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Erasmus Darwin loved seeing, touching, smelling, using, studying and celebrating plants and wanted others to share in his enjoyment, from members of his family to his patients, who utilised their virtues or powers as drugs to combat their illnesses and improve their lives. In Phytologia, his treatise upon agriculture and gardening, he exclaimed that ‘the beautiful colours of the petals of flowers with their polished surfaces’ were ‘scarcely rivalled’ by those of shells, feathers or ‘precious stones’. Many of these ‘transient beauties’ that gave such ‘brilliancy to our gardens’ delighted ‘the sense of smell with their odours’ and were employed extensively ‘as articles either of diet, medicine, or the arts’. Knowledge of plants was always important for Darwin, given that vegetable products were the basis of so much of the materia medica (substances prescribed as treatments), and botany was taught in the medical schools in order that practitioners could distinguish useful from useless or even dangerous plants.
During the 1770s and 1780s, however, botany and gardening assumed greater significance in Darwin’s life, encouraged by a community of plant enthusiasts and what Sylvia Bowerbank has described as literary ‘defenders’ of ‘environmental stewardship’ who were centred upon Lichfield and invested it with ‘deep feeling and value’ as a multilayered ‘storied place’. Among them were the poet Anna Seward, Rev. John Saville (1736–1803), Darwin’s future wife Elizabeth Pole and the members of the botanical society that Darwin formed, as noted above, with Brooke Boothby and William Jackson (1743/5–1798), who were engaged upon a project to translate some of the works of Carl Linnaeus (1707–1778) from Latin into English. Encouraged by his medical and scientific botanical concerns, his growing love of gardening and his experience of the countryside around Lichfield and the local coterie of plant lovers, Darwin developed a botanic garden in a small well-watered valley near the city, which inspired the two parts of his epic poem The Botanic Garden (1791). The formation of the Lichfield botanical garden was a crucial moment in both Darwin and Seward’s poetical careers. Through the success of the Botanic Garden, which, as the poet Samuel Taylor Coleridge (1772–1834) remarked, was ‘for some years greatly extolled, not only by the reading public in general’ but by poets of his generation, Darwin’s Lichfield creation became one of the most influential British botanical gardens.
Erasmus Darwin’s most important contribution to the science of farming was the publication Phytologia, a major treatise on agriculture and gardening that attracted some contemporary praise. More recently, Robert Schofield was puzzled that an ‘elderly, established doctor’ with ‘little public indication of an interest in agriculture’ should have published a treatise on the subject. And while Maureen McNeil argued that Darwin’s inspiration lay primarily in Scottish writings concerning agricultural improvement, the Agricultural Revolution and the ‘scarcity crisis of the 1790s’, along with some aspects of Linnaean botany and the creation of the Lichfield botanic garden, she still found it hard to explain how these provided ‘sufficient stimulus for a six-hundred page treatise on agriculture’. While some interest in the technologies of agricultural improvement and plant physiology were already evident in Darwin’s commonplace book from the 1770s, for McNeil ‘explanations of Darwin’s agrarian interest’ founded only upon his ‘personal situation’ are ‘inadequate’ and she saw ‘no necessary transition’ from prose and poetical ‘nature studies’ to agriculture. His medical interests did not provide a full explanation either, given the small part of agriculture that was devoted to generating ‘tools of medicine’. However, this underestimates the extent to which he mixed with farmers and landowners throughout his career, the extent of his experiences combating animal and plant diseases and the impact of his medical ideas and experiences upon his analyses of agriculture and horticulture.
Darwin was a strong supporter of the Georgian ideology of improvement, which, as Raymond Williams argued, like the notion of ‘cultivation’, contained meanings that were ‘historically linked but in practice so often contradictory’: ‘working agriculture’ existed alongside the costly ‘improvement of houses, parks, artificial landscapes’, interweaving the desire for increased wealth and productivity with landscape aesthetics reinforced by moral judgement. This chapter argues that Darwin’s belief that the sciences and medicine could be used to better harness nature and help realise a more productive countryside is evident in Phytologia, his medical treatise Zoonomia and the references to agriculture and gardening in his poetry and correspondence. McNeil has argued that, as such, his emphasis was on the ‘intellectual, rather than on the manual aspect’ of farming and that he was ‘eager to celebrate’ both agricultural as much as industrial ‘capitalists’ as ‘social heroes’ as well as those who helped encourage farmers to better organise their ‘space, capital and time’.
Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.
The light-induced reorientation of the cortical microtubule array in dark-grown Arabidopsis thaliana hypocotyl cells is a striking example of the dynamical plasticity of the microtubule cytoskeleton. A consensus model, based on katanin-mediated severing at microtubule crossovers, has been developed that successfully describes the onset of the observed switch between a transverse and longitudinal array orientation. However, we currently lack an understanding of why the newly populated longitudinal array direction remains stable for longer times and re-equilibration effects would tend to drive the system back to a mixed orientation state. Using both simulations and analytical calculations, we show that the assumption of a small orientation-dependent shift in microtubule dynamics is sufficient to explain the long-term lock-in of the longitudinal array orientation. Furthermore, we show that the natural alternative hypothesis that there is a selective advantage in severing longitudinal microtubules, is neither necessary nor sufficient to achieve cortical array reorientation, but is able to accelerate this process significantly.
Quantitative approaches in plant biology have a long history that have led to several ground-breaking discoveries and given rise to new principles, new paradigms and new methodologies. We take a short historical trip into the past to explore some of the many great scientists and influences that have led to the development of quantitative plant biology. We have not been constrained by historical fact, although we have tried not to deviate too much. We end with a forward look, expressing our hopes and ambitions for this exciting interdisciplinary field.
Efficient photosynthesis requires a balance of ATP and NADPH production/consumption in chloroplasts, and the exportation of reducing equivalents from chloroplasts is important for balancing stromal ATP/NADPH ratio. Here, we showed that the overexpression of purple acid phosphatase 2 on the outer membranes of chloroplasts and mitochondria can streamline the production and consumption of reducing equivalents in these two organelles, respectively. A higher capacity of consumption of reducing equivalents in mitochondria can indirectly help chloroplasts to balance the ATP/NADPH ratio in stroma and recycle NADP+, the electron acceptors of the linear electron flow (LEF). A higher rate of ATP and NADPH production from the LEF, a higher capacity of carbon fixation by the Calvin–Benson–Bassham (CBB) cycle and a greater consumption of NADH in mitochondria enhance photosynthesis in the chloroplasts, ATP production in the mitochondria and sucrose synthesis in the cytosol and eventually boost plant growth and seed yields in the overexpression lines.
Lateral organs arranged in spiral phyllotaxy are separated by the golden angle, ≈137.5°, leading to chirality: either clockwise or counter-clockwise. In some species, leaves are asymmetric such that they are smaller and curved towards the side ascending the phyllotactic spiral. As such, these asymmetries lead to mirroring of leaf shapes in plants of opposite phyllotactic handedness. Previous reports had suggested that the pin-stripe calathea (Goeppertia ornata) may be exclusively of one phyllotactic direction, counter-clockwise, but had limited sampling to a single population. Here, we use a citizen science approach leveraging a social media poll, internet image searches, in-person verification at nurseries in four countries and digitally-curated, research-grade observations to demonstrate that calatheas (Goeppertia spp.) around the world are biased towards counter-clockwise phyllotaxy. The possibility that this bias is genetic and its implications for models of phyllotaxy that assume handedness is stochastically specified in equal proportions is discussed.
Fruit shape is the result of the interaction between genetic, epigenetic, environmental factors and stochastic processes. As a core biological descriptor both for taxonomy and horticulture, the point at which shape stability is reached becomes paramount in apple cultivar identification, and authentication in commerce. Twelve apple cultivars were sampled at regular intervals from anthesis to harvest over two growing seasons. Linear and geometric morphometrics were analysed to establish if and when shape stabilised and whether fruit asymmetry influenced this. Shape stability was detected in seven cultivars, four asymmetric and three symmetric. The remaining five did not stabilise. Shape stability, as defined here, is cultivar-dependent, and when it occurs, it is late in the growing season. Geometric morphometrics detected stability more readily than linear, especially in symmetric cultivars. Key shape features are important in apple marketing, giving the distinctness and apparent uniformity between cultivars expected at point of sale.
Comparative transcriptomics can be used to translate an understanding of gene regulatory networks from model systems to less studied species. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. We find that different curve registration functions are required for different genes, indicating that there is no single common ‘developmental time’ between Arabidopsis and B. rapa. A detailed comparison between Arabidopsis and B. rapa and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa and highlights the importance of registration methods for the comparison of developmental gene expression data.
Phenotypic diversity of flowering plants stems from common basic features of the plant body pattern with well-defined body axes, organs and tissue organisation. Cell division and cell specification are the two processes that underlie the formation of a body pattern. As plant cells are encased into their cellulosic walls, directional cell division through precise positioning of division plane is crucial for shaping plant morphology. Since many plant cells are pluripotent, their fate establishment is influenced by their cellular environment through cell-to-cell signaling. Recent studies show that apart from biochemical regulation, these two processes are also influenced by cell and tissue morphology and operate under mechanical control. Finding a proper model system that allows dissecting the relationship between these aspects is the key to our understanding of pattern establishment. In this review, we present the Arabidopsis embryo as a simple, yet comprehensive model of pattern formation compatible with high-throughput quantitative assays.
Stem cells give rise to the entirety of cells within an organ. Maintaining stem cell identity and coordinately regulating stem cell divisions is crucial for proper development. In plants, mobile proteins, such as WUSCHEL-RELATED HOMEOBOX 5 (WOX5) and SHORTROOT (SHR), regulate divisions in the root stem cell niche. However, how these proteins coordinately function to establish systemic behaviour is not well understood. We propose a non-cell autonomous role for WOX5 in the cortex endodermis initial (CEI) and identify a regulator, ANGUSTIFOLIA (AN3)/GRF-INTERACTING FACTOR 1, that coordinates CEI divisions. Here, we show with a multi-scale hybrid model integrating ordinary differential equations (ODEs) and agent-based modeling that quiescent center (QC) and CEI divisions have different dynamics. Specifically, by combining continuous models to describe regulatory networks and agent-based rules, we model systemic behaviour, which led us to predict cell-type-specific expression dynamics of SHR, SCARECROW, WOX5, AN3 and CYCLIND6;1, and experimentally validate CEI cell divisions. Conclusively, our results show an interdependency between CEI and QC divisions.
Presenting a global and interdisciplinary approach to plant ecology, this much-awaited new edition of the book Plants and Vegetation integrates classical themes with the latest ideas, models, and data. Keddy draws on extensive teaching experience to bring the field to life, guiding students through essential concepts with numerous real-world examples and full-colour illustrations throughout. The chapters begin by presenting the wider picture of the origin of plants and their impact on the Earth, before exploring the search for global patterns in plants and vegetation. Chapters on resources, stress, competition, herbivory, and mutualism explore causation, and a concluding chapter on conservation addresses the concern that one-third of all plant species are at risk of extinction. The scope of this edition is broadened further by a new chapter on population ecology, along with extensive examples including South African deserts, the Guyana Highlands of South America, Himalayan forests and arctic alpine environments.
For almost a hundred years, the Willie Commelin Scholten laboratory was the hub of phytopathology research in the Netherlands, where generations of students learned the principles of plant pathology. In Splendid Isolation reconstructs the history of this unique institution, from its beginnings as a small private laboratory in the late nineteenth century to its final days as a renowned university research center. This unique volume chronicles how the laboratory's scientific reputation spread far beyond the country's borders as it diagnosed and researched thousands of plant diseases.
Genome editing with the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR associated protein) system allows mutagenesis of a targeted region of the genome using a Cas endonuclease and an artificial guide RNA. Both because of variable efficiency with which such mutations arise and because the repair process produces a spectrum of mutations, one needs to ascertain the genome sequence at the targeted locus for many individuals that have been subjected to mutagenesis. We provide a complete protocol for the generation of amplicons up until the identification of the exact mutations in the targeted region. CRISPR-finder can be used to process thousands of individuals in a single sequencing run. We successfully identified an ISOCHORISMATE SYNTHASE 1 mutant line in which the production of salicylic acid was impaired compared to the wild type, as expected. These features establish CRISPR-finder as a high-throughput, cost-effective and efficient genotyping method of individuals whose genomes have been targeted using the CRISPR/Cas9 system.
Plant shoot gravitropism is a complex phenomenon resulting from gravity sensing, curvature sensing (proprioception), the ability to uphold self-weight and growth. Although recent data analysis and modelling have revealed the detailed morphology of shoot bending, the relative contribution of bending force (derived from the gravi-proprioceptive response) and stretching force (derived from shoot axial growth) behind gravitropism remains poorly understood. To address this gap, we combined morphological data with a theoretical model to analyze shoot bending in wild-type and lazy1-like 1 mutant Arabidopsis thaliana. Using data from actual bending events, we searched for model parameters that minimized discrepancies between the data and mathematical model. The resulting model suggests that both the bending force and the stretching force differ significantly between the wild type and mutant. We discuss the implications of the mechanical forces associated with differential cell growth and present a plausible mechanical explanation of shoot gravitropism.
Attempts to demarcate the two processes of transportation: of inorganic, as well as organic nutrients in plants, dates back to the 17th century. A plant anatomist, Malpighi conducted a experiment in which he separated a ring of bark (phloem) from the wood (xylem) of young stems by detaching the two in the region of vascular cambium - ‘girdling’ or ‘ringing’ (Figure 13.1). Since the xylem remained intact, water and inorganic solutes kept on rising all the way upto the foliar region and the plant remained alive for a few days. However, girdled plants showed swelling of the bark in the area just above the girdle due to accumulation of photo-assimilates flowing downward. The downward stream also consisted of nitrogenous compounds and hormones, which caused cell enlargement above the girdle. Ultimately, the root system was subjected to starvation because of lack of nutrients and the girdled plants died away.
Evidences in Support of Phloem Transport
1. An analysis of phloem exudate obtained by making an incision into the phloem tissue provides evidence, supporting the fact that photoassimilates are translocated through the phloem.
2. Aphid technique: Aphids, constituting groups of small insects, feed on herbaceous plants by inserting a long mouth part (proboscis) deep into individual sieve-tube elements of the phloem. While aphids are feeding, they are anaesthetized with a gentle stream of CO2 and the proboscis is carefully removed with a sharp blade. Meanwhile, the uncontaminated phloem liquid continues to ooze out from the cut proboscis for a long period (Figure 13.2). This demonstrates that phloem sap is under pressure. The aphid technique has proved to be of great use in understanding the mechanism of phloem transport.
3. Radioactive tracers: Evidence is also garnered by employing radioactive elements, specifically 14C on the leaves of herbaceous and woody plants. The radioautographs that follow, reveal that radioactive photoassimilates being transported out from the leaves, are confined to only the phloem tissue.
Composition of the Photoassimilates Translocated in the Phloem
The major component of phloem sap in most of the plants is sucrose. But, a small number of plant families translocate oligosaccharides of the raffinose groups (raffinose, stachyose and verbascose) and sugar alcohols (mannitol and sorbitol).
The use of enzymes by mankind dates back to the Greek civilization, that first used enzymes in the process of fermentation to produce wine. After the discovery of the catalytic process in the early nineteenth century, a Swedish chemist, Brazelius (1836) suggested that the numerous chemical reactions in living organisms might depend upon the presence of catalysts within the tissues. In 1857, Louis Pasteur, a French scientist demonstrated the involvement of ‘living, intact’ yeast cells in the process of alcoholic fermentation and proposed the term ‘ferments’ for these biocatalysts. The term ‘enzyme’ was later coined by Kuhne (1878) for soluble ferment of yeast or bacteria. However, a significant breakthrough in the study of enzymes was made when the Buchner brothers (1897) in Germany accidentally discovered that the ‘squeezed out’ juice from non-living yeast extract when mixed with sugar could bring about fermentation. Yeast juice is now known to be a mixture of at least twelve different catalysts. The name ‘enzyme’ was coined for the postulated catalyst in juice.
The chemical nature of enzyme remained uncertain until Sumner (1926) purified and crystallized first, the enzyme ‘urease’ from Jackbean (Canavalia ensiformis) and further discovered that it was proteinaceous in nature. Thereafter, hundreds of enzymes have been separated in a pure or semi-pure state and all have proved to be proteins except for ribozymes.
Characteristics of Enzyme-catalyzed Reactions
• High rates of reaction: Enzyme-catalyzed reactions have typically 106–1012 times higher rates as compared to uncatalyzed reactions. Most of enzymes have the capability to convert thousands of substrate into product molecules every second.
• High specificity: Enzymes have the capablility to recognize extremely minute and specific differences in substrate as well as product molecules and can even distinguish between mirror images of any molecule (stereoisomers or enantiomers) e.g., D-Galactose and L-Galactose.
• Mild reaction conditions: Enzymatic reactions usually take place at atmospheric pressure, relatively low temperatures and within a narrow range of pH (approximately 7.0) except for certain protein-degrading enzymes in vacuoles which function at pHs near 4.0, or enzymes present in thermophilic bacteria that can survive in hot sulphur springs (at 100 °C).
Under both natural and agricultural situations, plants are often subjected to environmental stresses. Stress plays an important role in determining how soil and climate restrict the distribution of plant species. Stress is usually defined as a disadvantageous impact on the physiology of a plant, induced upon a sudden shift from optimal environmental condition where homeostasis is maintained to suboptimal level which disturbs the initial homeostatic state. In most cases, stress is measured in terms of plant survival, crop productivity or the primary assimilation processes, which are all co-related to overall growth.
Plant stress can be divided into two categories: Abiotic and Biotic.
Abiotic Stress
Plants grow and reproduce in hostile environments containing large numbers of abiotic chemical and physical variables, which differ both with time and geographical location. The primary abiotic environmental parameters that affect plant growth are light, water, carbon dioxide, oxygen, soil nutrient content and availability, temperature, salts, and heavy metals. Fluctuations of these abiotic factors generally have negative biochemical and physiological impact on plants. Being fixed, plants are unable to avoid abiotic stress by simply moving to a more suitable environment. Instead, plants have evolved the ability to compensate for stressful conditions by switching over physiological and developmental processes to maintain growth and reproduction.
Responses to abiotic stress depend on the extremity and time duration of the stress, developmental stage, tissue type and interactions between multiple stresses (Figure 18.1). Experiencing stress typically promotes alterations in gene expression and metabolism, and reactions are frequently centred on altered patterns of secondary metabolites. Plants are complex biological systems comprising of thousands of different genes, proteins, regulatory molecules, signalling agents, and chemical compounds that form hundreds of interlinked pathways and networks. Under normal growing conditions, the different biochemical pathways and signalling networks must act in a coordinated manner to balance environmental inputs with the plant's genetic imperative to grow and reproduce. When exposed to unfavourable environmental conditions, this complex interactive system adjusts homeostatically to minimize the negative impacts of stress and maintain metabolic equilibrium.