Performing abstraction: two ways of modelling<Emphasis Type="Italic"> Arabidopsis thaliana</Emphasis>

What is the best way to analyse abstraction in scientific modelling? I propose to focus on abstracting as an epistemic activity, which is achieved in different ways and for different purposes depending on the actual circumstances of modelling and the features of the models in question. This is in contrast to a more conventional use of the term ‘abstract’ as an attribute of models, which I characterise as black-boxing the ways in which abstraction is performed and to which epistemological advantage. I exemplify my claims through a detailed reconstruction of the practices involved in creating two types of models of the flowering plant Arabidopsis thaliana, currently the best-known model organism in plant biology. This leads me to distinguish between two types of abstraction processes: the ‘material abstracting’ required in the production of Arabidopsis specimens and the ‘intellectual abstracting’ characterising the elaboration of visual models of Arabidopsis genomics. Reflecting on the differences between these types of abstracting helps to pin down the epistemic skills and research commitments used by researchers to produce each model, thus clarifying how models are handled by researchers and with which epistemological implications.     

A fortunate choice: the history of Arabidopsis as a model plant

During the past 20 years, the flowering plant Arabidopsis thaliana has been adopted as a model organism by thousands of biologists. This community has developed important tools, resources and experimental approaches that have greatly stimulated plant biological research. Here, we review some of the key events that led to the uptake of Arabidopsis as a model plant and to the growth of the Arabidopsis community.     

Recent Progress in Arabidopsis Research in China： A Preface

In 2002, a workshop on Arabidopsis research in China was held in Shanghai, when a small group of Chinese plant scientists was working on this model species. Since then, we have witnessed the rapid growth of Arabidopsis research in China. This special issue of Journal of Integrative Plant Biology is dedicated exclusively to the Fourth Workshop on Arabidopsis Research in China, scheduled on November 30, 2005, in Beijing. In addition to reports collected in this special issue, the Chinese Arabidopsis community has been able to make significant contributions to many research fields. Here, I briefly summarize recent advances in Arabidopsis research in China.     

The impact of Arabidopsis on human health: diversifying our portfolio

Studies of the model plant Arabidopsis thaliana may seem to have little impact on advances in medical research, yet a survey of the scientific literature shows that this is a misconception. Many discoveries with direct relevance to human health and disease have been elaborated using Arabidopsis, and several processes important to human biology are more easily studied in this versatile model plant.     

Plant genomics takes root, branches out

For the past nine years, an international consortium of researchers have collaborated on a project to provide a full set of genomics tools for the model plant species Arabidopsis thaliana. Among the goals of this project were the complete sequence of the Arabidopsis genome, which may be completed in the year 2000, four years ahead of schedule. Arabidopsis was an appropriate choice as the first target of plant genomics because of its excellent genetics, outstanding research community and small genome size. Until very recently, it appeared that comprehensive high-throughput plant genomics in the public sector would largely begin and end with Arabidopsis. Over the past two years, this situation has changed completely.     

From bench to bountiful harvests: a road map for the next decade of Arabidopsis research

In the face of an increasing world population and climate instability, the demands for food and fuel will continue to rise. Plant science will be crucial to help meet these exponentially increasing requirements for food and fuel supplies. Fundamental plant research will play a major role in providing key advances in our understanding of basic plant processes that can then flow into practical advances through knowledge sharing and collaborations. The model plant Arabidopsis thaliana has played a major role in our understanding of plant biology, and the Arabidopsis community has developed many tools and resources to continue building on this knowledge. Drawing from previous experience of internationally coordinated projects, The international Arabidopsis community, represented by the Multinational Arabidopsis Steering Committee (MASC), has drawn up a road map for the next decade of Arabidopsis research to inform scientists and decision makers on the future foci of Arabidopsis research within the wider plant science landscape. This article provides a summary of the MASC road map.     

拟南芥——一把打开植物生命奥秘大门的钥匙

在过去的20年中,拟南芥作为模式植物广泛用于植物生命科学研究。历时10年的模式植物拟南芥的全基因组测序工作于2000年完成,通过测序获得的拟南芥基因组核苷酸序列全部公布在互联网上,有力地推动了植物生命科学研究向前发展。科学家提出的“2010计划”旨在通过全世界植物科学家的努力,到2010年能够尽可能多地了解拟南芥基因的功能。通过拟南芥研究所获得的信息将有助于人类对控制不同植物复杂生命活动机制的认识。     

Natural variation in innate immunity of a pioneer species

By 2010, we will have detailed knowledge about the genome of Arabidopsis thaliana from a Linnean-like effort by an international research community to identify nearly all of the genes in the species and to classify the products that these genes encode according to a primary function in a generic plant cell. To know the wild species, however, we will require knowledge of which genes provide the raw material for phenotypic variation and natural selection, and consequently affect the adaptability of individual plants and local populations across their geographic range, and ultimately survival of the species. Natural variation in innate immunity will be at the forefront of this exciting research frontier as a model for the molecular ecology of plant-microbe interactions.     

Hydroponics: A Versatile System to Study Nutrient Allocation and Plant Responses to Nutrient Availability and Exposure to Toxic Elements

Hydroponic systems have been utilized as one of the standard methods for plant biology research and are also used in commercial production for several crops, including lettuce and tomato. Within the plant research community, numerous hydroponic systems have been designed to study plant responses to biotic and abiotic stresses. Here we present a hydroponic protocol that can be easily implemented in laboratories interested in pursuing studies on plant mineral nutrition.This protocol describes the hydroponic system set up in detail and the preparation of plant material for successful experiments. Most of the materials described in this protocol can be found outside scientific supply companies, making the set up for hydroponic experiments less expensive and convenient.The use of a hydroponic growth system is most advantageous in situations where the nutrient media need to be well controlled and when intact roots need to be harvested for downstream applications. We also demonstrate how nutrient concentrations can be modified to induce plant responses to both essential nutrients and toxic non-essential elements.     

Mining the plant-herbivore interface with a leafmining Drosophila of Arabidopsis

Experimental infections of Arabidopsis thaliana (Arabidopsis) with genomically characterized plant pathogens such as Pseudomonas syringae have facilitated the dissection of canonical eukaryotic defence pathways and parasite virulence factors. Plants are also attacked by herbivorous insects, and the development of an ecologically relevant genetic model herbivore that feeds on Arabidopsis will enable the parallel dissection of host defence and reciprocal resistance pathways such as those involved in xenobiotic metabolism. An ideal candidate is Scaptomyza flava, a drosophilid fly whose leafmining larvae are true herbivores that can be found in nature feeding on Arabidopsis and other crucifers. Here, we describe the life cycle of S.?flava on Arabidopsis and use multiple approaches to characterize the response of Arabidopsis to S.?flava attack. Oviposition choice tests and growth performance assays on different Arabidopsis ecotypes, defence-related mutants, and hormone and chitin-treated plants revealed significant differences in host preference and variation in larval performance across Arabidopsis accessions. The jasmonate and glucosinolate pathways in Arabidopsis are important in mediating quantitative resistance against S.?flava, and priming with jasmonate or chitin resulted in increased resistance. Expression of xenobiotic detoxification genes was reduced in S.?flava larvae reared on Arabidopsis jasmonate signalling mutants and increased in plants pretreated with chitin. These results and future research directions are discussed in the context of developing a genetic model system to analyse insect-plant interactions.     

An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community

The future bioinformatics needs of the Arabidopsis community as well as those of other scientific communities that depend on Arabidopsis resources were discussed at a pair of recent meetings held by the Multinational Arabidopsis Steering Committee and the North American Arabidopsis Steering Committee. There are extensive tools and resources for information storage, curation, and retrieval of Arabidopsis data that have been developed over recent years primarily through the activities of The Arabidopsis Information Resource, the Nottingham Arabidopsis Stock Centre, and the Arabidopsis Biological Resource Center, among others. However, the rapid expansion in many data types, the international basis of the Arabidopsis community, and changing priorities of the funding agencies all suggest the need for changes in the way informatics infrastructure is developed and maintained. We propose that there is a need for a single core resource that is integrated into a larger international consortium of investigators. We envision this to consist of a distributed system of data, tools, and resources, accessed via a single information portal and funded by a variety of sources, under shared international management of an International Arabidopsis Informatics Consortium (IAIC). This article outlines the proposal for the development, management, operations, and continued funding for the IAIC.The Multinational Arabidopsis Steering Committee (MASC) and the North American Arabidopsis Steering Committee (NAASC) hosted workshops in Nottingham, UK (April 15 to 16, 2010) and Washington DC (May 10 to 11, 2010) to consider the future bioinformatics needs of the Arabidopsis community as well as other science communities that depend vitally on Arabidopsis resources. The outcomes of both workshops were presented and discussed at the International Conference on Arabidopsis Research (ICAR) in Yokohama, Japan. The focus of the workshops was on Arabidopsis because of its unique and essential role as a reference organism for all seed plant species. The development of the highly annotated “gold standard” Arabidopsis genome sequence has been an invaluable resource for plant and crop sciences. This platform provides important information and working practices for other species and for comparative genomic and evolutionary studies. Arabidopsis tools and resources for information storage, curation, and retrieval have been developed over recent years primarily through the activities of The Arabidopsis Information Resource (TAIR), the Nottingham Arabidopsis Stock Centre (NASC), and the Arabidopsis Biological Resource Center, among others. However, the Arabidopsis community and funding agencies recognize the need for a single data management infrastructure. The key challenge is to develop and fund this resource in a sustainable and transparent manner.Global challenges surrounding food and energy security require intelligent plant breeding strategies that will be dependent on a central Arabidopsis information resource to aid our understanding of gene function and associated phenotype in many different environments. The knowledge accrued in Arabidopsis informs our understanding of the genetic basis of plant processes and crop traits. To date, this has accumulated primarily through analysis of single genes. However, gene products do not act alone but rather in complex interacting networks. Thus, the challenge for the Arabidopsis community is to understand this higher level of complexity, to a significant extent through the application of new high volume, quantitative experimental techniques. The goals of these efforts are to develop gene/protein/metabolite networks that will enable systems-level modeling of plant processes and ultimately to translate these findings to crop plants. To achieve these goals, we must develop novel approaches to data management, integration, and access.The UK workshop addressed three principal issues: the types of data generated by the Arabidopsis community, the types of data used by the community, and future needs of the community. The objective was to produce recommendations for the type of infrastructure necessary to address the challenges and opportunities associated with the application of new technologies and recommendations for a sustainable funding model to support this infrastructure. These recommendations were considered and expanded upon at the US workshop with the ultimate goal of generating solutions to the issues discussed in the first meeting. It was recognized that cohesive, cooperative, and long-term international collaboration will be critical to successfully maintain an Arabidopsis database infrastructure that is essential for plant biology research worldwide.The workshop participants concluded that there is a continued need for a central Arabidopsis information resource, based on the productivity of the Arabidopsis community and the critical importance of the findings generated by this community. For example, ∼3000 Arabidopsis publications are currently published in peer-reviewed journals each year, a nearly 10-fold increase since the early 1990s; and in 2009, TAIR was accessed by 335,692 unique visitors and had nearly 20 million page views. Furthermore, the importance of a current, well-organized, and carefully curated Arabidopsis genome to researchers studying other plants, including crops, cannot be overstated. In the future, this resource should be part of a larger infrastructure that would be dynamic and responsive to new directions in plant biology research.     

A liquid chromatography–mass spectrometry platform for the analysis of phyllobilins,the major degradation products of chlorophyll in Arabidopsis thaliana

During senescence, chlorophyll is broken down to a set of structurally similar, but distinct linear tetrapyrrolic compounds termed phyllobilins. Structure identification of phyllobilins from over a dozen plant species revealed that modifications at different peripheral positions may cause complex phyllobilin composition in a given species. For example, in Arabidopsis thaliana wild‐type, eight different phyllobilins have structurally been characterized to date. Accurate phyllobilin identification and quantification, which classically have been performed by high performance liquid chromatography (HPLC) and UV/vis detection, are, however, hampered because of their similar physiochemical properties and vastly differing abundances in plant extracts. Here we established a rapid method for phyllobilin identification and quantification that couples ultra‐HPLC with high‐resolution/high‐precision tandem mass spectrometry. Using Arabidopsis wild‐type and mutant lines that are deficient in specific phyllobilin‐modifying reactions, we identified a total of 16 phyllobilins, among them two that have not been described before in Arabidopsis. The single and collision‐induced dissociation tandem mass spectrometry data of all 16 Arabidopsis phyllobilins were collected in a mass spectrometry library, which is available to the scientific community. The library allows rapid detection and quantification of phyllobilins within and across Arabidopsis genotypes and we demonstrate its potential use for high‐throughput approaches and genome‐wide association studies in chlorophyll breakdown. By extending the library with phyllobilin data from other plant species in the future, we aim providing a tool for chlorophyll metabolite analysis as a measure of senescence for practical applications, such as post‐harvest quality control.     

Plants Replacing Plants: The Future of Community Modeling and Research

Over the past few decades, several conceptual and mathematical models of plant community organization and dynamics have been put forward. While each of these models has attempted to explain important plant community patterns by attributing them to some aspect of plant niches, or to a higher-level process, their predictive success has been very limited. Here I explore why this has happened by reviewing and summarizing each model individually by highlighting the plant community pattern each is trying to explain and predict, by identifying the mechanisms, tolerances, and/or processes authors propose are producing those patterns and describing how they work within the model, and by examining the assumptions of each model. I then discuss common misconceptions and shortcomings among the models, and finally propose a unifying synthesis and comprehensive framework that can serve as a basis for future plant community modeling and research. This synthesis is composed of three key ideas (1) that plant-plant replacements are the “fundamental process” of plant communities which produce every community-level terrestrial plant pattern, (2) that plants respond to mechanisms and tolerances which work both in spaces inside plants and in those spaces outside plants that influence them and/or they may be able to influence, and (3) that those responses make up plant niches which may be able to predict how plants replace themselves over time and space. Consequently I suggest to future field researchers that the best way to understand plant community patterns is to study plant-plant replacements, first by sampling long-term vegetation plots in order to map them, and then by manipulating mechanisms and tolerances in field experiments in order to understand what causes them.     

Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species

Although Arabidopsis is well established as the premiere model species in plant biology, rice (Oryza sativa) is moving up fast as the second-best model organism. In addition to the availability of large sets of genetic, molecular, and genomic resources, two features make rice attractive as a model species: it represents the taxonomically distinct monocots and is a crop species. Plant structural genomics was pioneered on a genome-scale in Arabidopsis and the lessons learned from these efforts were not lost on rice. Indeed, the sequence and annotation of the rice genome has been greatly accelerated by method improvements made in Arabidopsis. For example, the value of full-length cDNA clones and deep expressed sequence tag resources, obtained in Arabidopsis primarily after release of the complete genome, has been recognized by the rice genomics community. For rice >250,000 expressed sequence tags and 28,000 full-length cDNA sequences are available prior to the completion of the genome sequence. With respect to tools for Arabidopsis functional genomics, deep sequence-tagged lines, inexpensive spotted oligonucleotide arrays, and a near-complete whole genome Affymetrix array are publicly available. The development of similar functional genomics resources for rice is in progress that for the most part has been more streamlined based on lessons learned from Arabidopsis. Genomic resource development has been essential to set the stage for hypothesis-driven research, and Arabidopsis continues to provide paradigms for testing in rice to assess function across taxonomic divisions and in a crop species.     

An improved,simple, hydroponic method for growing<Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Arabidopsis thaliana is one os the most studied plant model systems. Completing the genomic sequence ofA. thaliana has provided new opportunities for physiological and biochemical studies. While its small size is advantageous for genetic studies, the plant's low biomass makes it difficult to obtain enough plant material for biochemical and physiological research. The small size and rosette leaf structure, combined with the sensitivity of the apical meristem to flooding, make hydroponic growth of this model plant difficult. A few systems for hydroponic culture ofArabidopsis have been described. Gibeaut et al. (1997) introduced the use of rockwool forArabidopsis hydroponic culture. We have improved this system by introducing small-volume plastic containers with improved plugs to support the rockwool. This method is simpler than the original setup and provides improved germination and growth. The smaller containers enable the use of this system in growth chambers or small growth rooms for a large number of parallel experiments.     

The impact of Arabidopsis research on plant biotechnology

Arabidopsis thaliana, a small annual weed belonging to the mustard family, has become a widely used model in plant genetic research. It has a small genome, short life cycle, and is easy to mutagenize. Identification of genes based on phenotype alone, often a rather difficult part of molecular genetic research, is easiest in this plant. Laboratories working on the "model" plant Arabidopsis thaliana have created a network for sharing resources and ideas, so progress has been rapid. The importance of this plant to biotechnology is that genes isolated from Arabidopsis can be used to find their homologs in crop plants. Likewise, fundamental mechanisms can be understood in a model plant, and applied in crop plants.     

Environmental stress alters native-nonnative relationships at the community scale

The invasion of natural habitats by nonnative species is affected by both native biodiversity and environmental conditions; however few tests of facilitation between native community members and nonnative species have been conducted along disturbance and stress gradients. There is strong evidence for an increase in facilitation between native plant species with increasing levels of natural environmental stress, however it is unknown whether these same positive interactions occur between nonnative invaders and native communities. I investigated the effects of natural stress on community interactions between native heathland species and nonnative species with two field studies conducted at the landscape and community scale. At the landscape scale of investigation, nonnative species richness was positively related to native species richness. At the community level, nonnative invaders experienced facilitation with natives in the most stressful zones, whereas they experienced competition with native plants in the less stressful zones of the heathlands. Due to the observational nature of the landscape scale data, it is unclear whether nonnative diversity levels are responding positively to extrinsic factors or to native biodiversity. The experimental component of this research suggests that native community members may ameliorate stressful environmental conditions and facilitate invasion into high stress areas. I present a conceptual model which is a modification of the Shea and Chesson diversity-invasibility model and includes both facilitation as well as competition between the native community and nonnative invaders at the community level, summing to an overall positive relationship at the landscape scale.     

Re-thinking organisms: The impact of databases on model organism biology

Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards used by the curators of these databases for what counts as reliable evidence, acceptable terminology, appropriate experimental set-ups and adequate materials (e.g., specimens). On the one hand, these choices are informed by the collaborative research ethos characterising most model organism communities. On the other hand, the deployment of these standards in databases reinforces this ethos and gives it concrete and precise instantiations by shaping the skills, practices, values and background knowledge required of the database users. We conclude that the increasing reliance on community databases as vehicles to circulate data is having a major impact on how researchers conduct and communicate their research, which affects how they understand the biology of model organisms and its relation to the biology of other species.