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Mechanisms of Alternative Lengthening of Telomeres. 端粒替代性延长的机制
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-11-05 DOI: 10.1101/cshperspect.a041690
Roderick J O'Sullivan, Roger A Greenberg
{"title":"Mechanisms of Alternative Lengthening of Telomeres.","authors":"Roderick J O'Sullivan, Roger A Greenberg","doi":"10.1101/cshperspect.a041690","DOIUrl":"https://doi.org/10.1101/cshperspect.a041690","url":null,"abstract":"<p><p>In recent years, significant advances have been made in understanding the intricate details of the mechanisms underlying alternative lengthening of telomeres (ALT). Studies of a specialized DNA strand break repair mechanism, known as break-induced replication, and the advent of telomere-specific DNA damaging strategies and proteomic methodologies to profile the ribonucleoprotein composition of telomeres enabled the discovery of networks of proteins that coordinate the stepwise homology-directed DNA repair and DNA synthesis processes of ALT. These networks couple mediators of homologous recombination, DNA template-switching, long-range template-directed DNA synthesis, and DNA strand resolution with SUMO-dependent liquid condensate formation to create discrete nuclear bodies where telomere extension occurs. This review will discuss the recent findings of how these networks may cooperate to mediate telomere extension by the ALT mechanism and their impact on telomere function and integrity in ALT cancer cells.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582602","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
The Role of Microhomology-Mediated End Joining (MMEJ) at Dysfunctional Telomeres. 微同源物介导的端接（MMEJ）在功能障碍端粒中的作用
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-11-05 DOI: 10.1101/cshperspect.a041687
David Billing, Agnel Sfeir
{"title":"The Role of Microhomology-Mediated End Joining (MMEJ) at Dysfunctional Telomeres.","authors":"David Billing, Agnel Sfeir","doi":"10.1101/cshperspect.a041687","DOIUrl":"https://doi.org/10.1101/cshperspect.a041687","url":null,"abstract":"<p><p>DNA double-strand break (DSB) repair pathways are crucial for maintaining genome stability and cell viability. However, these pathways can mistakenly recognize chromosome ends as DNA breaks, leading to adverse outcomes such as telomere fusions and malignant transformation. The shelterin complex protects telomeres from activation of DNA repair pathways by inhibiting nonhomologous end joining (NHEJ), homologous recombination (HR), and microhomology-mediated end joining (MMEJ). The focus of this paper is on MMEJ, an error-prone DSB repair pathway characterized by short insertions and deletions flanked by sequence homology. MMEJ is critical in mediating telomere fusions in cells lacking the shelterin complex and at critically short telomeres. Furthermore, studies suggest that MMEJ is the preferred pathway for repairing intratelomeric DSBs and facilitates escape from telomere crisis. Targeting MMEJ to prevent telomere fusions in hematologic malignancies is of potential therapeutic value.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582607","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
Rediscovering and Unrediscovering Gregor Mendel: His Life, Times, and Intellectual Context. 重新发现和重新发现格里高尔-孟德尔：他的生平、时代和思想背景》（Rediscovering and Unrediscovering Gregor Mendel: His Life, Times, and Intellectual Context.
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-11-05 DOI: 10.1101/cshperspect.a041812
Sander Gliboff
{"title":"Rediscovering and Unrediscovering Gregor Mendel: His Life, Times, and Intellectual Context.","authors":"Sander Gliboff","doi":"10.1101/cshperspect.a041812","DOIUrl":"https://doi.org/10.1101/cshperspect.a041812","url":null,"abstract":"<p><p>Two things about Mendel were \"rediscovered\" in 1900: His famous paper of 1865 and the story of his life and long neglect. Unlike the paper, which anyone could read in its entirety, the story came out only gradually, and many of its elements were misconstrued by Western European scientists. They pictured him as a pure scientist like themselves and were puzzled by or disinterested in his career as a clergyman, his intellectual community in far-off Moravia, and the importance to him of practical plant breeding. This paper recapitulates the process of mythmaking that followed the rediscovery, then shows how more recent historical research has been able to undo it and, in a sense, \"unrediscover\" Mendel.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582604","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
Teaching School Genetics in the 2020s: Why "Naive" Mendelian Genetics Has to Go. 2020 年代的学校遗传学教学：为什么 "天真 "的孟德尔遗传学必须退出历史舞台？
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-11-05 DOI: 10.1101/cshperspect.a041679
Kostas Kampourakis
{"title":"Teaching School Genetics in the 2020s: Why \"Naive\" Mendelian Genetics Has to Go.","authors":"Kostas Kampourakis","doi":"10.1101/cshperspect.a041679","DOIUrl":"https://doi.org/10.1101/cshperspect.a041679","url":null,"abstract":"<p><p>Whereas Mendelian genetics is an important research program in the life sciences, its school version is problematic. On the one hand, it contains stereotypical representations of Gregor Mendel's work that misrepresent his findings and the historical context. This deprives students from gaining an authentic picture of how science is done. On the other hand, what most students end up learning in schools are extremely simplistic accounts of heredity, whereby alleles directly control traits and phenotypes, and thus exclusively depend on which allele an individual has. Such oversimplifications of Mendelian genetics as those that we still teach in schools were exploited by ideologues in the beginning of the twentieth century to provide the presumed \"scientific\" basis for eugenics. This paper addresses these problems of the school version of Mendelian genetics, which I call \"naive\" Mendelian genetics. It also proposes a shift in school education from teaching how the science of genetics is done using model systems to teaching the complexities of development through which heredity is materialized.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582605","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
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 : 2024-10-29 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":"<p><p>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.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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 : 2024-10-29 DOI: 10.1101/cshperspect.a041835
Shreya Lakhera, Elizabeth Herbert, Julijana Gjorgjieva
{"title":"Corrigendum: Modeling the Emergence of Circuit Organization and Function during Development.","authors":"Shreya Lakhera, Elizabeth Herbert, Julijana Gjorgjieva","doi":"10.1101/cshperspect.a041835","DOIUrl":"https://doi.org/10.1101/cshperspect.a041835","url":null,"abstract":"","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142544157","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
Calculating Relatedness: A Pedigree of Definitions. 计算亲缘关系：定义谱系
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-10-21 DOI: 10.1101/cshperspect.a041667
Matishalin Patel, J Arvid Ågren
{"title":"Calculating Relatedness: A Pedigree of Definitions.","authors":"Matishalin Patel, J Arvid Ågren","doi":"10.1101/cshperspect.a041667","DOIUrl":"https://doi.org/10.1101/cshperspect.a041667","url":null,"abstract":"<p><p>Biology can be viewed from both an organismal and a genic perspective. A good example is W.D. Hamilton's work on inclusive fitness and kin selection, which puts relatedness at the heart of our understanding of social behavior. Relatedness mediates how much an actor should value a specific behavior's effect on a relative compared to the cost incurred to itself. Despite its key explanatory role, relatedness is also a concept marred with misunderstanding. Part of the problem has been that the term has been used in different ways by different people. To help address this, we survey the history of how relatedness has been formally modeled, paying particular attention to how it is conceptualized from both a gene-centric and an organism-centric point of view.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142459788","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
Mitochondrial Maintenance in Skeletal Muscle. 骨骼肌中的线粒体维护
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-10-21 DOI: 10.1101/cshperspect.a041514
Laura M de Smalen, Christoph Handschin
{"title":"Mitochondrial Maintenance in Skeletal Muscle.","authors":"Laura M de Smalen, Christoph Handschin","doi":"10.1101/cshperspect.a041514","DOIUrl":"https://doi.org/10.1101/cshperspect.a041514","url":null,"abstract":"<p><p>Skeletal muscle is one of the tissues with the highest range of variability in metabolic rate, which, to a large extent, is critically dependent on tightly controlled and fine-tuned mitochondrial activity. Besides energy production, other mitochondrial processes, including calcium buffering, generation of heat, redox and reactive oxygen species homeostasis, intermediate metabolism, substrate biosynthesis, and anaplerosis, are essential for proper muscle contractility and performance. It is thus not surprising that adequate mitochondrial function is ensured by a plethora of mechanisms, aimed at balancing mitochondrial biogenesis, proteostasis, dynamics, and degradation. The fine-tuning of such maintenance mechanisms ranges from proper folding or degradation of individual proteins to the elimination of whole organelles, and in extremis, apoptosis of cells. In this review, the present knowledge on these processes in the context of skeletal muscle biology is summarized. Moreover, existing gaps in knowledge are highlighted, alluding to potential future studies and therapeutic implications.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142459789","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
Astrocyte Calcium Signaling. 星形胶质细胞的钙信号转导
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-10-01 DOI: 10.1101/cshperspect.a041353
Misha B Ahrens, Baljit S Khakh, Kira E Poskanzer
{"title":"Astrocyte Calcium Signaling.","authors":"Misha B Ahrens, Baljit S Khakh, Kira E Poskanzer","doi":"10.1101/cshperspect.a041353","DOIUrl":"10.1101/cshperspect.a041353","url":null,"abstract":"<p><p>Astrocytes are predominant glial cells that tile the central nervous system and participate in well-established functional and morphological interactions with neurons, blood vessels, and other glia. These ubiquitous cells display rich intracellular Ca<sup>2+</sup> signaling, which has now been studied for over 30 years. In this review, we provide a summary and perspective of recent progress concerning the study of astrocyte intracellular Ca<sup>2+</sup> signaling as well as discussion of its potential functions. Progress has occurred in the areas of imaging, silencing, activating, and analyzing astrocyte Ca<sup>2+</sup> signals. These insights have collectively permitted exploration of the relationships of astrocyte Ca<sup>2+</sup> signals to neural circuit function and behavior in a variety of species. We summarize these aspects along with a framework for mechanistically interpreting behavioral studies to identify directly causal effects. We finish by providing a perspective on new avenues of research concerning astrocyte Ca<sup>2+</sup> signaling.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11444304/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141070794","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
Synthesis and Scope of the Role of Postmating Prezygotic Isolation in Speciation. 交配后同种前隔离在物种形成中的作用的综合与范围。
IF 6.9 2区 生物学
Cold Spring Harbor perspectives in biology Pub Date : 2024-10-01 DOI: 10.1101/cshperspect.a041429
Martin D Garlovsky, Emma Whittington, Tomas Albrecht, Henry Arenas-Castro, Dean M Castillo, Graeme L Keais, Erica L Larson, Leonie C Moyle, Melissa Plakke, Radka Reifová, Rhonda R Snook, Murielle Ålund, Alexandra A-T Weber
{"title":"Synthesis and Scope of the Role of Postmating Prezygotic Isolation in Speciation.","authors":"Martin D Garlovsky, Emma Whittington, Tomas Albrecht, Henry Arenas-Castro, Dean M Castillo, Graeme L Keais, Erica L Larson, Leonie C Moyle, Melissa Plakke, Radka Reifová, Rhonda R Snook, Murielle Ålund, Alexandra A-T Weber","doi":"10.1101/cshperspect.a041429","DOIUrl":"10.1101/cshperspect.a041429","url":null,"abstract":"<p><p>How barriers to gene flow arise and are maintained are key questions in evolutionary biology. Speciation research has mainly focused on barriers that occur either before mating or after zygote formation. In comparison, postmating prezygotic (PMPZ) isolation-a barrier that acts after gamete release but before zygote formation-is less frequently investigated but may hold a unique role in generating biodiversity. Here we discuss the distinctive features of PMPZ isolation, including the primary drivers and molecular mechanisms underpinning PMPZ isolation. We then present the first comprehensive survey of PMPZ isolation research, revealing that it is a widespread form of prezygotic isolation across eukaryotes. The survey also exposes obstacles in studying PMPZ isolation, in part attributable to the challenges involved in directly measuring PMPZ isolation and uncovering its causal mechanisms. Finally, we identify outstanding knowledge gaps and provide recommendations for improving future research on PMPZ isolation. This will allow us to better understand the nature of this often-neglected reproductive barrier and its contribution to speciation.</p>","PeriodicalId":10494,"journal":{"name":"Cold Spring Harbor perspectives in biology","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11444258/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139048452","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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