Journal of Integrative Plant Biology对标国际著名植物学期刊的卓越之路

【目的】Journal of Integrative Plant Biology(JIPB)通过对标国际著名植物学期刊,探索追赶、超越发展的对策与举措,为我国加快国际一流科技期刊建设提供参考与借鉴。【方法】采用数据比较分析法和案例分析法。利用VOSviewer软件构建关键词共现网络图谱。通过与植物学领域国际著名期刊Journal of Experimental Botany(JXB)对标,分析JIPB与JXB的主要文献计量指标,包括期刊影响因子、总被引频次、国际论文比、期刊引文指标、作者分布、学科辐射范围、年发文量和顶尖论文方面的情况。【结果】JIPB受“中国科技期刊卓越行动计划”(以下简称“卓越计划”)资助以来,通过采取由国内外一线权威科学家深度参与办刊、发表具有原始创新性的重大成果、建立专业的期刊管理体系、提供高效优质的出版服务等一系列举措,追赶并部分超越JXB,建设成效显著。【结论】JIPB在“卓越计划”的资助下,以国际著名植物学期刊为标杆,不断提升学术水平和国际影响力,其国际化发展策略以及办刊实践是建设卓越期刊的有益尝试,探索出一条我国建设国际一流科技期刊的卓越之路。

Application of CRISPR/Cas9 in plant biology

The CRISPR/Cas(clustered regularly interspaced short palindromic repeats/CRISPRassociated proteins) system was first identified in bacteria and archaea and can degrade exogenous substrates. It was developed as a gene editing technology in 2013. Over the subsequent years, it has received extensive attention owing to its easy manipulation, high efficiency, and wide application in gene mutation and transcriptional regulation in mammals and plants. The process of CRISPR/Cas is optimized constantly and its application has also expanded dramatically. Therefore, CRISPR/Cas is considered a revolutionary technology in plant biology. Here, we introduce the mechanism of the type II CRISPR/Cas called CRISPR/Cas9, update its recent advances in various applications in plants, and discuss its future prospects to provide an argument for its use in the study of medicinal plants.

60 Years of Development of the Journal of Integrative Plant Biology

In celebration of JIPB＇s 60th anniversary, this paper summarizes and reviews the development process of the journal. To start, we offer our heartfelt thanks to JIPB＇s pioneer Editors-in-Chief who helped get the journal off the ground and make it successful. Academic achievement is the soul of academic journals, and this paper summarizes JIPB＇s course of academic development by analyzing it in four stages： the first two stages are mostly qualitative analyses, and the latter two stages are dedicated to quantitative analyses. Most-cited papers were statistically analyzed. Improvements in editing, pub- lication, distribution and online accessibility--which are detailed in this paper--contribute to JIPB＇s sustainable development. In addition, JIPB＇s evaluation index and awards are provided with accompany- ing pictures. At the end of the paper, JIPB＇s milestones are listed chronologically. We believe that JIPB＇s development, from a national journal to an international one, parallels the development of the Chinese plant sciences.

The Ever Expanding Role of Ubiquitin and SUMO in Plant Biology

When it was discovered in the 1970s as a ubiquitous protein, ubiquitin, a 76-aminoacid peptide, had no assigned function. It was not until later that ubiquitin was found to be a necessary cofactor in a vital cellular process： the degradation of proteins. Work by Avram Hershko, Aaron Ciechanover, and Irwin Rose （for which they received the 2004 Nobel Prize in Chemistry） showed that the covalent attachment of ubiquitin provide pro-teins with a tag that dispatches them to the proteasome, the main cell degradation machinery （Ciechanover 2012）. Subsequent work, has revealed that ubiquitin belongs to a broader family of ubiquitin-like proteins that can modify not only protein stability, but also subcellular localization and function.

Translational plant biology

The global demand on agricultural products is rapidly expanding because of a growing world population and other factors, such as the increasing consumption of meat and dairy. However, food supply is facing tremendous challenges includ- ing limited arable land, water and fertilizer resources, various biotic and abiotic stresses. To satisfy the demand of food, feed, fiber and other industrial purposes, by 2050 the amount of grain production must be doubled. Due to the limitation of traditional approaches in addressing the global challenge of food security, new tools are required to increase the agricultural productiv- ities. With the advance of genomics in model and crop plants, a number of genes/alleles controlling important agronomic traits have been identified and these discoveries offer new oppor- tunities to increase crop yield, quality and production stability using advanced breeding techniques. Furthermore, new technologies including high throughput DNA sequencing, high-density molecular markers, genome editing and compa- rative genomics speed up the identification of genes/alleles with economical importance. Additionally, the efficient trans- formation methods enable the characterization of predicted orthologs in crop species and translating the fundamental plant research to crops for agricultural improvement.

2nd International Symposium on Integrative Plant Biology

The 2nd International Symposium on August 26-28, 2011. The symposium will provide a Integrative Plant Biology will be held in Lanzhou, China, great occasion for members of the international plant science community, senior scientists as well as students, to meet and to discuss the latest trends and innovations in plant biology. The symposium will cover areas of plant growth and development, sexual reproduction, metabolic regulation, molecular ecology and evolution, and environmental physiology. Following the extremely successful 1st International Symposium on Integrative Plant Biology held 2009 in Yantai, we hope this meeting will provide an even better platform for the participants to communicate new ideas, to discuss new technologies, and to explore future collaborations.

Eigenvalues of Jacobian Matrices Report on Steps of Metabolic Reprogramming in a Complex Plant-Environment Interaction

Mathematical modeling of biochemical systems aims at improving the knowledge about complex regulatory networks. The experimental high-throughput measurement of levels of biochemical components, like metabolites and proteins, has become an integral part for characterization of biological systems. Yet, strategies of mathematical modeling to functionally integrate resulting data sets is still challenging. In plant biology, regulatory strategies that determine the metabolic output of metabolism as a response to changes in environmental conditions are hardly traceable by intuition. Mathematical modeling has been shown to be a promising approach to address such problems of plant-environment interaction promoting the comprehensive understanding of plant biochemistry and physiology. In this context, we recently published an inversely calculated solution for first-order partial derivatives, i.e. the Jacobian matrix, from experimental high-throughput data of a plant biochemical model system. Here, we present a biomathematical strategy, comprising 1) the inverse calculation of a biochemical Jacobian;2) the characterization of the associated eigenvalues and 3) the interpretation of the results with respect to biochemical regulation. Deriving the real parts of eigenvalues provides information about the stability of solutions of inverse calculations. We found that shifts of the eigenvalue real part distributions occur together with metabolic shifts induced by short-term and long-term exposure to low temperature. This indicates the suitability of mathematical Jacobian characterization for recognizing perturbations in the metabolic homeostasis of plant metabolism. Together with our previously published results on inverse Jacobian calculation this represents a comprehensive strategy of mathematical modeling for the analysis of complex biochemical systems and plant-environment interactions from the molecular to the ecosystems level.

From qualitative to quantitative:the state of the art and challenges for plant synthetic biology

Backgrounds:As an increasing number of synthetic switches and circuits have been created for plant systems and of synthetic products produced in plant chassis,plant synthetic biology is taking a strong foothold in agriculture and medicine.The ever-exploding data has also promoted the expansion of toolkits in this field.Genetic parts libraries and quantitative characterization approaches have been developed.However,plant synthetic biology is still in its infancy.The considerations for selecting biological parts to design and construct genetic circuits with predictable functions remain desired.Results:In this article,we review the current biotechnological progresses in field of plant synthetic biology.Assembly standardization and quantitative approaches of genetic parts and genetic circuits are discussed.We also highlight the main challenges in the iterative cycles of design-build-test-learn for introducing novel traits into plants.Conclusion:Plant synthetic biology promises to provide important solutions to many issues in agricultural production,human health care,and environmental sustainability.However,tremendous challenges exist in this field.For example,the quantitative characterization of genetic parts is limited;the orthogonality and the transfer functions of circuits are unpredictable;and also,the mathematical modeling-assisted circuits design still needs to improve predictability and reliability.These challenges are expected to be resolved in the near future as interests in this field are intensifying.

The CRISPR/Cas revolution continues: From efficient gene editing for crop breeding to plant synthetic biology

Since the discovery that nucleases of the bacterial CRISPR(clustered regularly interspaced palindromic repeat)-associated(Cas) system can be used as easily programmable tools for genome engineering,their application massively transformed different areas of plant biology. In this review, we assess the current state of their use for crop breeding to incorporate attractive new agronomical traits into specific cultivars of various crop plants. This can be achieved by the use of Cas9/12 nucleases for double-strand break induction,resulting in mutations by non-homologous recombinatr e-tion. Strategies for performing such experiments à from Rthe design of guide RNA to the use of different transformation technologies à are evaluated. Furtherweive-more, we sum up recent developments regarding the use of nuclease-deficient Cas9/12 proteins, as DNAbinding moieties for targeting different kinds of enzyme activities to specific sites within the genome. Progress in base deamination, transcriptional induction and transcriptional repression, as well as in imaging in plants, is also discussed. As different Cas9/12 enzymes are at hand, the simultaneous application of various enzyme activities, to multiple genomic sites, is now in reach to redirect plant metabolism in a multifunctional manner and pave the way for a new level of plant synthetic biology.

Plant synthetic biology: One answer to global challenges

In times of climate change, population growth and resource depletion, the future well-being of mankind will greatly depend on the ability to breed/engineer crop plants for high yield, low input and high quality.Based on the evaluation of historical yield increases, it seems that yield of major grain crops, such as rice or

Rhizosphere Microbiota and Microbiome of Medicinal Plants: From Molecular Biology to Omics Approaches

The rhizosphere is a narrow region of soil that is directly influenced by roots and associated soil microorganisms. Research on rhizosphere microbes of various medicinal plants is essential for microbial ecology, applied microbiology and industrial biotechnology with regard to the sustainable utilization of Chinese medicinal resources. However, the inability of culturing most rhizosphere microorganisms （around 99%） in the laboratory obviates the research progress. In recent years, there is enormous advances in applying non-culturing techniques based on molecular biology and omics to the study of rhizosphere microbial diversity and plant-microbe interactions. DGGE, T-RFLP, ARDRA, DNA cloning and Sanger sequencing are still useful in the rhizosphere studies, while various omics tools, such as FISH, SIP, microarray, next generation sequencing （NGS）, etc., evolve quickly to provide more comprehensive understanding of the rhizosphere microbiota and microbiome. Flexible applications of NGS technologies are here exemplified, e.g., amplicon sequencing, metagenomic sequencing, whole genome sequencing, and transcriptome sequencing, which address the biology and biotechnology potentials of the rhizosphere microbiome of medicinal plants. This review discusses recent findings and future challenges in the study of rhizosphere microbes, highlighting medicinal plant rhizosphere study, evolution of research methods, and innovative combinations of novel high-throughput techniques. The top-down approaches such as metagenomics and bottom-up approaches targeting individual species or strains should be integrated and combined with modeling approaches to afford a wide-ranging understanding of the microbial community as a whole.

Synthetic biology of plant natural products: From pathway elucidation to engineered biosynthesis in plant cells

Plant natural products(PNPs)are the main sources of drugs,food additives,and new biofuels and have become a hotspot in synthetic biology.In the past two decades,the engineered biosynthesis of many PNPs has been achieved through the construction of microbial cell factories.Alongside the rapid development of plant physiology,genetics,and plant genetic modification techniques,hosts have now expanded from single-celled microbes to complex plant systems.Plant synthetic biology is an emerging field that combines engineering principles with plant biology.In this review,we introduce recent advances in the biosynthetic pathway elucidation of PNPs and summarize the progress of engineered PNP biosynthesis in plant cells.Furthermore,a future vision of plant synthetic biology is proposed.Although we are still a long way from overcoming all the bottlenecks in plant synthetic biology,the ascent of this field is expected to provide a huge opportunity for future agriculture and industry.

Computational Biology Approaches to Plant Metabolism and Photosynthesis:Applications for Corals in Times of Climate Change and Environmental Stress

Knowledge of factors that are important in reef resilience helps us to understand how reef ecosystems react following major anthropogenic and environmental disturbances. The symbiotic relationship between the photosynthetic zooxanthellae algal cells and corals is that the zooxanthellae provide the coral with carbon, while the coral provides protection and access to enough light for the zooxanthellae to photosynthesise. This article reviews some recent advances in computational biology relevant to photosynthetic organisms, including Beyesian approaches to kinetics, computational methods for flux balances in metabolic processes, and determination of clades of zooxanthallae. Application of these systems will be important in the conservation of coral reefs in times of climate change and environmental stress.

Plant Vascular Biology and Agriculture

The evolution of animal and plant vascular systems played a pivotal role in the advancement from simple to complex organisms, through the provision of a delivery system for the distribution of components essential for both metabolism and growth. Interestingly, although these two vascular systems conform to the same general rules of fluid dynamics （Murray 1926; McCulloh et al. 2003）, the developmental mechanisms adopted by plants and animals, to generate these long-distance transport systems,

A brief view of international conference on plant cell wall biology 2017

The triennial International Conference on Plant Cell Wall Biology has been held 5 times since it was initiated in the United States.PCWB2017 for the first time is organized in China.The conference was attended with more than 220 participants and featured with oral and poster presentations,reflecting the contemporary status of plant cell wall studies.

Plant Metabolic Network 15:A resource of genome-wide metabolism databases for 126 plants and algae

To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we generated genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants(https://plantcyc.org).Of these, 104 have not been reported before.We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae,Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell typespecific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.