Recent advances in mammalian reproductive biology

Reproductive biology is a uniquely important topic since it is about germ cells, which are central for transmitting genetic information from generation to generation. In this review, we discuss recent advances in mammalian germ cell development,including preimplantation development, fetal germ cell development and postnatal development of oocytes and sperm. We also discuss the etiologies of female and male infertility and describe the emerging technologies for studying reproductive biology such as gene editing and single-cell technologies.     

Cell biology solves mysteries of reproduction

Reproduction and fertility have been objects of keen inquiry since the dawn of humanity. Medieval anatomists provided the first accurate depictions of the female reproductive system, and early microscopists were fascinated by the magnified sight of sperm cells. Initial successes were achieved in the in vitro fertilization of frogs and the artificial insemination of dogs. Gamete and embryo research was in the cradle of modern cell biology, providing the first evidence of the multi-cellular composition of living beings and pointing out the importance of chromosomes for heredity. In the 20th century, reproductive research paved the way for the study of the cytoskeleton, cell signaling, and the cell cycle. In the last three decades, the advent of reproductive cell biology has brought us human in vitro fertilization, animal cloning, and human and animal embryonic stem cells. It has contributed to the development of transgenesis, proteomics, genomics, and epigenetics. This Special Issue represents a sample of the various areas of reproductive biology, with emphasis on molecular and cell biological aspects. Advances in spermatology, ovarian function, fertilization, and maternal-fetal interactions are discussed within the framework of fertility and diseases such as endometriosis and diabetes.     

现代生物学对药物发现的影响

随着后基因组时代的到来,药物发现研究领域不断涌现出一系列新思路、新技术、新方法,从而迅速推进药物发现的多元化发展。一方面,基因组学、蛋白质组学、转录组学、代谢组学、生物信息学、系统生物学等新兴学科的崛起与发展,为药物发现提供更为广泛而深刻的理论基础;另一方面,计算机辅助药物设计、高通量筛选、高内涵筛选、生物芯片、转基因和RNA干扰等高新技术的发展和完善,为药物发现提供了新的技术手段和有力工具,极大地拓宽了药物发现的途径。本文结合近年来现代生物学的研究进展,综述现代生物学对药物发现过程的影响。     

Applying modelling experiences from the past to shape crop systems biology: the need to converge crop physiology and functional genomics

Functional genomics has been driven greatly by emerging experimental technologies. Its development as a scientific discipline will be enhanced by systems biology, which generates novel, quantitative hypotheses via modelling. However, in order to better assist crop improvement, the impact of developing functional genomics needs to be assessed at the crop level, given a projected diminishing effect of genetic alteration on phenotypes from the molecule to crop levels. This review illustrates a recently proposed research field, crop systems biology, which is located at the crossroads of crop physiology and functional genomics, and intends to promote communications between the two. Past experiences with modelling whole-crop physiology indicate that the layered structure of biological systems should be taken into account. Moreover, modelling not only plays a role in data synthesis and quantitative prediction, but certainly also in heuristics and system design. These roles of modelling can be applied to crop systems biology to enhance its contribution to our understanding of complex crop phenotypes and subsequently to crop improvement. The success of crop systems biology needs commitments from scientists along the entire knowledge chain of plant biology, from molecule or gene to crop and agro-ecosystem.     

Research on orchid biology and biotechnology

Orchidaceae constitute one of the largest families of angiosperms. They are one of the most ecological and evolutionary significant plants and have successfully colonized almost every habitat on earth. Because of the significance of plant biology, market needs and the current level of breeding technologies, basic research into orchid biology and the application of biotechnology in the orchid industry are continually endearing scientists to orchids in Taiwan. In this introductory review, we give an overview of the research activities in orchid biology and biotechnology, including the status of genomics, transformation technology, flowering regulation, molecular regulatory mechanisms of floral development, scent production and color presentation. This information will provide a broad scope for study of orchid biology and serve as a starting point for uncovering the mysteries of orchid evolution.     

基因组装技术在合成生物学中的应用

基因组装技术是合成生物学领域近年来发展起来的新型技术。它基于大规模基因组数据分析,发现新型的或隐藏的生物活性物质合成基因簇。利用基因组装技术,可提高或激活沉默的生物合成基因簇在微生物中的表达,从而合成潜在的、有价值的生物活性物质。本文旨在阐明最新的体内和体外基因组装技术的设计原理、关键策略及其应用。基因组装技术是合成生物学、代谢工程和功能基因组学研究的重要工具,对生物活性物质的高效生产及合成具有重要意义。     

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.     

ZFIQ: a software package for zebrafish biology

Rapid development, transparency and small size are the outstanding features of zebrafish that make it as an increasingly important vertebrate system for developmental biology, functional genomics, disease modeling and drug discovery. Zebrafish has been regarded as ideal animal specie for studying the relationship between genotype and phenotype, for pathway analysis and systems biology. However, the tremendous amount of data generated from large numbers of embryos has led to the bottleneck of data analysis and modeling. The zebrafish image quantitator (ZFIQ) software provides streamlined data processing and analysis capability for developmental biology and disease modeling using zebrafish model. AVAILABILITY: ZFIQ is available for download at http://www.cbi-platform.net.     

Fundamental issues in systems biology

In the context of scientists' reflections on genomics, we examine some fundamental issues in the emerging postgenomic discipline of systems biology. Systems biology is best understood as consisting of two streams. One, which we shall call 'pragmatic systems biology', emphasises large-scale molecular interactions; the other, which we shall refer to as 'systems-theoretic biology', emphasises system principles. Both are committed to mathematical modelling, and both lack a clear account of what biological systems are. We discuss the underlying issues in identifying systems and how causality operates at different levels of organisation. We suggest that resolving such basic problems is a key task for successful systems biology, and that philosophers could contribute to its realisation. We conclude with an argument for more sociologically informed collaboration between scientists and philosophers.     

Bovine embryo technologies

Embryo technologies are a combination of assisted reproduction, cellular and molecular biology and genomic techniques. Their classical use in animal breeding has been to increase the number of superior genotypes but with advancement in biotechnology and genomics they have become a tool for transgenesis and genotyping. Multiple ovulation and embryo transfer (MOET) has been well established for many years and still accounts for the majority of the embryos produced worldwide. However, no progress has been made in the last 20 years to increase the number of transferable embryos and to reduce the side effects on the reproductive performance of the donors. In vitro embryo production (IVP) is a newer and more flexible approach, although it is technically more demanding and requires specific laboratory expertise and equipment that are most important for the quality of the embryos produced. Somatic cell cloning is a rapidly developing area and a very valuable technique to copy superior genotypes and to produce or copy transgenic animals. More knowledge in oocyte and embryo biology is expected to shed new light on the early developmental events, including epigenetic changes and their long lasting effect on the newborn.Embryo technologies are here to stay and their use will increase as advances in the understanding of the mechanisms governing basic biological processes are made.     

Lignin valorization meets synthetic biology

Lignin, an abundant renewable resource in nature, is a highly heterogeneous biopolymer consisting of phenylpropanoid units. It is essential for sustainable utilization of biomass to convert lignin to value‐added products. However, there are technical obstacles for lignin valorization due to intrinsic heterogeneity. The emerging of synthetic biology technologies brings new opportunities for lignin breakdown and utilization. In this review, we discussed the applications of synthetic biology on lignin conversion, especially the production of value‐added products, such as aromatic chemicals, ring‐cleaved chemicals from lignin‐derived aromatics and bio‐active substances. Synthetic biology will offer new potential strategies for lignin valorization by optimizing lignin degradation enzymes, building novel artificial converting pathways, and improving the chassis of model microorganisms.     

Understanding bone cell biology requires an integrated approach: Reliable opportunities to study osteoclast biology in vivo

The relative simplicity of all in vitro methods to study bone cell biology will at best result in oversimplification of the development and functional capacity of the skeleton in vivo. We have shown this to be true for selected aspects of bone cell biology, but numerous other examples are available. One alternative is to undertake skeletal research in vivo. It is important that those in bone research be willing to move increasingly in this direction not only to understand the true complexitities of skeletal versatility, but also to avoid repetition and perpetuation of erroneous or irrelevant conclusions which waste resources. Toward this end we have described two situations, osteopetrosis and tooth eruption, in which reproducible abrogations or local activations of bone resorption can be examined in vivo. The application of emerging molecular and morphological techniques that permit the subcellular dissection of metabolic pathways and their precise cellular localization, such as a combination of the variety of in situ hybridzation technologies with PCR, antisense probes, and antibody blockase, will allow the investigator greater control of variables in vivo. We expect that these technologies, largely worked out in vitro, combined with highly selected, appropriate models, as we have oulined here for osteoclast biology worked out in vitro, combined with highly selected, appropriate models, as we have ourlined here for osteoclast biology, will make research in vivo less intimidating and increase the frequency with which the real biology is studied directly.     

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

The Functional Genomics Experiment data model (FuGE) has been developed to facilitate convergence of data standards for high-throughput, comprehensive analyses in biology. FuGE models the components of an experimental activity that are common across different technologies, including protocols, samples and data. FuGE provides a foundation for describing entire laboratory workflows and for the development of new data formats. The Microarray Gene Expression Data society and the Proteomics Standards Initiative have committed to using FuGE as the basis for defining their respective standards, and other standards groups, including the Metabolomics Standards Initiative, are evaluating FuGE in their development efforts. Adoption of FuGE by multiple standards bodies will enable uniform reporting of common parts of functional genomics workflows, simplify data-integration efforts and ease the burden on researchers seeking to fulfill multiple minimum reporting requirements. Such advances are important for transparent data management and mining in functional genomics and systems biology.     

Models for synthetic biology

Synthetic biological engineering is emerging from biology as a distinct discipline based on quantification. The technologies propelling synthetic biology are not new, nor is the concept of designing novel biological molecules. What is new is the emphasis on system behavior.     

A special issue on ＂Plant Molecular Biology＂

The use of molecular biology and genomics tools in plant biology research has greatly expanded our understandingof the molecular mechanisms that underlie plant development and physiology.The successful establishment of researchresources such as mutant populations has led to progress in a variety of fields,including plant reproductive develop-ment,signal transduction,hormone functions,defense responses and epigenetic control.In the future these advanceswill potentially facilitate crop improvement through molecular breeding.