Intrinsic and extrinsic regulators of developmental timing: from miRNAs to nutritional cues

A fundamental challenge in biology is to understand the reproducibility of developmental programs between individuals of the same metazoan species. This developmental precision reflects the meticulous integration of temporal control mechanisms with those that specify other aspects of pattern formation, such as spatial and sexual information. The cues that guide these developmental events are largely intrinsic to the organism but can also include extrinsic inputs, such as nutrition or temperature. This review discusses the well-characterized developmental timing mechanism that patterns the C. elegans epidermis. Components of this pathway are conserved, and their links to developmental time control in other species are considered, including the temporal patterning of the fly nervous system. Particular attention is given to the roles of miRNAs in developmental timing and to the emerging mechanisms that link developmental programs to nutritional cues.     

Apical constriction: A cell shape change that can drive morphogenesis

Biologists have long recognized that dramatic bending of a cell sheet may be driven by even modest shrinking of the apical sides of cells. Cell shape changes and tissue movements like these are at the core of many of the morphogenetic movements that shape animal form during development, driving processes such as gastrulation, tube formation, and neurulation. The mechanisms of such cell shape changes must integrate developmental patterning information in order to spatially and temporally control force production—issues that touch on fundamental aspects of both cell and developmental biology and on birth defects research. How does developmental patterning regulate force-producing mechanisms, and what roles do such mechanisms play in development? Work on apical constriction from multiple systems including Drosophila, Caenorhabditis elegans, sea urchin, Xenopus, chick, and mouse has begun to illuminate these issues. Here, we review this effort to explore the diversity of mechanisms of apical constriction, the diversity of roles that apical constriction plays in development, and the common themes that emerge from comparing systems.     

Integrins in development and cancer

The correct control of cell fate decisions is critical for metazoan development and tissue homeostasis. It is established that the integrin family of cell surface receptors regulate cell fate by mediating cell–cell and cell–extracellular matrix (ECM) interactions. However, our understanding of how the different family members control discrete aspects of cell biology, and how this varies between tissues and is temporally regulated, is still in its infancy. An emerging area of investigation aims to understand how integrins translate changes in tension in the surrounding microenvironment into biological responses. This is particularly pertinent due to changes in the mechanical properties of the ECM having been linked to diseases, such as cancer. In this review, we provide an overview of the roles integrins play in important developmental processes, such as proliferation, polarity, apoptosis, differentiation and maintenance of “stemness”. We also discuss recent advances in integrin mechanobiology and highlight the involvement of integrins and aberrant ECM in cancer.     

SCI/MIP-1 alpha: a potent stem cell inhibitor with potential roles in development.

The hemopoietic system represents a complex adult developmental system which allows the study of mechanisms of stem cell proliferative control and differentiation commitment. It is likely that information obtained from this model system will have implications for control processes regulating other hierarchical systems in the developing embryo as well as in the adult animal. We have recently identified and isolated a potent inhibitor of hemopoietic stem cell proliferation which we have labeled SCI/MIP-1 alpha. This inhibitor is also active on clonogenic epidermal cells and may thus be a more general stem cell inhibitor than was previously believed. The biology of this peptide is outlined in more detail below and the potential roles for such a factor in the developing embryo are also discussed.     

Mechanisms of size control

The study of organ size control is a discipline of developmental biology that is largely unexplored. Although the size of an organ or organism depends largely on cell numbers and cell size, studies have found that the simple deregulation of cell proliferation or cell growth does not necessarily lead to changes in organ size. Recent genetic screens in Drosophila suggest that mutations that do affect organ size can be classified into three broad categories on the basis of their underlying effects: patterning, proliferation, and growth. Overall, experimental data suggest that organ size might be regulated by a 'total mass checkpoint' mechanism which functions to link the regulation of cell size and cell proliferation. The mechanisms of organ size control could also be critical targets for evolutionary events or disease processes such as tumorigenesis.     

Developmental constraints vs. variational properties: How pattern formation can help to understand evolution and development

This article suggests that apparent disagreements between the concept of developmental constraints and neo-Darwinian views on morphological evolution can disappear by using a different conceptualization of the interplay between development and selection. A theoretical framework based on current evolutionary and developmental biology and the concepts of variational properties, developmental patterns and developmental mechanisms is presented. In contrast with existing paradigms, the approach in this article is specifically developed to compare developmental mechanisms by the morphological variation they produce and the way in which their functioning can change due to genetic variation. A developmental mechanism is a gene network, which is able to produce patterns in space though the regulation of some cell behaviour (like signalling, mitosis, apoptosis, adhesion, etc.). The variational properties of a developmental mechanism are all the pattern transformations produced under different initial and environmental conditions or IS-mutations. IS-mutations are DNA changes that affect how two genes in a network interact, while T-mutations are mutations that affect the topology of the network itself. This article explains how this new framework allows predictions not only about how pattern formation affects variation, and thus phenotypic evolution, but also about how development evolves by replacement between pattern formation mechanisms. This article presents testable inferences about the evolution of the structure of development and the phenotype under different selective pressures. That is what kind of pattern formation mechanisms, in which relative temporal order, and which kind of phenotypic changes, are expected to be found in development.     

Learning developmental biology has priority in the life sciences curriculum in Singapore

Singapore has embraced the life sciences as an important discipline to be emphasized in schools and universities. This is part of the nation's strategic move towards a knowledge-based economy, with the life sciences poised as a new engine for economic growth. In the life sciences, the area of developmental biology is of prime interest, since it is not just intriguing for students to know how a single cell can give rise to a complex, coordinated, functional life that is multicellular and multifaceted, but more importantly, there is much in developmental biology that can have biomedical implications. At different levels in the Singapore educational system, students are exposed to various aspects of developmental biology. The author has given many guest lectures to secondary (ages 12-16) and high school (ages 17-18) students to enthuse them about topics such as embryo cloning and stem cell biology. At the university level, some selected topics in developmental biology are part of a broader course which caters for students not majoring in the life sciences, so that they will learn to comprehend how development takes place and the significance of the knowledge and impacts of the technologies derived in the field. For students majoring in the life sciences, the subject is taught progressively in years two and three, so that students will gain specialist knowledge in developmental biology. As they learn, students are exposed to concepts, principles and mechanisms that underlie development. Different model organisms are studied to demonstrate the rapid advances in this field and to show the interconnectivity of developmental themes among living things. The course inevitably touches on life and death matters, and the social and ethical implications of recent technologies which enable scientists to manipulate life are discussed accordingly, either in class, in a discussion forum, or through essay writing.     

Rheb is an essential regulator of S6K in controlling cell growth in Drosophila

Understanding the mechanisms through which multicellular organisms regulate cell, organ and body growth is of relevance to developmental biology and to research on growth-related diseases such as cancer. Here we describe a new effector in growth control, the small GTPase Rheb (Ras homologue enriched in brain). Mutations in the Drosophila melanogaster Rheb gene were isolated as growth-inhibitors, whereas overexpression of Rheb promoted cell growth. Our genetic and biochemical analyses suggest that Rheb functions downstream of the tumour suppressors Tsc1 (tuberous sclerosis 1)-Tsc2 in the TOR (target of rapamycin) signalling pathway to control growth, and that a major effector of Rheb function is ribosomal S6 kinase (S6K).     

The interface between cell and developmental biology

Cell differentiation, morphology, migration, polarity, intercellular communication and adhesion are all cellular processes that control embryo morphogenesis and lie at the interface of cell and developmental biology. The interface between these two fields is best illustrated, however, in studies of axiation and cytoskeletal remodeling during development. Recent advances reveal novel mechanisms for axiation, including the role of RNA and protein degradation in regulating the timely expression of morphogenetic signals. Significant progress has also been made in identifying components of the cytoskeleton and the extracellular matrix that mediate embryonic cell migration and polarity. Cellular processes at the interface of cell and developmental biology are overseen by the Wnt signaling cascade that coordinates both axiation and cytoskeletal remodeling during development.     

哺乳动物卵母细胞及早期胚胎蛋白质组学研究进展

雌性生殖细胞发育是动物繁殖的基石,哺乳动物卵母细胞和早期胚胎在其生长发育过程中有许多独特的现象和规律,涉及一系列蛋白质合成/降解和磷酸化等状态的动态改变。对卵母细胞分裂、成熟调控机理以及植入前胚胎发育规律的研究是发育生物学领域的一项重要课题。蛋白质组学是以细胞或组织内全部的蛋白质为研究对象,系统鉴定、定量蛋白质并研究这些蛋白质功能的科学。随着蛋白质分离、鉴定技术的快速发展,蛋白质组学为卵母细胞发生、分化、成熟以及质量控制等相关研究提供了新的方法和内容,如在蛋白质定量、修饰、定位和相互作用等方面提供其他组学技术不可获得的重要信息。这些信息将有助于揭示哺乳动物卵母细胞成熟和早期胚胎发育的分子机制,对于进一步完善卵母细胞的体外成熟培养体系,提高胚胎体外生产、体细胞克隆和转基因动物生产效率具有重要意义。     

Genetic control of plant organ growth

CONTENTS: Summary 319 I. Introduction 320 II. The cell biology and biophysics of growth 320 III. Timing is everything: what determines when proliferation gives way to expansion? 323 IV. Anisotropic growth and the importance of polarity 325 V. How does organ identity and developmental patterning modulate growth behaviour? 326 VI. Coordination of growth at different scales 327 VII. Conclusions 329 Acknowledgements 329 References 330 SUMMARY: The growth of plant organs is under genetic control. Work in model species has identified a considerable number of genes that regulate different aspects of organ growth. This has led to an increasingly detailed knowledge about how the basic cellular processes underlying organ growth are controlled, and which factors determine when proliferation gives way to expansion, with this transition emerging as a critical decision point during primordium growth. Progress has been made in elucidating the genetic basis of allometric growth and the role of tissue polarity in shaping organs. We are also beginning to understand how the mechanisms that determine organ identity influence local growth behaviour to generate organs with characteristic sizes and shapes. Lastly, growth needs to be coordinated at several levels, for example between different cell layers and different regions within one organ, and the genetic basis for such coordination is being elucidated. However, despite these impressive advances, a number of basic questions are still not fully answered, for example, whether and how a growing primordium keeps track of its size. Answering these questions will likely depend on including additional approaches that are gaining in power and popularity, such as combined live imaging and modelling.     

Morphogenetic fields in embryogenesis, regeneration, and cancer: Non-local control of complex patterning

Establishment of shape during embryonic development, and the maintenance of shape against injury or tumorigenesis, requires constant coordination of cell behaviors toward the patterning needs of the host organism. Molecular cell biology and genetics have made great strides in understanding the mechanisms that regulate cell function. However, generalized rational control of shape is still largely beyond our current capabilities. Significant instructive signals function at long range to provide positional information and other cues to regulate organism-wide systems properties like anatomical polarity and size control. Is complex morphogenesis best understood as the emergent property of local cell interactions, or as the outcome of a computational process that is guided by a physically encoded map or template of the final goal state? Here I review recent data and molecular mechanisms relevant to morphogenetic fields: large-scale systems of physical properties that have been proposed to store patterning information during embryogenesis, regenerative repair, and cancer suppression that ultimately controls anatomy. Placing special emphasis on the role of endogenous bioelectric signals as an important component of the morphogenetic field, I speculate on novel approaches for the computational modeling and control of these fields with applications to synthetic biology, regenerative medicine, and evolutionary developmental biology.     

Gene networks capable of pattern formation: from induction to reaction-diffusion

One of the main aims of developmental biology is to understand how a single and apparently homogeneous egg cell achieves the intricate complexity of the adult. Here we present two models to explain the generation of developmental patterns through interactions at the gene level. One model considers direct-contact induction between cells while the other takes into account diffusion of hormones. We show that sets of cells involving identical gene networks and communicating through hormones spontaneously exhibit ordered patterns. We have characterized these patterns and the specific networks responsible for them. The models allow to (i) compare diffusion and direct-contact induction processes as mechanisms of pattern generation; (ii) identify the possible range of behaviour of real gene networks and (iii) suggest causal mechanisms to generate known patterns. The evolutionary implications are discussed.     

Physical forces modulate cell differentiation and proliferation processes

Currently, the predominant hypothesis explains cellular differentiation and behaviour as an essentially genetically driven intracellular process, suggesting a gene‐centrism paradigm. However, although many living species genetic has now been described, there is still a large gap between the genetic information interpretation and cell behaviour prediction. Indeed, the physical mechanisms underlying the cell differentiation and proliferation, which are now known or suspected to guide such as the flow of energy through cells and tissues, have been often overlooked. We thus here propose a complementary conceptual framework towards the development of an energy‐oriented classification of cell properties, that is, a mitochondria‐centrism hypothesis based on physical forces‐driven principles. A literature review on the physical–biological interactions in a number of various biological processes is analysed from the point of view of the fluid and solid mechanics, electricity and thermodynamics. There is consistent evidence that physical forces control cell proliferation and differentiation. We propose that physical forces interfere with the cell metabolism mostly at the level of the mitochondria, which in turn control gene expression. The present perspective points towards a paradigm shift complement in biology.     

A primary cell culture of Drosophila postembryonic larval neuroblasts to study cell cycle and asymmetric division

Drosophila melanogaster is a key model system that has greatly contributed to the advance of developmental biology through its extensive and sophisticated genetics. Nevertheless, only a few in vitro approaches are available in Drosophila to complement genetic studies in order to better elucidate developmental mechanisms at the cellular and molecular level. Here we present a dissociated cell culture system generated from the optic lobes of Drosophila larval brain. This culture system makes it feasible to study the proliferative properties of Drosophila postembryonic Nbs by allowing BrdU pulse and chase assays, as well as detailed immunocytochemical analysis with molecular markers. These immunofluorescence experiments allowed us to conclude that localization of asymmetric cell division markers such as Inscuteable, Miranda, Prospero and Numb is cell autonomous. By time-lapse video recording we have observed interesting cellular features of postembryonic neurogenesis such us the polarized genesis of the neuroblast progeny, the extremely short ganglion mother cell (GMC) cell cycle, and the last division of a neuroblast lineage. The combination of this cell culture system and genetic tools of Drosophila will provide a powerful experimental model for the analysis of cell cycle and asymmetric cell division of neural progenitor cells.     

纤毛及纤毛相关疾病研究进展

纤毛是一种以细胞微管为主形成的突出于细胞表面的结构,分布于哺乳动物体内的大多数细胞。近年来研究发现,很多人类疾病都与纤毛结构、长度的失调相关,所以有关纤毛的研究是目前研究的热点领域。越来越多的证据证明,纤毛除了提供流体推动力参与细胞的运动功能之外,还具有信号传导的功能,在细胞生命活动的各个方面发挥着多种关键作用。它参与调控细胞生理活动、增殖与分化以及动物个体发育。因此,深入地探索纤毛调控机理对基础生物学理论的发展和人类纤毛相关疾病的攻克有重要意义。该文简要介绍了纤毛的结构、组装与解聚的机制、参与信号传导的功能以及纤毛缺陷同人类疾病的关系。     

Cell Differentiation and Organ Initiation at the Shoot Apical Meristem

Plants continuously generate organs at the flanks of their shoot apical meristems (SAMs). The patterns in which these organs are initiated, also called patterns of phyllotaxis, are highly stereotypic and characteristic for a particular species or developmental stage. This stable, predictable behaviour of the meristem has led to the idea that organ initiation must be based on simple and robust mechanisms. This conclusion is less evident, however, if we consider the very dynamic behaviour of the individual cells. How dynamic cellular events are coordinated and how they are linked to the regular patterns of organ initiation is a major issue in plant developmental biology.     

Pathway landscapes and epigenetic regulation in breast cancer and melanoma cell lines

Understanding how developmental systems evolve over time is a key question in stem cell and developmental biology research. However, due to hurdles of existing experimental techniques, our understanding of these systems as a whole remains partial and coarse. In recent years, we have been constructing in-silico models that synthesize experimental knowledge using software engineering tools. Our approach integrates known isolated mechanisms with simplified assumptions where the knowledge is limited. This has proven to be a powerful, yet underutilized, tool to analyze the developmental process. The models provide a means to study development in-silico by altering the model’s specifications, and thereby predict unforeseen phenomena to guide future experimental trials. To date, three organs from diverse evolutionary organisms have been modeled: the mouse pancreas, the C. elegans gonad, and partial rodent brain development. Analysis and execution of the models recapitulated the development of the organs, anticipated known experimental results and gave rise to novel testable predictions. Some of these results had already been validated experimentally. In this paper, I review our efforts in realistic in-silico modeling of stem cell research and developmental biology and discuss achievements and challenges. I envision that in the future, in-silico models as presented in this paper would become a common and useful technique for research in developmental biology and related research fields, particularly regenerative medicine, tissue engineering and cancer therapeutics.