Seminars in cell & developmental biology最新文献

{"title":"Engineering the ovarian niche: Environmental control of folliculogenesis in vitro","authors":"Arezoo Dadashzadeh ,&nbsp;Saeid Moghassemi ,&nbsp;Saba Nikanfar ,&nbsp;Ellen C.R. Leonel ,&nbsp;Shunran Zhang ,&nbsp;Maria João Sousa ,&nbsp;Thalles Fernando Rocha Ruiz ,&nbsp;Christiani A. Amorim","doi":"10.1016/j.semcdb.2025.103639","DOIUrl":"10.1016/j.semcdb.2025.103639","url":null,"abstract":"<div><div>Advancements in cancer therapies have significantly improved patient survival, but gonadotoxic treatments often compromise fertility, particularly in female patients. While ovarian tissue cryopreservation and transplantation are well-established fertility preservation options, they are not recommended for patients with blood-borne cancers or highly metastatic malignancies due to the risk of ovarian involvement. In these cases, follicle in vitro culture offers a promising alternative. However, folliculogenesis is a complex process that requires meticulous environmental control to mimic the ovarian niche. Key factors include biochemical signals delivered through culture media, biophysical support provided by three-dimensional biomaterials or the native extracellular matrix, and crucial cellular interactions that drive follicular development. Recent advances in biomaterial design have led to the creation of scaffolds that not only preserve structural integrity but also facilitate nutrient exchange and cell communication. Moreover, dynamic culture systems have shown superior outcomes compared to static models, offering a more physiologically relevant environment. This review explores the interplay of biochemical, biophysical, and mechanical factors in in vitro folliculogenesis. By synthesizing current innovations in scaffold design, culture systems, and bioactive supplementation, we outline key strategies for optimizing in vitro follicular development. These advances pave the way toward safer and more effective fertility preservation approaches for patients at high risk of ovarian metastasis and offer broader insights into reproductive biology and regenerative medicine. However, to fully realize this potential, further standardization, long-term safety studies, and critical evaluation of emerging technologies remain essential to enable robust clinical translation and personalized reproductive applications.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"175 ","pages":"Article 103639"},"PeriodicalIF":6.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144867375","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}

{"title":"Distributed computing inspired by biology","authors":"Matthias Függer ,&nbsp;Thomas Nowak ,&nbsp;Kerian Thuillier","doi":"10.1016/j.semcdb.2025.103666","DOIUrl":"10.1016/j.semcdb.2025.103666","url":null,"abstract":"<div><div>Biological systems are mastering the art of composing cells into colonies, tissues, and organisms. This article reviews striking similarities and differences between such biological systems and distributed computing systems, where computational units are composed to form larger systems with the goal of increasing computational power, enhancing system robustness, or overcoming spatial distances.</div><div>A problem that recurs in many contexts in distributed systems is obtaining a consistent view of part of the system by its agents. Such problems, known as agreement problems in distributed computing, have been extensively studied across different computational models, varying, for example, in the extent to which the network is stable or dynamic.</div><div>Motivated by the importance of agreement problems, we discuss examples ranging from simple to more complex cases, the latter in the context of optimization: agents solving graph optimization problems, searching for optima in arbitrary loss landscapes, and applying gradient-based techniques closely related to widely adopted artificial neural networks.</div><div>We then discuss the reverse direction: distributed systems implemented with biological material. In particular, we detail a theoretical distributed computing model and algorithm targeted toward implementation in bacterial populations.</div><div>We conclude with an outlook on what we consider the beginning of a promising intersection between distributed computing and biology, highlighting opportunities for both understanding natural systems and engineering novel distributed systems, both biological and in silico.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"175 ","pages":"Article 103666"},"PeriodicalIF":6.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145550521","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}

{"title":"For special issue: Collective cell migration in vivo","authors":"Mie Wong,&nbsp;Tetsuya Hiraiwa","doi":"10.1016/j.semcdb.2025.103663","DOIUrl":"10.1016/j.semcdb.2025.103663","url":null,"abstract":"","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"175 ","pages":"Article 103663"},"PeriodicalIF":6.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145355793","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}

{"title":"Chlamydomonas as a model system for the study of cilia and eukaryotic flagella","authors":"Xuecheng Li ,&nbsp;Qingqing Liu ,&nbsp;Junmin Pan","doi":"10.1016/j.semcdb.2025.103658","DOIUrl":"10.1016/j.semcdb.2025.103658","url":null,"abstract":"<div><div><em>Chlamydomonas</em> is a haploid, unicellular green alga that serves as an excellent model system for studying ciliary biology. It possesses two motile cilia of equal length, making it ideal for investigating both ciliogenesis and ciliary motility, as well as cilia-based signaling. The organism's ease of cultivation, the simplicity of cilia isolation, and the availability of well-established experimental systems for rapid and synchronous cilia regeneration and disassembly contribute to its utility in laboratory research. Furthermore, <em>Chlamydomonas</em> is highly amenable to a variety of genetic approaches, enhancing its value as a model organism. Due to the high degree of conservation in the core mechanisms governing ciliary structure and function, discoveries made in <em>Chlamydomonas</em> have significantly advanced our understanding of cilia across species and have provided important insights into cilia-related human disorders. In this overview, we summarize the key cellular features, life cycle stages, ciliary architecture and dynamics, ciliary behavior, biochemical and genetic advantages of <em>Chlamydomonas</em> as a model organism. Our goal is to provide a foundational perspective for those new to ciliary research in <em>Chlamydomonas</em> - including early-career scientists, experienced researchers transitioning from other fields, and cilia experts working with alternative model systems.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"175 ","pages":"Article 103658"},"PeriodicalIF":6.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145092394","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}

{"title":"How to get the most out of your cancer spatial transcriptomics data","authors":"David I. Kaplan ,&nbsp;Xiang Guo ,&nbsp;Sasuni D. Hirimuthugoda ,&nbsp;Lachlan Cain ,&nbsp;Sirui Weng ,&nbsp;David Le ,&nbsp;James Comben ,&nbsp;Anna S. Trigos","doi":"10.1016/j.semcdb.2025.103657","DOIUrl":"10.1016/j.semcdb.2025.103657","url":null,"abstract":"<div><div>Spatial transcriptomics (ST) has emerged as a powerful tool in cancer research, significantly expanding our capacity to study the complexity of tumour ecosystems. Together with the diversity of ST platforms, a plethora of analysis approaches and tools have been developed with the goal of extracting distinct aspects of biological information contained in the data. From visualizing gene expression in the context of tissue structure and cell morphology, to the exploitation of machine learning and spatial statistics to identify cell neighbourhoods, quantify tumour heterogeneity and map cell-cell signalling networks, there is a current explosion of novel analyses techniques. Unfortunately, this makes it challenging to develop workflows and strategies for data analysis, especially for those new to the field. This review serves to offer a path to cancer researchers who recognise the potential of ST and would like to start their data analysis journey. We cover the main analysis approaches used to address common research questions associated with ST data in cancer, highlighting commonly used tools, as well as discuss emerging analysis techniques that hold the potential to leverage the richness of the data at an unprecedented scale. Finally, we end by highlighting considerations when designing ST projects, from experimental design, to assembling teams and managing the rapid flux of ST technologies. We anticipate this review will be useful resource for researchers to not just seek analysis strategies to answer their current research questions, but also provide inspiration to further take advantage of the wealth of information provided by ST data.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"175 ","pages":"Article 103657"},"PeriodicalIF":6.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318449","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}

{"title":"Approximating the living","authors":"Rob Phillips","doi":"10.1016/j.semcdb.2025.103646","DOIUrl":"10.1016/j.semcdb.2025.103646","url":null,"abstract":"<div><div>Is a herd of wildebeest better thought of as a series of individual animals, each with its own glorious and unmanageable volition, or as a field of moving arrows? Are the morphogen gradients that set up the coordinate systems for embryonic anterior–posterior patterning a smooth and continuous concentration field or instead a chaotic collection of protein molecules each jiggling about in the haphazard way first described by Robert Brown in his microscopical observations of pollen? Is water, the great liquid ether of the living world, a collection of discrete molecules or instead a perfectly continuous medium with a density of <span><math><mo>≈</mo></math></span>1000 kg/m<span><math><msup><mrow></mrow><mrow><mn>3</mn></mrow></msup></math></span>? In this article, I will argue that these questions pose a false dichotomy since there are many different and powerful representations of the world around us. Different representations suit us differently at different times and it is often useful to be able to hold these seemingly contradictory notions in our heads simultaneously. Indeed, mathematics is not only the language of representation, but often is also the engine of reconciliation of such disparate views. In a letter to Alfred Russel Wallace on 14 April 1869, Charles Darwin noted that Lord Kelvin’s “views on the recent age of the world have been for some time one of my sorest troubles”. Here, I will argue that one of the highest attainments of the scientific enterprise is a coherent picture of the world, a picture in which our stories about the geological age of the Earth are coherent with our stories of how whales populated the oceans, our understanding of the living jibes with our understanding of the inanimate, our insights into the dynamics of genes and molecular structures are consonant with our physical understanding of the laws of statistical physics. The underpinnings of such coherency are often best revealed when viewed through the lens of mathematics.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"175 ","pages":"Article 103646"},"PeriodicalIF":6.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144922768","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}

{"title":"The mechanics of shaping organs in plants","authors":"Ankita Dash ,&nbsp;Mabel Maria Mathew ,&nbsp;Kalika Prasad","doi":"10.1016/j.semcdb.2025.103640","DOIUrl":"10.1016/j.semcdb.2025.103640","url":null,"abstract":"<div><div>Mechanical forces are instrumental to shaping lifeforms, influencing development from the subcellular scale to the organismal scale. Here, we explore how mechanical forces manifest themselves in plants, driving deformations such as tissue folding, buckling, undulating patterns, and edge curving. These deformations result from modulations in fundamental cellular processes such as cell division, cell expansion, cell wall mechanics, and cytoskeletal organization. Cytoskeletal structure like microtubules, actin filaments respond to mechanical cues by generating localized stress patterns that shape cell structure and function. Mechanical forces can also regulate gene expression and gate mechanosensitive channels to regulate ion fluxes, thereby integrating physical forces with biochemical properties. We draw parallels between plant and animal kingdoms to show how these two kingdoms utilize mechanochemical effects to drive growth and morphogenesis.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"175 ","pages":"Article 103640"},"PeriodicalIF":6.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144813846","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}

{"title":"In vitro modeling of cell types in cardiogenesis and congenital heart disease","authors":"Sanjeev S. Ranade","doi":"10.1016/j.semcdb.2025.103656","DOIUrl":"10.1016/j.semcdb.2025.103656","url":null,"abstract":"<div><div>Congenital heart defects (CHD) are present in nearly 1 % of live births and are a leading cause of infant mortality. Despite advances in genome sequencing technologies and an increased understanding of the genes necessary for heart development, the etiology of a majority of CHD cases remains undefined. Recent breakthroughs in single-cell genomics, lineage tracing, and live imaging in animal models of cardiogenesis have revealed the precise spatiotemporal dynamics of discrete cell types in heart development. Here, I review how these findings have informed the development of new human pluripotent stem cell methods to generate a diverse range of cells in cardiogenesis. A key unifying theme is that multipotent cardiac progenitor cells are extraordinarily responsive to slight changes to signaling factors administered at various stages of cardiac differentiation. I highlight how the ability to make a range of cardiac cell types can be used to define context specific mechanisms of CHD. I then describe how <em>in vitro</em> human models of cardiogenesis are especially important in cases of severe forms of CHD, such as single ventricle disorders, for which the complex genetic underlying mechanisms are poorly defined and animal models are lacking.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"175 ","pages":"Article 103656"},"PeriodicalIF":6.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200934","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}

{"title":"Mechanics of force transmission in epithelia: From cell-to-cell propagation to nuclear response","authors":"Ronan Bouzignac,&nbsp;Magali Suzanne","doi":"10.1016/j.semcdb.2025.103662","DOIUrl":"10.1016/j.semcdb.2025.103662","url":null,"abstract":"<div><div>Mechanical forces play essential roles during morphogenesis, enabling cells to change shape or reorganize to form new structures. Recent questions in the field of mechanobiology focus on how these locally generated forces propagate and the extent of their propagation. This phenomenon can be observed at multiple scales (across tissues, where supracellular actomyosin structures interconnected at cell–cell junctions transmit forces, or within individual cells, where mechanical cues can influence the nucleus). In the first part of this review, we highlight recent advances in our understanding of force propagation along epithelial apical surfaces, including factors that facilitate it, such as tissue curvature and polarity. In the second part, we examine how mechanical forces affect nuclear shape and integrity at the single-cell level, beginning with <em>in vitro</em> studies of nuclear responses to mechanical stress and extending to the less-explored mechanical behavior of nuclei in more complex, integrated model systems.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"175 ","pages":"Article 103662"},"PeriodicalIF":6.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145308365","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}

{"title":"The mechanics behind the Drosophila egg","authors":"Megha Maria Jacob,&nbsp;Muriel Grammont","doi":"10.1016/j.semcdb.2025.103638","DOIUrl":"10.1016/j.semcdb.2025.103638","url":null,"abstract":"<div><div>The formation and the development of the <em>Drosophila</em> egg involves multiple mechanical cross-talks between germline cells, somatic cells and the surrounding basement membrane. In this review, we discuss several development stages when the sources, as well as the roles, of mechanical forces in egg shape establishment are well defined. The examples described here illustrate the diversity of these forces as well as of the tools used to measure them and of the outcome each of them generates. We examine their contributions and their integration to morphogenesis. We discuss the limitations of our current knowledge, the importance of developing novel approaches and the support that modelling could bring to tackle some issues. One major future challenge is to understand how robustness in shaping the egg is achieved when the contributors act in different cell types and at different times. Studying <em>Drosophila</em> egg formation thus remains an exciting model in developmental biology as it must integrate a variety of biomechanical inputs from its environment, in addition of the biochemical signals discovered in the past.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"175 ","pages":"Article 103638"},"PeriodicalIF":6.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144878521","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}