An overview of NMR-based metabolomics to identify secondary plant compounds involved in host plant resistance

Secondary metabolites provide a potential source for the generation of host plant resistance and development of biopesticides. This is especially important in view of the rapid and vast spread of agricultural and horticultural pests worldwide. Multiple pests control tactics in the framework of an integrated pest management (IPM) programme are necessary. One important strategy of IPM is the use of chemical host plant resistance. Up to now the study of chemical host plant resistance has, for technical reasons, been restricted to the identification of single compounds applying specific chemical analyses adapted to the compound in question. In biological processes however, usually more than one compound is involved. Metabolomics allows the simultaneous detection of a wide range of compounds, providing an immediate image of the metabolome of a plant. One of the most universally used metabolomic approaches comprises nuclear magnetic resonance spectroscopy (NMR). It has been NMR which has been applied as a proof of principle to show that metabolomics can constitute a major advancement in the study of host plant resistance. Here we give an overview on the application of NMR to identify candidate compounds for host plant resistance. We focus on host plant resistance to western flower thrips (Frankliniella occidentalis) which has been used as a model for different plant species.     

Laser Microdissection (LM): Applications to plant materials

Abstract

In recent years, Laser Microdissection (LM), which has been widely used in animal biology, has been adapted to plant tissues. This short paper focuses on some technical aspects concerning plant sample preparation for LM technology, with particular attention to the application of gene expression and proteomics studies. Examples derived from the use of different LM methods are reported and their applications to plant–microbe interactions are explored.     

One fungus, one name promotes progressive plant pathology

The robust and reliable identification of fungi underpins virtually every element of plant pathology, from disease diagnosis to studies of biology, management/control, quarantine and, even more recently, comparative genomics. Most plant diseases are caused by fungi, typically pleomorphic organisms, for which the taxonomy and, in particular, a dual nomenclature system have frustrated and confused practitioners of plant pathology. The emergence of DNA sequencing has revealed cryptic taxa and revolutionized our understanding of relationships in the fungi. The impacts on plant pathology at every level are already immense and will continue to grow rapidly as new DNA sequencing technologies continue to emerge. DNA sequence comparisons, used to resolve a dual nomenclature problem for the first time only 19 years ago, have made it possible to approach a natural classification for the fungi and to abandon the confusing dual nomenclature system. The journey to a one fungus, one name taxonomic reality has been long and arduous, but its time has come. This will inevitably have a positive impact on plant pathology, plant pathologists and future students of this hugely important discipline on which the world depends for food security and plant health in general. This contemporary review highlights the problems of a dual nomenclature, especially its impact on plant pathogenic fungi, and charts the road to a one fungus, one name system that is rapidly drawing near.     

Plant tissue culture. Biotechnology. Milestones

Summary The progress in the development of the technologies of plant tissue and cell culture over the past four decades has been remarkable. This article covers my personal reflections on the various topics and is based on my involvement in the field during that period. There are three fundamental technologies which constitute most of what is referred to as plant in vitro technologies or tissue culture. The origin and some of the key persons involved in the development of each of these procedures will be discussed. The technology that is most common is growing plant tissue on gel-solidified nutrient media. That technology is being used in the most vital procedures, namely the regeneration of plants from cultured cells. The culture of plant cells in liquid suspension was developed very shortly after that, and has become a very effective technology for plant regeneration by somatic embryogenesis. The method of meristem culture arose out of a need for developing plants that were virus-free. In many species the technique is now being used to produce virus-free crop plants. Another important technology is the culture of anthers and microspores for producing haploid and homozygous plants. Included with plant tissue culture is the development of the plant protoplast and cell fusion technologies for the production of new plant hybrids. The final aspect of the development concerns the integration of tissue culture with molecular genetics, which has developed into the rapidly expanding field of biotechnology.     

How genetic modification of roots affects rhizosphere processes and plant performance

Genetic modification of plants has become common practice. However, root-specific genetic modifications have only recently been advocated. Here, a review is presented regarding how root-specific modifications can have both plant internal and rhizosphere-mediated effects on aboveground plant properties and plant performance. Plant internal effects refer to pleiotropic processes such as transportation of the modified gene product. Rhizosphere-mediated effects refer to altered plant-rhizosphere interactions, which subsequently feed back to the plant. Such plant-soil feedback mechanisms have been demonstrated both in natural systems and in crops. Here how plant internal and rhizosphere-mediated effects could enhance or counteract improvements in plant properties for which the genetic modification was intended is discussed. A literature survey revealed that rice is the most commonly studied crop species in the context of root-specific transgenesis, predominantly in relation to stress tolerance. Phytoremediation, a process in which plants are used to clean up pollutants, is also often an objective when transforming roots. These two examples are used to review potential effects of root genetic modifications on shoots. There are several examples in which root-specific genetic modifications only lead to better plant performance if the genes are specifically expressed in roots. Constitutive expression can even result in modified plants that perform worse than non-modified plants. Rhizosphere effects have rarely been examined, but clearly genetic modification of roots can influence rhizosphere interactions, which in turn can affect shoot properties. Indeed, field studies with root-transformed plants frequently show negative effects on shoots that are not seen in laboratory studies. This might be due to the simplified environments that are used in laboratories which lack the full range of plant-rhizosphere interactions that are present in the field.     

The utility of transposable elements as tools for the isolation of plant genes

Transposable elements are segments of DNA which have the unique capability of being able to excise from one site in the genome and reintegrate into new, different sites elsewhere in the genome. When transposition takes place and integration occurs within a gene locus, mutations are frequently generated producing variegated or recessive phenotypes. This ability of transposable elements to act as mutagenic agents through their association with particular gene sequences has lead to the development of the procedure of transposon tagging or gene tagging in higher plants. Through this technique, transposable elements can be used to clone and isolate genes of interest for which little or nothing is known about the final product (i.e., polypeptide). This offers tremendous potential for the isolation of a variety of agronomically important genes, which are virtually impossible to recover by other currently available gene cloning methodologies. To date, the technique has been used successfully to isolate genes from corn and snapdragon. Using gene transfer technologies, the potential now exists to extend this approach to clone genes from other plant species. Advantages and limitations of transposon tagging for isolating plant genes will be discussed.     

Functional–structural plant models: a growing paradigm for plant studies

A number of research groups in various areas of plant biology as well as computer science and applied mathematics have addressed modelling the spatiotemporal dynamics of growth and development of plants. This has resulted in development of functional–structural plant models (FSPMs). In FSPMs, the plant structure is always explicitly represented in terms of a network of elementary units. In this respect, FSPMs are different from more abstract models in which a simplified representation of the plant structure is frequently used (e.g. spatial density of leaves, total biomass, etc.). This key feature makes it possible to build modular models and creates avenues for efficient exchange of model components and experimental data. They are being used to deal with the complex 3-D structure of plants and to simulate growth and development occurring at spatial scales from cells to forest areas, and temporal scales from seconds to decades and many plant generations. The plant types studied also cover a broad spectrum, from algae to trees. This special issue of Annals of Botany features selected papers on FSPM topics such as models of morphological development, models of physical and biological processes, integrated models predicting dynamics of plants and plant communities, modelling platforms, methods for acquiring the 3-D structures of plants using automated measurements, and practical applications for agronomic purposes.     

Initiation, growth and cryopreservation of plant cell suspension cultures

Methods described in this paper are confined to in vitro dedifferentiated plant cell suspension cultures, which are convenient for the large-scale production of fine chemicals in bioreactors and for the study of cellular and molecular processes, as they offer the advantages of a simplified model system for the study of plants when compared with plants themselves or differentiated plant tissue cultures. The commonly used methods of initiation of a callus from a plant and subsequent steps from callus to cell suspension culture are presented in the protocol. This is followed by three different techniques for subculturing (by weighing cells, pipetting and pouring cell suspension) and four methods for growth measurement (fresh- and dry-weight cells, dissimilation curve and cell volume after sedimentation). The advantages and disadvantages of the methods are discussed. Finally, we provide a two-step (controlled rate) freezing technique also known as the slow (equilibrium) freezing method for long-term storage, which has been applied successfully to a wide range of plant cell suspension cultures.     

Economic plant species associated with prehistoric agriculture in the Maya lowlands

The issue of plant species used by the ancient Maya of the Yucatan region previous to A.D. 900–1,000 has involved a number of types of arguments, 5 of which are identified: ecological speculation, ethnobotany, plant relicts, linguistics/ iconography, and plant remains/fossils. Recent emphasis on uncovering and analyzing plant remains from Maya occupational and agricultural relics demonstrates that direct evidence from archaeological contexts can be obtained. This evidence, including fossil pollen, seeds, and stem and wood fragments, is used to evaluate various issues involving those species proposed to have been used by the Maya. The results support views dealing with the dominance of maize as a staple and the use of squash, agave, cotton, and tree species. Propositions concerning significance of ramón, cacao, root crops, and amaranth are not yet supported by direct evidence.     

Deep insights into the plant proteome by pretreatment with combinatorial hexapeptide ligand libraries

Proteome analyses suffer from the large complexity of even small proteomes. Additionally, in many protein samples a few highly abundant proteins are hindering detailed proteomic studies, since they mask low abundant proteins. Recently, a new technology has emerged, which reduces dynamic range of protein concentrations within a given sample using combinatorial hexapeptide ligand libraries (CPLLs). This technique has been widely used in the microbial, animal and human fields and is now going to enter plant research. It can be a useful tool for fractionation of protein samples and might help to get a deeper insight into specific plant proteomes. In this review we describe the CPLL protein fractionation, summarize its possible applications in the plant field and discuss the limitations of this method.     

Plant peptides and peptidomics

Extracellular plant peptides perform a large variety of functions, including signalling and defence. Intracellular peptides often have physiological functions or may merely be the products of general proteolysis. Plant peptides have been identified and, in part, functionally characterized through biochemical and genetic studies, which are lengthy and in some cases impractical. Peptidomics is a branch of proteomics that has been developed over the last 5 years, and has been used mainly to study neuropeptides in animals and the degradome of proteases. Peptidomics is a fast, efficient methodology that can detect minute and transient amounts of peptides and identify their post-translational modifications. This review describes known plant peptides and introduces the use of peptidomics for the detection of novel plant peptides.     

Molecular approaches for improvement of medicinal and aromatic plants

Medicinal and aromatic plants (MAPs) are important sources for plant secondary metabolites, which are important for human healthcare. Improvement of the yield and quality of these natural plant products through conventional breeding is still a challenge. However, recent advances in plant genomics research has generated knowledge leading to a better understanding of the complex genetics and biochemistry involved in biosynthesis of these plant secondary metabolites. This genomics research also concerned identification and isolation of genes involved in different steps of a number of metabolic pathways. Progress has also been made in the development of functional genomics resources (EST databases and micro-arrays) in several medicinal plant species, which offer new opportunities for improvement of genotypes using perfect markers or genetic transformation. This review article presents an overview of the recent developments and future possibilities in genetics and genomics of MAP species including use of transgenic approach for their improvement.     

Spin-lattice relaxation of water protons in plant and animal cells

NMR-spin echo method has been used to study spin-lattice relaxation time of protons T1 in plant and animal cells ?? muscle tissue of fish, the cells of which unlike plant cells have no developed system of vacuoles, plastids and a solid cell wall. According to the values of T1 time a new NMR parameter K, a coefficient of relaxation effectiveness of a cell structure, has been calculated. This parameter can be used for quantitative characterization of the influence of different cell structures, the tissue water interact with, for a time of spin-lattice relaxation of water protons. It has been ascertained that the values of K coefficient in animal tissue and in storing tissues of some plants differ little; it may be stipulated by permanent transmembrane water exchange which occurs at high rate in the living cell. It has been concluded that there exists a certain similarity between water state in protoplast of plant and animal cells.     

病毒诱导的基因沉默技术及其在植物中的研究进展

病毒诱导的基因沉默(virus-induced gene silencing,VIGS)是近年来发现的一种转录后基因沉默现象,是植物抵抗病毒侵染的一种自然机制。现已被开发为快速鉴定植物基因功能的一种反向遗传学新技术。与传统的植物转基因技术相比,VIGS无需构建转基因植株,而且具有操作简便、获得表型快速等优点,目前已广泛应用于与植物抗病、逆境胁迫、细胞信号转导以及生长发育等相关基因功能的研究。该文就VIGS技术的作用机理、主要操作规程、在植物基因功能研究方面的应用以及存在的问题进行综述。     

Flow cytometry of plant cells with applications in large-scale bioprocessing

In recent years, there has been a significant upsurge in the application of flow cytometry to plant cells and plant cell cultures. As well as a range of uses in plant biology, flow cytometry offers many advantages for monitoring plant cell cultures used in large-scale bioprocessing operations. This review summarizes the current status of the field, concentrating on methods for DNA measurement and multiparameter cell cycle analysis. Techniques for screening and selection of elite cell lines with high productivity of secondary metabolites are also addressed.     

采用稳定同位素技术判定喀斯特地区植物水分来源的挑战与可能应对方案

占全球陆地面积约15%的喀斯特地区,有着不同于绝大多数非喀斯特地区的水文地质结构,使得许多在非喀斯特地区行之有效的研究方法难以直接用于喀斯特地区,而且这种限制在植物水分来源的研究上体现得尤为明显.本文从为什么要在喀斯特地区开展植物水分来源的研究、为什么一定要用稳定同位素的方法、使用该方法在喀斯特地区有何挑战,以及应对这些挑战的可能解决方案是什么等4个方面,综述了喀斯特地区植物水分来源研究普遍关注问题的由来和可能应对方案.文中重点阐述了与其他方法相比,稳定同位素技术在喀斯特地区植物水分来源研究中的优势以及难以完全满足其前提条件的挑战,结合现有相关研究的有益探索,提出在喀斯特地区的研究不必过分追求对各水源在具体深度上的细致划分,从水源特性的角度进行区分是更为适宜的途径.     

Progress and challenges for abiotic stress proteomics of crop plants

Plants are continually challenged to recognize and respond to adverse changes in their environment to avoid detrimental effects on growth and development. Understanding the mechanisms that crop plants employ to resist and tolerate abiotic stress is of considerable interest for designing agriculture breeding strategies to ensure sustainable productivity. The application of proteomics technologies to advance our knowledge in crop plant abiotic stress tolerance has increased dramatically in the past few years as evidenced by the large amount of publications in this area. This is attributed to advances in various technology platforms associated with MS‐based techniques as well as the accessibility of proteomics units to a wider plant research community. This review summarizes the work which has been reported for major crop plants and evaluates the findings in context of the approaches that are widely employed with the aim to encourage broadening the strategies used to increase coverage of the proteome     

FQA:一种基于物种保守性的植物区系质量评价方法

植物区系质量评价法(FQA)是一种利用植物物种对特定生境的保守性和植物群落的物种丰富度快速评估栖息地质量的方法.基于样方物种组成和专家赋值的植物物种保守系数,运用简单的公式即可计算出样方的植物区系质量指数(FQI).该指数能够反映植被的完整性和退化程度,可以用于对栖息地质量进行时空对比,已经在美国、加拿大等十余个国家广泛应用.本文介绍该方法的原理、计算公式和应用案例,为生态管理工作者和研究人员提供一种简单、可重复、可对比的生境质量评估工具.