Embryogenomics: developmental biology meets genomics

Fundamental questions in developmental biology are: what genes are expressed, where and when they are expressed, what is the level of expression and how are these programs changed by the functional and structural alteration of genes? These questions have been addressed by studying one gene at a time, but a new research field that handles many genes in parallel is emerging. The methodology is at the interface of large-scale genomics approaches and developmental biology. Genomics needs developmental biology because one of the goals of genomics – collection and analysis of all genes in an organism – cannot be completed without working on embryonic tissues in which many genes are uniquely expressed. However, developmental biology needs genomics – the high-throughput approaches of genomics generate information about genes and pathways that can give an integrated view of complex processes. This article discusses these new approaches and their applications to mammalian developmental biology.     

The long reach of philosophy of biology

The Oxford Handbook of Philosophy of Biology covers a broad range of topics in this field. It is not just a textbook focusing on evolutionary theory but encompasses ethics, social science and behaviour too. This essay outlines the scope of the work, discusses some points on methodology in the philosophy of biology, and then moves on to a more detailed analysis of cultural evolution and the applicability of a philosophy of biology toolkit to the social sciences. It is noted that concepts like the species concept may generalise to other domains whilst failing to account for the nature of all species. Finally, the author notes the omission of any discussion of information in biology.     

Boris Balinsky: transition from embryology to developmental biology

This is the story of a textbook that students of developmental biology have used for 45 years. "An Introduction to Embryology" was released soon after a role for genes in the control of development became finally recognized but not yet well documented. Thus this book manifested the transition from embryology to developmental biology. The story of its author, Boris Balinsky, who against all odds survived to write this book, is remarkable on its own. He started his scientific career in the USSR, but due to 20th century social and political upheavals, ended it in South Africa. This article will shed light on the life of Boris Balinsky, a scientist and writer and will explore the origins of his book.     

医学院校中生物化学与分子生物学实验课教学的改革实践

为进一步提高生物化学与分子生物学实验课的教学质量,培养学生的综合素质和创新能力,在生物化学与分子生物学实验教学中开展了一系列改革,取得了很好的效果。对改革教学法、丰富教学内容、编订新教材、开放实验室及建立完善综合考核制度等方面改革的必要性及近年来在这些方面实施改革的特色性进行总结,为医学院校实验课教学提供参考。     

文昌鱼特异的基因倍增

进化生物学和发育生物学的结合产生了一门新兴学科——进化发育生物学,近年来该领域研究取得了丰硕的成果。头索动物文昌鱼是现存生物中最近似于脊椎动物直接祖先的生物,在与脊椎动物分化后形态改变很小,其基因组未曾经历大规模的基因组倍增,在一定程度上反映了脊椎动物祖先型基因组的特征,但在漫长的独立进化历程中基因组自身还是经历了一些变化。本文介绍了在几例在文昌鱼支系中独立发生的基因倍增事件(Hox; Evx; HNF-3; Calmodulin-like),有力地揭示了文昌鱼虽然与脊椎动物直接祖先极其接近,但其基因组有其自身特性,不能简单地将之等同于脊椎动物直接祖先。Abstract: The union of the two complementary disciplines, developmental biology and evolutionary biology resulted in a new division of evolutionary developmental biology, namely “Evo-Devo”. Recently, the research on this field has been fruitful in understanding the origin and development of vertebrates. The cephalochordate amphioxus, which remains in relatively invariant morphology since the divergence from the vertebrate lineage, is the closest living relative to vertebrates. The vertebrate-like simple body plan and preduplicative genome provide amphioxus genes the privilege to serve as key landmark to understand morphological evolution. However, the amphioxus genome has not escaped evolution. In this paper several examples of independent gene (Hox; Evx; HNF-3 and Calmodulin-like) duplications in the cephalochordate lineage were summarized. These particularities and oddities remind the fact that amphioxus is not an immediate ancestor of the vertebrates but ‘only’ the closest living relative to the ancestor, with a mix of prototypical and amphioxus-specific features in its genome.     

Using models to enhance the intellectual content of learning in developmental biology

Models have been particularly useful in developmental biology over the last 30 years. At first, underlying control mechanisms were poorly understood, but over time a wealth of detailed information became available to provide an increasingly detailed knowledge of underlying mechanisms, at levels from genes through cells to organs, organisms and populations. Models are also of great value in teaching developmental biology, as they allow students to explore phenomena hard to perceive directly because of their scale, accessibility, expense or other considerations. A model may allow students to "experiment" in ways which would be impractical in real life, as well as give them a deep understanding of competing hypotheses of development. Lastly, students can be challenged to produce models of their own, whereas only rarely are they able to carry out original experiments. I discuss two main kinds of models and their uses in generating, testing and expounding hypotheses and point out dangers in the use of models in education. Models may draw upon and reflect the consensus paradigm in the field: a researcher may be able to appreciate that models are interim conditional statements of probability and use them to generate new knowledge. A student may be less able to do so and may fail to appreciate where new knowledge will come from. And unlike physics, biology is stochastic and contingent and can never be entirely deduced from first principles, implying that models can never be as perfect in any biological field as they can be in some other fields.     

面向中学生物教育的高师遗传学教学改革

遗传学知识,在中学生物教学中占有较大比重,随着中学新课改的实施,生物教材在教学内容上也有了一些变化。为使高师院校的遗传学教学适应中学生物教学的需要以及高师院校对师范生的培养要求,作者对遗传学教学内容进行了改革,使其与中学生物教学内容和特点紧密结合,同时在遗传学教学中渗透了对学生生物教学技能的培养。     

Theoretical models for branch formation in plants

Various branch architectures are observed in living organisms including plants. Branch formation has traditionally been an area of interest in the field of developmental biology, and theoretical approaches are now commonly used to understand the complex mechanisms involved. In this review article, we provide an overview of theoretical approaches including mathematical models and computer simulations for studying plant branch formation. These approaches cover a wide range of topics. In particular, we focus on the importance of positional information in branch formation, which has been especially revealed by theoretical research in plants including computations of developmental processes.

     

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。     

Book review of evolutionary genetics: Concepts,analysis, and practice

Recent technological advances have expanded and increased the resolution of studies in evolutionary biology, creating a need for a modern textbook that highlights the latest developments in the field. Evolutionary Genetics: Concepts, Analysis, and Practice, by Glenn‐Peter Sætre and Mark Ravinet (2019), as well as the book's accompanying online tutorials, provide a clear, up‐to‐date, and enjoyable introduction to evolutionary biology and genetics that explains fundamental evolutionary concepts, illustrates recent exciting findings, and offers hands‐on experience in analysing and interpreting genomic data. The book's accessible nature and emphasis on developing practical skills make it a valuable resource for undergraduate courses on evolutionary biology.     

Evolutionary developmental biology its roots and characteristics

The rise of evolutionary developmental biology was not the progressive isolation and characterization of developmental genes and gene networks. Many obstacles had to be overcome: the idea that all genes were more or less involved in development; the evidence that developmental processes in insects had nothing in common with those of vertebrates.Different lines of research converged toward the creation of evolutionary developmental biology, giving this field of research its present heterogeneity. This does not prevent all those working in the field from sharing the conviction that a precise characterization of evolutionary variations is required to fully understand the evolutionary process.Some evolutionary developmental biologists directly challenge the Modern Synthesis. I propose some ways to reconcile these apparently opposed visions of evolution. The turbulence seen in evolutionary developmental biology reflects the present entry of history into biology.     

Synthetic spatial patterning in bacteria: advances based on novel diffusible signals

Engineering multicellular patterning may help in the understanding of some fundamental laws of pattern formation and thus may contribute to the field of developmental biology. Furthermore, advanced spatial control over gene expression may revolutionize fields such as medicine, through organoid or tissue engineering. To date, foundational advances in spatial synthetic biology have often been made in prokaryotes, using artificial gene circuits. In this review, engineered patterns are classified into four levels of increasing complexity, ranging from spatial systems with no diffusible signals to systems with complex multi-diffusor interactions. This classification highlights how the field was held back by a lack of diffusible components. Consequently, we provide a summary of both previously characterized and some new potential candidate small-molecule signals that can regulate gene expression in Escherichia coli. These diffusive signals will help synthetic biologists to successfully engineer increasingly intricate, robust and tuneable spatial structures.     

Modeling new conceptual interpretations of development

In April 2011, researchers from diverse background met at the Gulbenkian Institute (Oeiras, Portugal) to discuss the emerging input of biophysics into the field of developmental biology. The scope of the workshop was to bring together scientists working in different model systems and to discuss some of the most recent advances towards understanding how physical forces affect embryonic development. Discussions and talks highlighted two main trends: that many aspects of embryogenesis can be accurately quantified and translated into a limited number of physical forces and biochemical parameters; and that simulations and modeling provide new conceptual interpretations of classical developmental questions.     

Mouse models and the evolutionary developmental biology of the skull

Understanding development is relevant to understanding evolutionbecause developmental processes structure the expression ofphenotypic variation upon which natural selection acts. Advancesin developmental biology are fueling a new synthesis of developmentaland evolutionary biology, but it remains unclear how to usedevelopmental information that largely derives from a few modelorganisms to test hypotheses about the evolutionary developmentalbiology of taxa such as humans and other primates that havenot been or are not amenable to direct study through experimentaldevelopmental biology. In this article, we discuss how and whenmodel organisms like mice are useful for studying the evolutionarydevelopmental biology of even rather distantly related and morphologicallydifferent groups like primates. A productive approach is tofocus on processes that are likely to play key roles in producingevolutionarily significant phenotypic variation across a largephylogenetic range. We illustrate this approach by applyingthe analysis of craniofacial variation in mouse mutant modelsto primate and human evolution.     

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.     

Evolution of animal body plans: the role of metazoan phylogeny at the interface between pattern and process

SUMMARY Comprehensive integrative studies are the hallmark of evolutionary developmental biology. A properly defined phylogenetic framework takes a central place in such analyses as the meeting ground for observation and inference. Molecular phylogenies take this place in many current studies on animal body plan evolution. In particular, 18S rRNA/DNA sequence analyses have yielded a new view of animal evolution that is often contrasted with a presumed traditional or classical view. First, I expose this traditional view to be a simplified historical abstraction that became textbook dogma. Second, I discuss how two recent important studies of animal body plan evolution, examining the evolution of the platyhelminth body plan and the evolutionary significance of indirect development and set-aside cells, have actively incorporated two problematic aspects of the newly emerging molecular view of animal evolution: incomplete and unresolved phylogenies.     

Homology in comparative, molecular, and evolutionary developmental biology: the radiation of a concept

The present paper analyzes the use and understanding of the homology concept across different biological disciplines. It is argued that in its history, the homology concept underwent a sort of adaptive radiation. Once it migrated from comparative anatomy into new biological fields, the homology concept changed in accordance with the theoretical aims and interests of these disciplines. The paper gives a case study of the theoretical role that homology plays in comparative and evolutionary biology, in molecular biology, and in evolutionary developmental biology. It is shown that the concept or variant of homology preferred by a particular biological field is used to bring about items of biological knowledge that are characteristic for this field. A particular branch of biology uses its homology concept to pursue its specific theoretical goals.