Assessing the evolution of research topics in a biological field using plant science as an example.

Scientific advances due to conceptual or technological innovations can be revealed by examining how research topics have evolved. But such topical evolution is difficult to uncover and quantify because of the large body of literature and the need for expert knowledge in a wide range of areas in a field. Using plant biology as an example, we used machine learning and language models to classify plant science citations into topics representing interconnected, evolving subfields. The changes in prevalence of topical records over the last 50 years reflect shifts in major research trends and recent radiation of new topics, as well as turnover of model species and vastly different plant science research trajectories among countries. Our approaches readily summarize the topical diversity and evolution of a scientific field with hundreds of thousands of relevant papers, and they can be applied broadly to other fields.

Measuring stomatal and guard cell metrics for plant physiology and growth using StoManager1.

Automated guard cell detection and measurement are vital for understanding plant physiological performance and ecological functioning in global water and carbon cycles. Most current methods for measuring guard cells and stomata are laborious, time-consuming, prone to bias, and limited in scale. We developed StoManager1, a high-throughput tool utilizing geometrical, mathematical algorithms, and convolutional neural networks to automatically detect, count, and measure over 30 guard cell and stomatal metrics, including guard cell and stomatal area, length, width, stomatal aperture area/guard cell area, orientation, stomatal evenness, divergence, and aggregation index. Combined with leaf functional traits, some of these StoManager1-measured guard cell and stomatal metrics explained 90% and 82% of tree biomass and intrinsic water use efficiency (iWUE) variances in hardwoods, making them substantial factors in leaf physiology and tree growth. StoManager1 demonstrated exceptional precision and recall (mAP@0.5 over 0.96), effectively capturing diverse stomatal properties across over 100 species. StoManager1 facilitates the automation of measuring leaf stomatal and guard cells, enabling broader exploration of stomatal control in plant growth and adaptation to environmental stress and climate change. This has implications for global gross primary productivity (GPP) modeling and estimation, as integrating stomatal metrics can enhance predictions of plant growth and resource usage worldwide. Easily accessible open-source code and standalone Windows executable applications are available on a GitHub repository (https://github.com/JiaxinWang123/StoManager1) and Zenodo (https://doi.org/10.5281/zenodo.7686022).

Spatial regulation of immunity: unmasking the secrets of abaxial immunity to powdery mildew.

This article comments on: Wu Y, Sexton WK, Zhang Q, Bloodgood D, Wu Y, Hooks C, Coker F, Vasquez A, Wei C-I, Xiao S. 2024. Leaf abaxial immunity to powdery mildew in Arabidopsis is conferred by multiple defense mechanisms. Journal of Experimental Botany 75, 1465-1478.

Botany and geogenomics: Constraining geological hypotheses in the neotropics with large-scale genetic data derived from plants.

Decades of empirical research have revealed how the geological history of our planet shaped plant evolution by establishing well-known patterns (e.g., how mountain uplift resulted in high rates of diversification and replicate radiations in montane plant taxa). This follows a traditional approach where botanical data are interpreted in light of geological events. In this synthesis, I instead describe how by integrating natural history, phylogenetics, and population genetics, botanical research can be applied alongside geology and paleontology to inform our understanding of past geological and climatic processes. This conceptual shift aligns with the goals of the emerging field of geogenomics. In the neotropics, plant geogenomics is a powerful tool for the reciprocal exploration of two long standing questions in biology and geology: how the dynamic landscape of the region came to be and how it shaped the evolution of the richest flora. Current challenges that are specific to analytical approaches for plant geogenomics are discussed. I describe the scale at which various geological questions can be addressed from biological data and what makes some groups of plants excellent model systems for geogenomics research. Although plant geogenomics is discussed with reference to the neotropics, the recommendations given here for approaches to plant geogenomics can and should be expanded to exploring long-standing questions on how the earth evolved with the use of plant DNA.

A Comprehensive Review on Botany, Phytochemistry, Traditional Uses, Pharmacology, Analytical Methods, Processing Methods, Pharmacokinetics and Toxicity of Pulsatilla chinensis.

Objective: To lay the foundation for further research and clinical application of Pulsatilla chinensi (Bge.) Regel (PR). Method: The information presented in this paper is based on scientific databases (such as Baidu Academic, CNKI, Google Academic, PubMed, Science Direct, Web of Science, SciFinder Scholar), traditional Chinese medicine classics, Chinese Pharmacopoeia, doctoral and master's dissertations, etc. Various compounds were identified and isolated through HPLC analysis, including glycosides, polysaccharides, organic acids, phenylpropane, and flavonoids. Results: These compounds have demonstrated a range of pharmacological effects such as anti-cancer, anti-inflammatory, insecticidal, immune-enhancing, antimutagenic, antioxidant, antiviral, antibacterial, hepatoprotective, and antidiarrheal properties. Its chemical composition and pharmacological effects are complex and diverse. Conclusion: There is a need for further studies to investigate its mechanism, potential coordination, and antagonism.

Special Issue "State-of-the-Art Molecular Plant Sciences in Japan".

Food shortages are one of the most serious problems caused by global warming and population growth in this century [...].

Trollius chinensis Bunge: A Comprehensive Review of Research on Botany, Materia Medica, Ethnopharmacological Use, Phytochemistry, Pharmacology, and Quality Control.

Trollius chinensis Bunge, a perennial herb belonging to the Ranunculaceae family, has been extensively used in traditional Chinese medicine. Documented in the Supplements to the Compendium of Materia Medica, its medicinal properties encompass a spectrum of applications, including heat clearance, detoxification, alleviation of oral/throat sores, earaches, eye pain, cold-induced fever, and vision improvement. Furthermore, T. chinensis is used in clinical settings to treat upper respiratory infections, pharyngitis, tonsillitis, esoenteritis, canker, bronchitis, etc. It is mainly used to treat inflammation, such as inflammation of the upper respiratory tract and nasal mucosa. This comprehensive review explores the evolving scientific understanding of T. chinensis, covering facets of botany, materia medica, ethnopharmacological use, phytochemistry, pharmacology, and quality control. In particular, the chemical constituents and pharmacological research are reviewed. Polyphenols, mainly flavonoids and phenolic acids, are highly abundant among T. chinensis and are responsible for antiviral, antimicrobial, and antioxidant activities. The flower additionally harbors trace amounts of volatile oil, polysaccharides, and other bioactive compounds. The active ingredients of the flower have fewer side effects, and it is used in children because of its minimal side effects, which has great research potential. These findings validate the traditional uses of T. chinensis and lay the groundwork for further scientific exploration. The sources utilized in this study encompass Web of Science, Pubmed, CNKI site, classic monographs, Chinese Pharmacopoeia, Chinese Medicine Dictionary, and doctoral and master's theses.

The Study of Geographical Distribution in the Analysis of Domestication as an Evolutionary Process: Tensions in Alphonse de Candolle's Approach.

Interest in the study of domesticated plants increased near the end of the 18th century, mainly because of their economic potential. In the 19th century, there was a new focus on the historical understanding of species, their origin, changes in their distribution, and their evolutionary history. Charles Darwin developed an extended interpretation of species domestication, considering variations, reproduction, inheritance, and modification as standard processes between wild and domesticated organisms. In this context, one relatively neglected aspect was the geographical distribution of domesticated species. Alphonse de Candolle addressed and developed in detail the question of the geographical origin of cultivated plants. Since 1836 Alphonse de Candolle had been studying the topic and obtained evidence that contributed to understanding aspects such as the center of origin, dispersion, competition, selection, and time of domestication. Although Darwin himself admitted that Géographie botanique raisonnée (de Candolle, Alphonse,de. Géographie botanique raisonnée; ou, exposition des faits principaux et des lois concernant la distribution géographique des plantes de l'epoque actuelle, 2ème tome. Paris: Masson.) was of great help to him in the development of his evolutionary theory, the importance of de Candolle's contribution is seldom recognized. Our purpose is to detail the dialogue between Alphonse de Candolle and Darwin on the geography of domesticated plants, to understand some of the most critical discussions that contributed to the reinterpretation of domestication under the Darwinian proposal of modified descent.

Andrographolide, diterpenoid constituent of Andrographis paniculata: Review on botany, phytochemistry, molecular docking analysis, and pharmacology.

Andrographispaniculata (kalmegh) is also known as "king of bitters", is an herbaceous plant belongs to family Acanthaceae. The therapeutic effect is due to presence of diterpenoid lactone derivatives of A. paniculata mainly andrographolide. The main purpose of this review includes detailed (past and present) study of A. paniculata and its most important component andrographolide a diterpenoid lactone with respect to its botany, phytochemistry, molecular docking analysis and pharmacological effects i.e., therapeutic benefits. In reference to the search, we also compiled variety of dosage forms available, which are made up of A. paniculata extract and Andrographolide such as tablets and capsules. This review also discusses reported methods of extraction of phytoconstituents, pharmacokinetics of main components, their molecular docking analysis data and main therapeutic applications with their proposed mechanism of actions in various diseases. According to data collected, A. paniculata is becoming more and more valuable as a therapeutic herb.

REPRISAL: mapping lignification dynamics using chemistry, data segmentation, and ratiometric analysis.

This article describes a methodology for detailed mapping of the lignification capacity of plant cell walls that we have called "REPRISAL" for REPorter Ratiometrics Integrating Segmentation for Analyzing Lignification. REPRISAL consists of the combination of three separate approaches. In the first approach, H*, G*, and S* monolignol chemical reporters, corresponding to p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol, are used to label the growing lignin polymer in a fluorescent triple labeling strategy based on the sequential use of three main bioorthogonal chemical reactions. In the second step, an automatic parametric and/or artificial intelligence segmentation algorithm is developed that assigns fluorescent image pixels to three distinct cell wall zones corresponding to cell corners, compound middle lamella and secondary cell walls. The last step corresponds to the exploitation of a ratiometric approach enabling statistical analyses of differences in monolignol reporter distribution (ratiometric method [RM] 1) and proportions (RM 2) within the different cell wall zones. We first describe the use of this methodology to map developmentally related changes in the lignification capacity of wild-type Arabidopsis (Arabidopsis thaliana) interfascicular fiber cells. We then apply REPRISAL to analyze the Arabidopsis peroxidase (PRX) mutant prx64 and provide further evidence for the implication of the AtPRX64 protein in floral stem lignification. In addition, we also demonstrate the general applicability of REPRISAL by using it to map lignification capacity in poplar (Populus tremula × Populus alba), flax (Linum usitatissimum), and maize (Zea mays). Finally, we show that the methodology can be used to map the incorporation of a fucose reporter into noncellulosic cell wall polymers.

Next generation editors.

The Journal of Experimental Botany is pleased to announce the appointment of six early career researchers as editorial interns: Francesca Bellinazzo (Wageningen University and Research, the Netherlands), Konan Ishida (University of Cambridge, UK), Nishat Shayala Islam (Western University, Ontario, Canada), Chao Su (University of Freiburg, Germany), Catherine Walsh (Lancaster University, UK), and Arpita Yadav (University of Massachusetts Amherst, MA, USA) (Fig. 1). The aim of this programme is to help train the next generation of editors.

Acorus tatarinowii Schott: A Review of Its Botany, Traditional Uses, Phytochemistry, and Pharmacology.

Acorus tatarinowii Schott (A. tatarinowii) is a natural medicinal plant. It plays an indispensable role in the treatment of diseases by the empirical medicine system and has achieved remarkable curative effects. A. tatarinowii is often used to treat various diseases, such as depression, epilepsy, fever, dizziness, heartache, stomachache, etc. More than 160 compounds of different structural types have been identified in A. tatarinowii, including phenylpropanoids, terpenoids, lignans, flavonoids, alkaloids, amides, and organic acids. These bioactive ingredients make A. tatarinowii remarkable for its pharmacological effects, including antidepressant, antiepileptic, anticonvulsant, antianxiety, neuroprotective, antifatigue, and antifungal effects, improving Alzheimer's disease, and so on. It is noteworthy that A. tatarinowii has been widely used in the treatment of brain diseases and nervous system diseases and has achieved satisfactory therapeutic effects. This review focused on the research publications of A. tatarinowii and aimed to summarize the advances in the botany, traditional uses, phytochemistry, and pharmacology, which will provide a reference for further studies and applications of A. tatarinowii.

Decolonizing Botany: Indonesia, UNESCO, and the Making of a Global Science.

Decolonization created new opportunities for international scientific research collaboration. In Indonesia this began in the late 1940s, as Indonesian scientists and officials sought to remake the formerly colonial botanical gardens in the city of Bogor into an international research center. Indonesia sponsored the Flora Malesiana project, a flora of all of island Southeast Asia. This project was formally centered in Bogor, Indonesia, with participation from tropical botanists from around the world. The international orientation of Indonesian science led to the establishment of one of UNESCO's Field Science Co-operation Offices in Jakarta, and to a period of close collaboration between Indonesian botanists and UNESCO. This paper examines the importance of UNESCO's Humid Tropics research program, which initially provided further opportunities for Indonesian botanists to participate in international scientific networks. The paper concludes by showing that the Humid Tropics program led to the slow erosion of Indonesian agency and authority over tropical botany, and the assertion of Western control and management over tropical botany research.

"From the Known to the Unknown:" Nature's Diversity, Materia Medica, and Analogy in 18th Century Botany, Through the Work of Tournefort, the Jussieu Brothers, and Linnaeus.

The growth of botany following European expansion and the consequent increase of plants necessitated significant development in classification methodology, during the key decades spanning the late 17th to the mid-18th century, leading to the emergence of a "natural method." Much of this development was driven by the need to accurately identify medicinal plants, and was founded on the principle of analogy, used particularly in relation to properties. Analogical reasoning established correlations (affinities) between plants, moreover between their external and internal characteristics (here, medicinal properties). The diversity of plants, names, and botanical information gathered worldwide amplified confusion. This triggered the systematisation of the collection and referencing of data, prioritizing the meticulous observation of plant characteristics and the recording of medicinal properties as established by tradition: it resulted in principled methods of natural classification and nomenclature, represented by the genus, to enhance reliability of plant knowledge, which was crucial in medical contexts. The scope of botany increased dramatically, with new methods broadening studies beyond traditional medicinal plants. The failure of chemical methods to predict properties, particularly of unknown flora, amplified the reliance on analogy and on natural affinities.

Relevance of DNA preservation for future botany and ecology.

The use of molecular methods in plant systematics and taxonomy has increased during the last decades; however, the accessibility of curated genetic samples and their metadata is a bottleneck for DNA-based genetic studies in botany. Plant biodiversity DNA banks and DNA-friendly collections could be critical suppliers of curated genetic material for researchers in the current context of plant biodiversity loss. Here, we aimed to understand the potential of plant DNA banks and DNA-friendly collections to enhance the growth and openness of scientific knowledge. The preservation of genetic material should become part of a natural collection's process for the generation of extended specimens enabling the preservation of both the phenotype and genotype and contributing to the generation of data networks which cross-fertilize other fields. These curated collections are advantageous in endangered species research, detecting processes related to extinction, giving a genetic dimension to IUCN assessments or completing the Leipzig Catalogue of Vascular Plants. Therefore, DNA collections are fundamental in producing FAIR data, responsible research and innovation (RRI) and meeting the goals of international conservation programmes. The completion of natural collections is important for current research efforts and furthermore vital to support future research in an era of ongoing plant biodiversity loss.

Optical topometry and machine learning to rapidly phenotype stomatal patterning traits for maize QTL mapping.

Stomata are adjustable pores on leaf surfaces that regulate the tradeoff of CO2 uptake with water vapor loss, thus having critical roles in controlling photosynthetic carbon gain and plant water use. The lack of easy, rapid methods for phenotyping epidermal cell traits have limited discoveries about the genetic basis of stomatal patterning. A high-throughput epidermal cell phenotyping pipeline is presented here and used for quantitative trait loci (QTL) mapping in field-grown maize (Zea mays). The locations and sizes of stomatal complexes and pavement cells on images acquired by an optical topometer from mature leaves were automatically determined. Computer estimated stomatal complex density (SCD; R2 = 0.97) and stomatal complex area (SCA; R2 = 0.71) were strongly correlated with human measurements. Leaf gas exchange traits were genetically correlated with the dimensions and proportions of stomatal complexes (rg = 0.39-0.71) but did not correlate with SCD. Heritability of epidermal traits was moderate to high (h2 = 0.42-0.82) across two field seasons. Thirty-six QTL were consistently identified for a given trait in both years. Twenty-four clusters of overlapping QTL for multiple traits were identified, with univariate versus multivariate single marker analysis providing evidence consistent with pleiotropy in multiple cases. Putative orthologs of genes known to regulate stomatal patterning in Arabidopsis (Arabidopsis thaliana) were located within some, but not all, of these regions. This study demonstrates how discovery of the genetic basis for stomatal patterning can be accelerated in maize, a C4 model species where these processes are poorly understood.