Seminars in cell & developmental biology最新文献

Agent-based modeling of complex molecular mechanisms 基于agent的复杂分子机制建模

IF 6.2 2区生物学

Seminars in cell & developmental biology Pub Date : 2025-06-17 DOI: 10.1016/j.semcdb.2025.103626

Margot Riggi , Janet H. Iwasa

{"title":"Agent-based modeling of complex molecular mechanisms","authors":"Margot Riggi , Janet H. Iwasa","doi":"10.1016/j.semcdb.2025.103626","DOIUrl":"10.1016/j.semcdb.2025.103626","url":null,"abstract":"<div><div>The diverse molecular mechanisms that orchestrate cellular processes typically involve a complex network of actors and span broad ranges of spatial and temporal scales that no single experimental or computational technique can cover. While several multiscale methods are increasingly capable of connecting across scales, bridging molecular and cellular levels remains a challenge. Agent-based modeling (ABM) is a computational paradigm that models a complex system and its emergent properties from the perspective of its individual components whose behaviors are governed by a set of predefined rules. As long as these rules are biophysically accurate, the flexibility of this framework makes it uniquely positioned to fill the gap between spatially detailed and computationally efficient approaches and emerge as an effective mesoscopic modeling method that could bring valuable mechanistic insight into how complex behaviors arise in cellular environments. In this review, we summarize ABM principles and current capabilities in the realm of molecular biology and discuss potential directions for the development of additional features that would further broaden the scope of the method.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"172 ","pages":"Article 103626"},"PeriodicalIF":6.2,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144297587","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 open and closed case for Class I HDACs in cardiac development I类hdac在心脏发育中的开放和封闭案例

IF 6.2 2区生物学

Seminars in cell & developmental biology Pub Date : 2025-06-09 DOI: 10.1016/j.semcdb.2025.103621

Drishti Rajesth, Veronica Uribe , Kelly A. Smith

{"title":"The open and closed case for Class I HDACs in cardiac development","authors":"Drishti Rajesth, Veronica Uribe , Kelly A. Smith","doi":"10.1016/j.semcdb.2025.103621","DOIUrl":"10.1016/j.semcdb.2025.103621","url":null,"abstract":"<div><div>Gene expression in cardiac development is regulated through complex epigenetic mechanisms. Histone deacetylases (HDACs) are one of the many layers of epigenetic modulation, whereby they remove acetylation marks on histone tails, prompting chromatin tightening and therefore bring about gene repression. The most extensively characterised HDACs in cardiac development are HDACs 1–3, all belonging to the Class I HDAC family. Global as well as tissue-specific knockout models in mice have provided insight into the phenotypes generated by loss of these key molecular regulators. In some instances, molecular processes that individual HDACs regulate within cardiac development have also been revealed, although the epigenetic targets and binding partners of HDACs within cardiac development are still relatively understudied. Knowledge has also been contributed from <em>in vitro</em> studies using stem cell-derived models as well as burgeoning research using the zebrafish model. The aim of this review is to summarise the current knowledge of class I HDAC function during key stages of cardiac development, including cardiac specification and differentiation, looping morphogenesis, and second heart field development. The role of class I HDACs in non-cardiomyocyte populations, such as the endocardium, valves, and epicardium is also discussed.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"172 ","pages":"Article 103621"},"PeriodicalIF":6.2,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144239566","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

Cardiac trabeculation in vertebrates: Convergent evolution or evolutionary adaptations associated with heart complexity? 脊椎动物心脏小梁：趋同进化还是与心脏复杂性相关的进化适应？

IF 6.2 2区生物学

Seminars in cell & developmental biology Pub Date : 2025-06-05 DOI: 10.1016/j.semcdb.2025.103622

Yen T.H. Tran , Diptarka Saha , Gonzalo del Monte-Nieto

{"title":"Cardiac trabeculation in vertebrates: Convergent evolution or evolutionary adaptations associated with heart complexity?","authors":"Yen T.H. Tran , Diptarka Saha , Gonzalo del Monte-Nieto","doi":"10.1016/j.semcdb.2025.103622","DOIUrl":"10.1016/j.semcdb.2025.103622","url":null,"abstract":"<div><div>One of the most important processes during early heart development is the formation of trabecular myocardium. Cardiac trabeculation is the process by which the ventricular chambers develop a complex sponge-like myocardium essential for optimal cardiac function to provide efficient oxygenation and nourishment to the developing embryo. Indeed, its importance is highlighted by the fact that defects in trabecular formation lead to embryonic lethality and congenital heart disease. In the last decades, our understanding of cardiac trabeculation in different vertebrate models has advanced significantly. However, instead of reinforcing cardiac trabeculation as a highly evolutionarily conserved process across vertebrates, these studies have identified significant differences in the way the process occurs and how it is regulated in different vertebrate species. In this review, we assembled the current knowledge on cardiac trabeculation in different vertebrate species and examined if trabecular myocardium development can be achieved through different morphogenetic processes across vertebrates or if these differences are associated with evolutionary adaptations required to develop more complex vertebrate hearts.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"172 ","pages":"Article 103622"},"PeriodicalIF":6.2,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144220836","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

Dynamical systems of fate and form in development 发展中的命运和形式的动力系统

IF 6.2 2区生物学

Seminars in cell & developmental biology Pub Date : 2025-06-03 DOI: 10.1016/j.semcdb.2025.103620

Alex M. Plum, Mattia Serra

引用次数: 0

Ploidy in cardiovascular development and regeneration 心血管发育和再生的倍性

IF 6.2 2区生物学

Seminars in cell & developmental biology Pub Date : 2025-05-20 DOI: 10.1016/j.semcdb.2025.103618

Tian Lan , Sabrina Kaminsky , Chi-Chung Wu

{"title":"Ploidy in cardiovascular development and regeneration","authors":"Tian Lan , Sabrina Kaminsky , Chi-Chung Wu","doi":"10.1016/j.semcdb.2025.103618","DOIUrl":"10.1016/j.semcdb.2025.103618","url":null,"abstract":"<div><div>Somatic polyploidy, a non-inheritable form of genome multiplication, plays cell-type specific and context-dependent roles in organ development and regeneration. In the mammalian heart, embryonic cardiomyocytes are primarily diploid, which lose their ability to complete cell division and become polyploid as they mature. Unlike lower vertebrates like zebrafish, polyploid cardiomyocytes are commonly found across mammals, including humans. Intriguingly, the degree, timing, and modes of cardiomyocyte polyploidization vary greatly between species. In addition to the association with cardiomyocyte development and maturation, recent studies have established polyploidy as a barrier against cardiomyocyte proliferation and heart regeneration following cardiac injury. Hence, a thorough understanding of how and why cardiomyocyte become polyploid will provide insights into heart development and may help develop therapeutic strategies for heart regeneration. Here, we review the dynamics of cardiomyocyte polyploidization across species and how cardiomyocyte-intrinsic, -extrinsic, and environmental factors regulate this process as well as the impact of cardiomyocyte polyploidization on heart development and regeneration.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"172 ","pages":"Article 103618"},"PeriodicalIF":6.2,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144099845","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

Cardiac regeneration: Unraveling the complex network of intercellular crosstalk 心脏再生：揭示细胞间串扰的复杂网络

IF 6.2 2区生物学

Seminars in cell & developmental biology Pub Date : 2025-05-13 DOI: 10.1016/j.semcdb.2025.103619

Bailin Wu , Florian Constanty , Arica Beisaw

{"title":"Cardiac regeneration: Unraveling the complex network of intercellular crosstalk","authors":"Bailin Wu , Florian Constanty , Arica Beisaw","doi":"10.1016/j.semcdb.2025.103619","DOIUrl":"10.1016/j.semcdb.2025.103619","url":null,"abstract":"<div><div>The heart is composed of multiple cell types, including cardiomyocytes, endothelial/endocardial cells, fibroblasts, resident immune cells and epicardium and crosstalk between these cell types is crucial for proper cardiac function and homeostasis. In response to cardiac injury or disease, cell-cell interactions and intercellular crosstalk contribute to remodeling to compensate reduced heart function. In some vertebrates, the heart can regenerate following cardiac injury. While cardiomyocytes play a crucial role in this process, additional cell types are necessary to create a pro-regenerative microenvironment in the injured heart. Here, we review recent literature regarding the importance of cellular crosstalk in promoting cardiac regeneration and provide insight into emerging technologies to investigate cell-cell interactions <em>in vivo</em>. Lastly, we explore recent studies highlighting the importance of inter-organ communication in response to injury and promotion of cardiac regeneration. Importantly, understanding how intercellular and inter-organ crosstalk promote cardiac regeneration is essential for the development of therapeutic strategies to stimulate regeneration in the human heart.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"171 ","pages":"Article 103619"},"PeriodicalIF":6.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143936965","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

A near death experience: The secret stem cell life of caspase-3 濒死体验：caspase-3干细胞生命的秘密

IF 6.2 2区生物学

Seminars in cell & developmental biology Pub Date : 2025-05-08 DOI: 10.1016/j.semcdb.2025.103617

Mahasen Sarji , Roi Ankawa , Matan Yampolsky , Yaron Fuchs

引用次数: 0

Artery regeneration: Molecules, mechanisms and impact on organ function 动脉再生：分子、机制及对器官功能的影响

IF 6.2 2区生物学

Seminars in cell & developmental biology Pub Date : 2025-05-02 DOI: 10.1016/j.semcdb.2025.103611

Swarnadip Ghosh , Bhavnesh Bishnoi , Soumyashree Das

{"title":"Artery regeneration: Molecules, mechanisms and impact on organ function","authors":"Swarnadip Ghosh , Bhavnesh Bishnoi , Soumyashree Das","doi":"10.1016/j.semcdb.2025.103611","DOIUrl":"10.1016/j.semcdb.2025.103611","url":null,"abstract":"<div><div>Replenishment of artery cells to repair or create new arteries is a promising strategy to re-vascularize ischemic tissue. However, limited understanding of cellular and molecular programs associated with artery (re-)growth impedes our efforts towards designing optimal therapeutic approaches. In this review, we summarize different cellular mechanisms that drive injury-induced artery regeneration in distinct organs and organisms. Artery formation during embryogenesis includes migration, self-amplification, and changes in cell fates. These processes are coordinated by multiple signaling pathways, like Vegf, Wnt, Notch, Cxcr4; many of which, also involved in injury-induced vascular responses. We also highlight how physiological and environmental factors determine the extent of arterial re-vascularization. Finally, we discuss different <em>in vitro</em> cellular reprogramming and tissue engineering approaches to promote artery regeneration, <em>in vivo</em>. This review provides the current understanding of endothelial cell fate reprogramming and explores avenues for regenerating arteries to restore organ function through efficient revascularization.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"171 ","pages":"Article 103611"},"PeriodicalIF":6.2,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898562","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

Immune-mediated cardiac development and regeneration 免疫介导的心脏发育和再生

IF 6.2 2区生物学

Seminars in cell & developmental biology Pub Date : 2025-05-01 DOI: 10.1016/j.semcdb.2025.103613

Timothy C. Byatt , Ehsan Razaghi , Selin Tüzüner , Filipa C. Simões

引用次数: 0

Why cellular computations challenge our design principles 为什么细胞计算挑战我们的设计原则

IF 6.2 2区生物学

Seminars in cell & developmental biology Pub Date : 2025-04-30 DOI: 10.1016/j.semcdb.2025.103616

Lewis Grozinger , Bruno Cuevas-Zuviría , Ángel Goñi-Moreno

{"title":"Why cellular computations challenge our design principles","authors":"Lewis Grozinger , Bruno Cuevas-Zuviría , Ángel Goñi-Moreno","doi":"10.1016/j.semcdb.2025.103616","DOIUrl":"10.1016/j.semcdb.2025.103616","url":null,"abstract":"<div><div>Biological systems inherently perform computations, inspiring synthetic biologists to engineer biological systems capable of executing predefined computational functions for diverse applications. Typically, this involves applying principles from the design of conventional silicon-based computers to create novel biological systems, such as genetic Boolean gates and circuits. However, the natural evolution of biological computation has not adhered to these principles, and this distinction warrants careful consideration. Here, we explore several concepts connecting computational theory, living cells, and computers, which may offer insights into the development of increasingly sophisticated biological computations. While conventional computers approach theoretical limits, solving nearly all problems that are computationally solvable, biological computers have the opportunity to outperform them in specific niches and problem domains. Crucially, biocomputation does not necessarily need to scale to rival or replicate the capabilities of electronic computation. Rather, efforts to re-engineer biology must recognise that life has evolved and optimised itself to solve specific problems using its own principles. Consequently, intelligently designed cellular computations will diverge from traditional computing in both implementation and application.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"171 ","pages":"Article 103616"},"PeriodicalIF":6.2,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143892090","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