Cold Spring Harbor perspectives in biology最新文献_第7页

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 : 2025-04-01 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":"10.1101/cshperspect.a041653","url":null,"abstract":"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.","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960702/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Facioscapulohumeral Dystrophy: Molecular Basis and Therapeutic Opportunities. 面岬肱骨营养不良症：分子基础和治疗机会。

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2025-04-01 DOI: 10.1101/cshperspect.a041492

Tessa Arends, Danielle C Hamm, Silvère van der Maarel, Stephen J Tapscott

引用次数: 0

Epigenetics of Human Telomeres. 人类端粒的表观遗传学。

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2025-03-17 DOI: 10.1101/cshperspect.a041706

Nicole Bettin, Mélina Vaurs, Anabelle Decottignies

{"title":"Epigenetics of Human Telomeres.","authors":"Nicole Bettin, Mélina Vaurs, Anabelle Decottignies","doi":"10.1101/cshperspect.a041706","DOIUrl":"https://doi.org/10.1101/cshperspect.a041706","url":null,"abstract":"Human telomeric heterochromatin is unusual in that it does not show the enrichment of canonical repressive histone marks H3K9me3 or H4K20me3 seen in constitutive heterochromatin. Instead, human telomeres exhibit both facultative heterochromatin and euchromatin marks, consistent with their epigenetically regulated transcription into TERRA noncoding RNA. Additionally, telomeric DNA is out of phase with the DNA helical repeat and has no nucleosome positioning signal. Yet, human telomeric DNA forms a columnar structure of tightly stacked nucleosomes, alternating with open states, and regulated by histone tails and shelterin protein binding. We discuss the proposed mechanisms regulating human telomeric chromatin and the consequences that telomeric chromatin properties have on various cellular processes, such as telomere transcription, the regulation of shelterin binding, and the activation of the alternative lengthening of telomeres mechanism. Together, we summarize current evidence on the combination of hetero- and euchromatic properties of human telomeres that may help explain their crucial protective functions and plasticity to regulate telomere maintenance pathways and damage signaling.","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647562","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

In the Loop: Unusual DNA Structures at Telomeric Repeats and Their Impact on Telomere Function. 在循环中：端粒重复的不寻常DNA结构及其对端粒功能的影响。

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2025-03-17 DOI: 10.1101/cshperspect.a041694

Elia Zanella, Ylli Doksani

{"title":"In the Loop: Unusual DNA Structures at Telomeric Repeats and Their Impact on Telomere Function.","authors":"Elia Zanella, Ylli Doksani","doi":"10.1101/cshperspect.a041694","DOIUrl":"https://doi.org/10.1101/cshperspect.a041694","url":null,"abstract":"Telomeric repeats recruit the shelterin complex to prevent activation of the double-strand break response at chromosome ends. Thousands of TTAGGG repeats are present at each chromosome end to ensure telomere function. This abundance of G-rich repeats comes with the propensity to generate unusual DNA structures. The telomere loop (t-loop) structure, generated by strand invasion of the 3' overhang in the internal repeats, contributes to telomere function. G4-DNA is promoted by the stretches of G-rich repeats in a single-stranded form and may affect telomere replication and elongation by telomerase. The intramolecular homology can lead to the formation of internal loops (i-loops) via intramolecular recombination at sites of telomeric damage, which can promote the excision of telomeric repeats as extrachromosomal circular DNA. Shelterin promotes t-loops, counteracting the accumulation of pathological structures either directly or via the recruitment of specialized helicases. Here, we will discuss the current evidence for the formation of unusual DNA structures at telomeres and possible implications for telomere function.","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647564","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

Multiple Sclerosis and Other Acquired Demyelinating Diseases of the Central Nervous System. 多发性硬化症和其他后天性中枢神经系统脱髓鞘疾病。

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2025-03-03 DOI: 10.1101/cshperspect.a041374

Michael D Kornberg, Peter A Calabresi

引用次数: 0

Corrigendum: Modeling the Emergence of Circuit Organization and Function during Development. 更正：模拟发育过程中电路组织和功能的出现。

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2025-03-03 DOI: 10.1101/cshperspect.a041835

Shreya Lakhera, Elizabeth Herbert, Julijana Gjorgjieva

引用次数: 0

Speciation. 物种。

IF 8.4 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2025-03-03 DOI: 10.1101/cshperspect.a041735

Catherine L Peichel, Daniel I Bolnick, Åke Brännström, Ulf Dieckmann, Rebecca J Safran

引用次数: 0

Maintaining Telomeres without Telomerase in Drosophila: Novel Mechanisms and Rapid Evolution to Save a Genus. 果蝇在没有端粒酶的情况下维持端粒：拯救一个属的新机制和快速进化。

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2025-03-03 DOI: 10.1101/cshperspect.a041708

Stefano Cacchione, Giovanni Cenci, Anne-Marie Dion-Côté, Daniel A Barbash, Grazia Daniela Raffa

{"title":"Maintaining Telomeres without Telomerase in Drosophila: Novel Mechanisms and Rapid Evolution to Save a Genus.","authors":"Stefano Cacchione, Giovanni Cenci, Anne-Marie Dion-Côté, Daniel A Barbash, Grazia Daniela Raffa","doi":"10.1101/cshperspect.a041708","DOIUrl":"10.1101/cshperspect.a041708","url":null,"abstract":"Telomere maintenance is crucial for preventing the linear eukaryotic chromosome ends from being mistaken for DNA double-strand breaks, thereby avoiding chromosome fusions and the loss of genetic material. Unlike most eukaryotes that use telomerase for telomere maintenance, Drosophila relies on retrotransposable elements-specifically HeT-A, TAHRE, and TART (collectively referred to as HTT)-which are regulated and precisely targeted to chromosome ends. Drosophila telomere protection is mediated by a set of fast-evolving proteins, termed terminin, which bind to chromosome termini without sequence specificity, balancing DNA damage response factors to avoid erroneous repair mechanisms. This unique telomere capping mechanism highlights an alternative evolutionary strategy to compensate for telomerase loss. The modulation of recombination and transcription at Drosophila telomeres offers insights into the diverse mechanisms of telomere maintenance. Recent studies at the population level have begun to reveal the architecture of telomere arrays, the diversity among the HTT subfamilies, and their relative frequencies, aiming to understand whether and how these elements have evolved to reach an equilibrium with the host and to resolve genetic conflicts. Further studies may shed light on the complex relationships between telomere transcription, recombination, and maintenance, underscoring the adaptive plasticity of telomeric complexes across eukaryotes.","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11875090/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853176","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 Mechanics of Building Functional Organs. 构建功能器官的机制

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2025-03-03 DOI: 10.1101/cshperspect.a041520

Toby G R Andrews, Rashmi Priya

引用次数: 0

Modeling the Emergence of Circuit Organization and Function during Development. 模拟发育过程中电路组织和功能的出现

IF 6.9 2区生物学

Cold Spring Harbor perspectives in biology Pub Date : 2025-02-03 DOI: 10.1101/cshperspect.a041511

Shreya Lakhera, Elizabeth Herbert, Julijana Gjorgjieva

{"title":"Modeling the Emergence of Circuit Organization and Function during Development.","authors":"Shreya Lakhera, Elizabeth Herbert, Julijana Gjorgjieva","doi":"10.1101/cshperspect.a041511","DOIUrl":"10.1101/cshperspect.a041511","url":null,"abstract":"Developing neural circuits show unique patterns of spontaneous activity and structured network connectivity shaped by diverse activity-dependent plasticity mechanisms. Based on extensive experimental work characterizing patterns of spontaneous activity in different brain regions over development, theoretical and computational models have played an important role in delineating the generation and function of individual features of spontaneous activity and their role in the plasticity-driven formation of circuit connectivity. Here, we review recent modeling efforts that explore how the developing cortex and hippocampus generate spontaneous activity, focusing on specific connectivity profiles and the gradual strengthening of inhibition as the key drivers behind the observed developmental changes in spontaneous activity. We then discuss computational models that mechanistically explore how different plasticity mechanisms use this spontaneous activity to instruct the formation and refinement of circuit connectivity, from the formation of single neuron receptive fields to sensory feature maps and recurrent architectures. We end by highlighting several open challenges regarding the functional implications of the discussed circuit changes, wherein models could provide the missing step linking immature developmental and mature adult information processing capabilities.","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11864115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300243","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