pull themselves together and the strongest ones internalize. Finally, the blastocyst forms after the pressurized lumen breaks the radial symmetry of the embryo before expanding in cycles of collapses and regrowth. In this review, we delineate the force patterns sculpting the blastocyst, based on our knowledge on the mouse and, to some extent, human embryos.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":6.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141476124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 0
Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models. 组织活性物质：将力学和信号传导整合到动力学模型中。
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-07-01 DOI: 10.1101/cshperspect.a041653
David B Brückner, Edouard Hannezo
{"title":"Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.","authors":"David B Brückner, Edouard Hannezo","doi":"10.1101/cshperspect.a041653","DOIUrl":"https://doi.org/10.1101/cshperspect.a041653","url":null,"abstract":"<p><p>The importance of physical forces in the morphogenesis, homeostatic function, and pathological dysfunction of multicellular tissues is being increasingly characterized, both theoretically and experimentally. Analogies between biological systems and inert materials such as foams, gels, and liquid crystals have provided striking insights into the core design principles underlying multicellular organization. However, these connections can seem surprising given that a key feature of multicellular systems is their ability to constantly consume energy, providing an active origin for the forces that they produce. Key emerging questions are, therefore, to understand whether and how this activity grants tissues novel properties that do not have counterparts in classical materials, as well as their consequences for biological function. Here, we review recent discoveries at the intersection of active matter and tissue biology, with an emphasis on how modeling and experiments can be combined to understand the dynamics of multicellular systems. These approaches suggest that a number of key biological tissue-scale phenomena, such as morphogenetic shape changes, collective migration, or fate decisions, share unifying design principles that can be described by physical models of tissue active matter.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":6.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141476127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 0
Fisher's Geometric Model as a Tool to Study Speciation. 费雪几何模型作为研究物种的工具。
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-07-01 DOI: 10.1101/cshperspect.a041442
Hilde Schneemann, Bianca De Sanctis, John J Welch
{"title":"Fisher's Geometric Model as a Tool to Study Speciation.","authors":"Hilde Schneemann, Bianca De Sanctis, John J Welch","doi":"10.1101/cshperspect.a041442","DOIUrl":"10.1101/cshperspect.a041442","url":null,"abstract":"<p><p>Interactions between alleles and across environments play an important role in the fitness of hybrids and are at the heart of the speciation process. Fitness landscapes capture these interactions and can be used to model hybrid fitness, helping us to interpret empirical observations and clarify verbal models. Here, we review recent progress in understanding hybridization outcomes through Fisher's geometric model, an intuitive and analytically tractable fitness landscape that captures many fitness patterns observed across taxa. We use case studies to show how the model parameters can be estimated from different types of data and discuss how these estimates can be used to make inferences about the divergence history and genetic architecture. We also highlight some areas where the model's predictions differ from alternative incompatibility-based models, such as the snowball effect and outlier patterns in genome scans.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":null,"pages":null},"PeriodicalIF":6.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11216183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 0
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