Decoding and recoding plant development

The development of multicellular organisms has been studied for centuries, yet many critical events and mechanisms of regulation remain challenging to observe directly. Early research focused on detailed observational and comparative studies. Molecular biology has generated insights into regulatory mechanisms, but only for a limited number of species. Now, synthetic biology is bringing these two approaches together, and by adding the possibility of sculpting novel morphologies, opening another path to understanding biology. Here, we review a variety of recently invented techniques that use CRISPR/Cas9 and phage integrases to trace the differentiation of cells over various timescales, as well as to decode the molecular states of cells in high spatiotemporal resolution. Most of these tools have been implemented in animals. The time is ripe for plant biologists to adopt and expand these approaches. Here, we describe how these tools could be used to monitor development in diverse plant species, as well as how they could guide efforts to recode programs of interest.

One-sentence summary: Recent advances in tracking cell lineage and molecular states could inspire new strategies to understand and engineer plant development.     

Imaging and modeling growth and morphogenesis in plants

The growth of tissues, organs or organisms derives from the coordinated activities of complex genetic regulatory networks. In addition to its molecular underpinnings, growth also generally involves significant changes in geometry. To fully understand morphogenesis in its molecular and physical contexts the development of an interdisciplinary approach is required associating biology, mathematics, and physics, which held together by computer science. Growth quantitation and digital simulations have been developed to generate and test the plausibilities of complex hypotheses. Increasingly, real-time live imaging protocols are becoming an essential part of this process. In this review, I discuss the evolution of imaging techniques in plant developmental biology and briefly examine the different ways in which these studies have shed light on growth and morphogenesis in plants.     

Key players in regulatory RNA realm of bacteria

Precise regulation of gene expression is crucial for living cells to adapt for survival in diverse environmental conditions. Among the common cellular regulatory mechanisms, RNA-based regulators play a key role in all domains of life. Discovery of regulatory RNAs have made a paradigm shift in molecular biology as many regulatory functions of RNA have been identified beyond its canonical roles as messenger, ribosomal and transfer RNA. In the complex regulatory RNA network, riboswitches, small RNAs, and RNA thermometers can be identified as some of the key players. Herein, we review the discovery, mechanism, and potential therapeutic use of these classes of regulatory RNAs mainly found in bacteria. Being highly adaptive organisms that inhabit a broad range of ecological niches, bacteria have adopted tight and rapid-responding gene regulation mechanisms. This review aims to highlight how bacteria utilize versatile RNA structures and sequences to build a sophisticated gene regulation network.     

园艺作物花青素合成调控研究进展

花青素是一类保护植物免受生物和非生物胁迫的重要次生代谢产物,因其赋予植物丰富的色彩和对人体的保健功能而受到广泛关注。花青素合成调控机理的相关研究是目前园艺作物分子生物学研究的前沿课题,对于园艺作物花青素含量的提高、种质品质的提升等具有重要的意义。结合国内外园艺作物中花青素生物合成调控方面的最新研究进展,介绍了环境因素、酶与激素、DNA甲基化与泛素化和调控基因等对花青素生物合成的作用,以及花青素抵御外界胁迫的功能机制,综述了近年来园艺作物中花青素生物合成调控的研究成果,以期利用基因工程为提升园艺作物的色彩丰富度提供理论参考。     

Biological evolution as an expression of body-plan potentialities.

A growing bulk of recent data from different fields as molecular biology, developmental biology, genetics, paleontology and phylogenetics shows that organisms play a more active role in their evolution than what postulated by the random variation-natural selection paradigm of the neo-Darwinian synthesis. Organisms show during development and morphogenesis autopoietic processes which are related to their body-plan potentialities. These potentialities are expressed through regulatory networks in which a plastic genome participates together with proteins and other substances in an epigenetic space. The epigenetic systems which arise from this interaction may be inherited and then assume a significant role in evolution becoming the source of new acquired characters. The acquisition of new traits through the epigenetic systems is influenced directly by environmental cues. If this process is coherent with the environmental demands it co-operates with natural selection in organism adaptation. An outstanding role in this context may be played by phenotypic plasticity if, as emerges in recent views, it may constitute a general basis for genetic assimilation processes.     

Genetic Causation in Complex Regulatory Systems: An Integrative Dynamic Perspective

The logic of genetic discovery has changed little over time, but the focus of biology is shifting from simple genotype–phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the traditional reductionist view of individual genes as privileged difference-making causes of phenotypes is re-examined. The scope and nature of genetic effects in complex regulatory systems, in which dynamics are driven by regulatory feedback and hierarchical interactions across levels of organization are considered. This review argues that it is appropriate to treat genes as specific actual difference-makers for the molecular regulation of gene expression. However, they are often neither stable, proportional, nor specific as causes of the overall dynamic behavior of regulatory networks. Dynamical models, properly formulated and validated, provide the tools to probe cause-and-effect relationships in complex biological systems, allowing to go beyond the limitations of genetic reductionism to gain an integrative understanding of the causal processes underlying complex phenotypes.     

植物抗冷分子生物学研究进展（综述）

温度是植物生长的必要条件,然而低温却是限制作物生产的重要因素,为此,各国政府及研究部门一直都把植物低温适应性问题作为一个重要的研究课题．按照低温的不同程度,植物的低温伤害可分为冷害（ｃｈｉｌｌｉｎｇ ｉｎｊｕｒｙ;零上低温对植物的伤害）和冻害（ｆｒｅｅｚｉｎｇ ｉｎｊｕｒｙ;零下低温对植物的伤害）两大类。早期关于植物冷害机理和抗冷机理的研究,是从比较冷敏感（ｃｈｉｌｌｉｎｇ－ｓｅｎｓｉｔｉｖｅ）植物和抗冷（ｃｈｉｌｌｉｎｇ－ｉｎｓｅｎｓｉｔｉｖｅ）植物或比较未经冷驯化的植物（ｎｏｎ－ｃｏｌｄ－ａｃ…     

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.     

Nuclear microenvironments and cancer

Nucleic acids and regulatory proteins are architecturally organized in nuclear microenvironments. The compartmentalization of regulatory machinery for gene expression, replication and repair, is obligatory for fidelity of biological control. Perturbations in the organization, assembly and integration of regulatory machinery have been functionally linked to the onset and progression of tumorigenesis. The combined application of cellular, molecular, biochemical and in vivo genetic approaches, together with structural biology, genomics, proteomics and bioinformatics, will likely lead to new approaches in cancer diagnostics and therapy.     

Biological Signal Processing with a Genetic Toggle Switch

Complex gene regulation requires responses that depend not only on the current levels of input signals but also on signals received in the past. In digital electronics, logic circuits with this property are referred to as sequential logic, in contrast to the simpler combinatorial logic without such internal memory. In molecular biology, memory is implemented in various forms such as biochemical modification of proteins or multistable gene circuits, but the design of the regulatory interface, which processes the input signals and the memory content, is often not well understood. Here, we explore design constraints for such regulatory interfaces using coarse-grained nonlinear models and stochastic simulations of detailed biochemical reaction networks. We test different designs for biological analogs of the most versatile memory element in digital electronics, the JK-latch. Our analysis shows that simple protein-protein interactions and protein-DNA binding are sufficient, in principle, to implement genetic circuits with the capabilities of a JK-latch. However, it also exposes fundamental limitations to its reliability, due to the fact that biological signal processing is asynchronous, in contrast to most digital electronics systems that feature a central clock to orchestrate the timing of all operations. We describe a seemingly natural way to improve the reliability by invoking the master-slave concept from digital electronics design. This concept could be useful to interpret the design of natural regulatory circuits, and for the design of synthetic biological systems.