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Artificial intelligence (AI) is advancing rapidly and continually evolving in various fields. Recently, the release of ChatGPT has sparked significant public interest. In this study, we revisit the '100 Important Questions Facing Plant Science' by leveraging ChatGPT as a valuable tool for generating thought-provoking questions relevant to plant science. These questions primarily revolve around the utilization of plants in product development, understanding plant mechanisms, plant–environment interactions, and enhancing plant traits, with an emphasis on sustainable product development. While ChatGPT may not capture certain crucial aspects highlighted by scientists, it offers valuable insights into the questions generated by experts. Our analysis demonstrates that ChatGPT can be cautiously employed as a supportive tool to facilitate, streamline, and expedite specific tasks in plant science. Large language models (LLMs) were recently made widely available to the public. ChatGPT is an LLM released in late 2022, which has received massive public attention and interest. A need has emerged to evaluate how ChatGPT and other such artificial intelligence (AI) tools can benefit plant science. Proper use of such AI tools can improve and expedite the scientific process. [ABSTRACT FROM AUTHOR]

This article celebrates the 100-year anniversary of the American Society of Plant Biologists (ASPB) and highlights its role in publishing high-quality plant science. It presents a compendium of review articles covering various topics in plant biology, including plant metabolism, development, reproduction, cell biology, genomics, evolution, and phytohormones. The reviews provide insights into the history, current research, and future directions in these areas. Two specific reviews focus on the trafficking of transcription factors and the regulation of mRNA translation in plants. The article acknowledges that the collection of reviews is not exhaustive and hopes that readers find them instructive and inspirational for future plant biology research. [Extracted from the article]

Turkey is expected to be affected considerably in future adverse climatic conditions. Plant species are one of the most vulnerable to these climatic changes. In this study, we aimed to investigate current and future potential distribution areas of Ferulago humilis Boiss., which is an endemic vascular plant species for Turkey, using CMIP5 projected to year 2070. For this purpose, we obtained occurence data (presence-only) from Global Biodiversity Information Facility (GBIF). Regarding bioclimatic data we used WorldClim dataset with 10 km² resolution. Using both plant occurrence and bioclimatic data, we performed species distribution modelling analysis. We used two methods namely Boosted Regression Trees (BRT) and Random Forest (RF). Additionally, we used bootstrapping method as partitioning resampling for all analysis. Our analysis has showed that potential distribution areas of the species has slightly changed for the future projection. The species movement is towards slightly upwards as higher latitudes. We believe that our study shows the importance and relevance of the endemic species in the scope of species distribution models for plant conservation topics. [ABSTRACT FROM AUTHOR]

Pitaya (Hylocereus spp.) is a member of the cactus family that is native to Central and South America but is now cultivated throughout the sub-tropical and tropical regions of the world. It is of great importance due to its nutritional, ornamental, coloring, medicinal, industrial, and high consumption values. In order to effectively utilize and develop the available genetic resources, it is necessary to appreciate and understand studies pertaining to the usage, origin, nutrition, diversity, evaluation, characterization, conservation, taxonomy, and systematics of the genus Hylocereus. Additionally, to gain a basic understanding of the biology of the plant, this review has also discussed how biotechnological tools, such as cell and tissue culture, micropropagation (i.e., somatic embryogenesis, organogenesis, somaclonal variation, mutagenesis, androgenesis, gynogenesis, and altered ploidy), virus-induced gene silencing, and molecular marker technology, have been used to enhance pitaya germplasm. [ABSTRACT FROM AUTHOR]

This special issue reflects the diversity of approaches to new and old problems in plant biology, showcasing the wide range of applications of bioinformatics in plant biology, and we hope that it will support the continuing development of bioinformatics tools and methods for a new generation of technological advance. Bioinformatics has revolutionized plant biology, enabling researchers to harness analytical advancements and reveal the enormous complexity of plant genomes, relationships, and biology. Despite advances in genome assembly methods, genome annotation remains one of the most challenging bottlenecks facing plant genome science, with intron length variation, divergent TE dynamics, and low sequence conservation hampering the annotation efforts of non-model genome projects. [Extracted from the article]

This article discusses the advancements in seed ecology and evolutionary biology research, specifically focusing on the study of seed dormancy. The authors highlight the importance of collaboration between physiologists and ecologists in understanding the functions of seeds. They also emphasize the significance of open science and the availability of large datasets in testing hypotheses related to seed dispersal, persistence in soil seedbanks, and germination. The article presents a recent study on the diversity of seed dormancy across different biomes and addresses criticisms regarding the selection of predictors for seed dormancy and the role of fire in its evolution. The authors acknowledge the limitations of current data and call for further research and data sharing to enhance our understanding of seed ecology and evolution. [Extracted from the article]

This account presents information on all aspects of the biology of Viscum album L. (Mistletoe) that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the standard framework of the Biological Flora of Britain and Ireland: distribution, habitat, communities, responses to biotic factors, responses to environment, structure and physiology, phenology, floral and seed characters, herbivores and disease, history, and conservation.Viscum album is a widespread obligate hemiparasite on a wide range of angiosperm and gymnosperm trees. Once thought to take just water and nutrients from its host via a haustorium, it is now suggested to also take carbon. Heavy infestations can reduce host vitality through prolific water use and carbon removal.Flowers are highly reduced but are primarily pollinated by flies, ants and bees. Seeds are dispersed by birds. Removal of the epicarp is necessary for successful seedling establishment, and seeds have a sticky viscin coat, adhering it to the host bark. Vegetative spread also happens under the bark of its host resulting in densities of >700 Mistletoe plants per host.Viscum album is a lowland species, most frequent in open human‐made habitats extending into woodlands in Europe. It has been widely planted for folklore use centred around Christmas. Despite conservation concerns following removal of Mistletoe‐laden old orchards, the species is thriving and needs control in some areas. Viscotoxins and lectins in leaves and shoots have been widely used in herbal medicine and now potentially in complementary cancer therapy. [ABSTRACT FROM AUTHOR]

Now characterised by high-throughput sequencing methods that enable the study of microbes without lab culture, the human "microbiome" (the microbial flora of the body) is said to have revolutionary implications for biology and medicine. According to many experts, we must now understand ourselves as "holobionts" like lichen or coral, multispecies superorganisms that consist of animal and symbiotic microbes in combination, because normal physiological function depends on them. Here I explore the 1960s research of biologist René Dubos, a forerunner figure mentioned in some historical accounts of the microbiome, and argue that he arrived at the superorganism concept 40 years before the Human Microbiome Project. This raises the question of why his contribution was not hailed as revolutionary at the time and why Dubos is not remembered for it. [ABSTRACT FROM AUTHOR]

The adoption of a holistic approach to root research, that is, one that takes into account all categories of root traits, from anatomy to root morphology, physiology and architecture, as well as interactions with the rhizosphere microbiota, was emphasised as a crucial step in facing the challenges posed by global change. Keywords: Ambassador Program; ISRR11; rhizosphere; root phenotyping; root traits; Rooting2021; roots EN Ambassador Program ISRR11 rhizosphere root phenotyping root traits Rooting2021 roots 2149 2154 6 08/22/22 20220915 NES 220915 Emerging frontiers: root and rhizosphere research in the context of global environmental chan... Natural ecosystems and agricultural production have been threatened by multifaceted global environmental changes. ISRR11, rhizosphere, root traits, Ambassador Program, root phenotyping, Rooting2021, roots Root biology never sleeps: 11th Symposium of the International Society of Root Research (ISRR11) and the 9th International Symposium on Root Development (Rooting2021), 24-28 May 2021. [Extracted from the article]

This account provides information on all aspects of the biology of Neottia nidus‐avis (L.) Rich. (Bird's‐nest Orchid) that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the standard framework of the Biological Flora of Britain and Ireland: distribution, habitat, communities, responses to biotic factors, responses to environment, structure and physiology, phenology, reproductive characteristics, herbivory, history and conservation.Neottia nidus‐avis is a native mycoheterotrophic orchid; it is found most frequently in the deep humus of densely shaded beech woodlands, on limestone or chalky soils in the British Isles. The species extends throughout temperate Eurasia.Neottia nidus‐avis is a perennial, mostly monocarpic herb with mixed mode of reproduction and many adaptations to autogamy. The perennating organ is a short rhizome; vegetative reproduction by rhizome branching or root‐sprouting is rather infrequent. Because of its achlorophyllous nature, N. nidus‐avis is entirely dependent on its mycorrhizal basidiomycetes from the family Sebacinaceae for nutrition.Plastid genome of N. nidus‐avis has been reduced as a result of the relaxation of functional constraints on photosynthesis as in other mycoheterotrophic plants. Despite this, the plant has retained all enzymes to produce chlorophyll as well as some photoprotective metabolites, such as zeaxanthin and tocopherol, whose function in the mycoheterotrophic plant remains unresolved.The species flowers from May to June, depending on latitude and altitude. The flowers emit a sweet scent and produce little nectar. They may be pollinated by flies, crawling thrips and ants but self‐pollination is presumed to be the main mode of reproduction. Between 75% and 97% of open flowers set fruits.Neottia nidus‐avis is classified as Vulnerable in Great Britain. The species is scattered throughout much of the British Isles, but it is very scarce except in southern England, where it is locally abundant. The main threats are deforestation, changes in woodland management and coniferization. [ABSTRACT FROM AUTHOR]

RNAseq analysis revealed differential expression of 645 genes due to salt stress, and some of the salt stress-related genes we found upregulated are given below: GDSL esterase/lipase, glucan-1,3-beta-glucosidase, and glyceraldehyde-3-phosphate dehydrogenase. Another line contains an active herbicide resistance gene I bar i , recombinase gene I Cre i and I FLO/LFY i homolog gene guide RNA (sgRNA), and an inactive stress-regulating gene, I AVP1 i . Three target genes; I 9-cis-Epoxycarotenoid Dioxygenase-1 i ( I NCED1), Salt/drought-stress response/antifungal domain protein i ( I SalT) i , and I Light-harvesting protein i ( I Bio-PSII) i and reference gene, I Regulatory subunit of phosphatase 2A-protein (VuPp2A) i for comparing were evaluated by quantitative reverse transcription PCR (qRT-PCR). Our study reports the first case of achieving high T-DNA-free gene editing frequency through transient suppression of the POLQ gene in plants, which is of great impact on the application of CRIPSR genome editing in clonally propagated plant species. [Extracted from the article]

Croton crassifolius Geisel. (C. crassifolius), belonging to the family Euphorbiaceae, is a traditional Chinese medicine primarily distributed in Asia. This medicinal plant is commonly used for moving qi and relieving pain, dispelling wind and swelling, relaxing tendons and activating collaterals in traditional Chinese medicine (TCM) to treat rheumatic arthritis, bruises and injuries, gastric and duodenal ulcers, sore throat, and so on. To date, no comprehensive review on C. crassifolius has been published. The purpose of this review is to provide a thorough overview of the botany, traditional uses, phytochemistry, pharmacology, and quality control of C. crassifolius. We mainly focus on phytochemical and pharmacological investigations of C. crassifolius. Furthermore, perspectives for possible future studies on C. crassifolius are also discussed. A thorough search of published articles up to May 2023 was conducted, focusing on original publications related to C. crassifolius, using numerous literature databases, including China National Knowledge Infrastructure (CKNI) (http://www.cnki.net), PubMed Database (https://pubmed.ncbi.nlm.nih.gov), Wanfang Data (http://www.wanfangdata.com.cn/), and Web of Science database (http://apps.webofknowledge.com/). More than 250 chemical compounds, including terpenoids, volatile oils, pyran-2-one derivatives, and flavonoids have been isolated and identified from C. crassifolius. Among these compounds, terpenoids form the main components. Modern pharmacological studies have shown that the plant possesses antiangiogenic, anti-inflammatory, antitumor, antibacterial, and antiviral properties. After the initial search, we reviewed the deficiencies of pharmacological mechanism and quality control studies and suggested workable solutions, which will be of great use in future research. In this review we have conducted a thorough overview of C. crassifolius and offered new perspectives on research regarding quality control, substance basis, and pharmacological mechanism, providing theoretical guidance for the clinical application and development of Chinese medicine. However, several defects, such as pharmacological mechanism determination, quality control, pharmacokinetic establishment, and toxicology assessment of C. crassifolius need further study. [Display omitted] • The study first discussed quality control, which has not been explored in previous reviews. • The study first reviewed the limitations of pharmacological mechanism and quality control studies and proposed appropriate solutions, which are of great practical significance to subsequent studies. • This is the first systematic critical review of studies on Croton crassifolius Geisel. [ABSTRACT FROM AUTHOR]

Buddleja officinalis Maxim. (B. officinalis), commonly known as "Menghua" "Yangerduo" is a widely recognized traditional herbal medicine in China, Korea, and Vietnam. For thousands of years, it has been used to treat dry eye disease, conjunctivitis, keratitis, eye ulcers, eye pain, cough, asthma, hemoptysis, and other medical conditions. This review article aims to provide a concise summary of the botany, ethnopharmacology, phytochemistry, pharmacology, medicinal potential, and application of B. officinalis in treating ophthalmic diseases and critically evaluates the existing literature to establish a scientific basis for its reasonable utilization and further investigation. The information reviewed in this study was collected from various electronic resources, including the Web of Science, PubMed, and Google Scholar. To date, 80 structurally diverse compounds have been isolated and characterized from B. officinalis , primarily flavonoids, phenylethanoids, triterpenoids, and monoterpenes. Extracts and compounds derived from B. officinalis have been reported to possess broad pharmacological effects including anti-dry eye disease, anti-inflammation, anti-oxidation, anti-diabetes, anti-obesity, improving osteoporosis and treatment of skin diseases. This review provides a reference for the future studies on of B. officinalis. As a natural medicinal plant, B. officinalis is worthy of further development in botany, ethnopharmacology, phytochemistry, pharmacology, and therapeutic potential for ophthalmic diseases. Although some components have demonstrated multiple pharmacological activities, their mechanisms of action remain unclear. Further studies on the underlying molecular basis and mechanism of action are warranted. [Display omitted] • B. officinalis is a common natural medicinal plant with multiple therapeutic effects. • The phytochemical compositions of B. officinalis have various biological activities. • B. officinalis has great potential to treat dry eye diseases. [ABSTRACT FROM AUTHOR]

For much of the twentieth century, plant physiologists considered themselves in an ideal position to study and explain the functions and processes of plants. Much of that authority stemmed from plant physiologists' long-standing commitment to experimental control and the integration of the physical sciences into biological practice. This article places plant physiology back in the center of the story of the recent life sciences. It shows the development of parallel experimental research programs into environmental as well as genetic effects on growth and development in plant physiology and genetics, and notes that the pursuit of an experimental environment was celebrated as much as (and occasionally more than) a molecular vision of life throughout most of the twentieth century by much of the plant science community. Thus, this article concludes that the history of the recent life sciences needs new complementary narratives of plant physiology with genetics, new concepts with technological tools, and plant-sized scales with the molecular. The history of the 'Age of Biology,' as the plant scientists saw it, helps confront the issue first posed by Evelyn Fox Keller, namely that the history of genetics has overshadowed a larger history of experimental life science. My answer here is through a larger narrative of the rise of the complementary experimental sciences of genes and environments in the life sciences. [ABSTRACT FROM AUTHOR]

This article is meant for a wider educational and scientific public. It reflects the results of our monitoring of the zoological literacy of students at selected grammar schools in the Prešov region. (We assume that analogous or very similar results would also be found in other regions of Slovakia.) This monitoring was conducted in 2013 by a test. The test was taken by 318 students, including 151 fourth-grade students and 167 third-grade students(111 boys and 207 girls). The test consisted of 16 theoretical and 22 practical questions. The task of the practical part of the test was to identify 22 species of known and easily identifiable animals, including 9 protected species. From a knowledge perspective, the results of the test were very dis- appointing. The correct answers in the theoretical part of the test was at 31%, less than one third. The results of the practical part of the test were even worse: 28.8%, and after excluding three rather simple species (the broad-bodied chaser, the fire salamander, and the Eurasian otter), only 18.75%. The results of the monitoring indicate the sad fact that contemporary youth know almost nothing about the natural world. An appalling fact is that only one student (0.3%) was able to identify the clouded Apollo (Parnassius mnemosyne), despite its being a protected species of European importance! This highly unfavorable state of affairs (approaching zoological illiteracy) is a consequence of the sterile, verbal-and-theoretical model of biology education. Unfortunately, the teaching of the subject is missing the very topic which is “the most biological”: individual plant and animal species and their higher taxa (and as a note: the huge kingdom of fungi is almost completely over-looked). The rapid decline of zoological (and, in general, biological) literacy has a dire effect and especially will have such effect in the more distant future. The number of people in Slovakia that are able to determine knowledgeably individual species of organisms (including plants, fungi, vertebrates, mollusks, spiders, beetles, and bugs) is constantly decreasing. If this trend continues for another 20 years, studies of flora and fauna in Slovakia will be carried out by foreign specialists, as is the case in the Third World. Unfortunately, it seems that this development will benefit some. When we know little about the flora and fauna of the various regions and sites of Slovakia, it might be exploited even more and “without remorse“. The fundamental problem is how to change this unsustainable situation. The answer is crystal clear. In order to achieve a gradual, and at least partial, improvement, a comprehensive and fundamental revision of the model of teaching biology in primary schools and especially grammar schools is necessary; including, of course, the curricula and textbooks. There is an urgent need to start a public discussion on this issue. [ABSTRACT FROM AUTHOR]

Key message: Advances in deep learning are providing a powerful set of image analysis tools that are readily accessible for high-throughput phenotyping applications in plant reproductive biology. High-throughput phenotyping systems are becoming critical for answering biological questions on a large scale. These systems have historically relied on traditional computer vision techniques. However, neural networks and specifically deep learning are rapidly becoming more powerful and easier to implement. Here, we examine how deep learning can drive phenotyping systems and be used to answer fundamental questions in reproductive biology. We describe previous applications of deep learning in the plant sciences, provide general recommendations for applying these methods to the study of plant reproduction, and present a case study in maize ear phenotyping. Finally, we highlight several examples where deep learning has enabled research that was previously out of reach and discuss the future outlook of these methods. [ABSTRACT FROM AUTHOR]

Species distribution models (SDMs) are useful tools for future potential distribution patterns of species in the face of climate change. Turkey is expected to be affected considerably from climatic change i.e., up to 6°C increase in temperature and 50% decrease in precipitation by 2070. Therefore, there is an urgent need for conservation and management practices for future patterns of species. It is aimed current and future (using CMIP5 projected to 2070) potential distribution areas of Campanula lyrata Lam., which is formerly an endemic species. To do this, presence-only data was used, which is obtained from the Global Biodiversity Information Facility (GBIF). Bioclimatic data from was downloaded from WorldClim dataset with 10 km² resolution. Species distribution modelling was performed using R program. Two regression techniques and two machine learning techniques namely Generalized Linear Models (GLMs), Generalized Additive Models (GAMs), Support Vector Machine (SVM) and Random Forest (RF), were used, respectively. The bootstrapping method as partitioning resampling was also used for all analysis. Considerably high model performances as well as AUC values for all possible models were found. Significant range shifts between current and future climatic conditions were found. The most relevant relative importance variables were precipitation seasonality and precipitation of the wettest month. This study reveals the importance of the future distributional areas of species. [ABSTRACT FROM AUTHOR]

Here, we briefly review the historic and contemporary contributions that botanists have made in invasion biology and argue that botanists will continue to play a critical role in revolutionizing invasion biology. Keywords: colonization; establishment; genomics; herbaria; introduced species; weed science EN colonization establishment genomics herbaria introduced species weed science 549 552 4 04/28/21 20210401 NES 210401 Although botanists have been at the center of invasion biology since its inception, few botanists identify as invasion biologists. MOVING INVASION BIOLOGY FORWARD The examples above demonstrate the significant contributions that botanists are making to invasion biology, but botanists are also well poised to overcome some of the mechanistic hurdles that have long encumbered invasion biology as a field. [Extracted from the article]

In this study, transgenic T1 soybean plants, expressing a dominant-negative Arabidopsis ERECTA mutant ( ER) gene, were grown in a greenhouse and evaluated phenotypically for grain yield (YLD, kg.ha-1), number of grains per pod (GP), weight of dry matter of the shoot (WDM) and weight of one hundred grains (100G). In theory, it allows to combine into the same cell not only the nuclear genome of one parent, but also the cytoplasm genome of the second by producing new cytoplasmic-nuclear genome combinations at both ploidy levels (diploid and tetraploid) to enhance the diversity of gene pools in the new germplasm. We are also pioneering gene editing methods which, by avoiding the incorporation of foreign DNA into a plant's genome, are expected to obviate GMO concerns and drawn-out regulatory hurdles, easing adoption of improved cassava cultivars. [Extracted from the article]

Machine learning approaches are affecting all aspects of modern society, from autocorrect applications on cell phones to self-driving cars to facial recognition, personalized medicine, and precision agriculture. However, manual scoring of insect damage to herbarium specimens is extremely laborious, and the possibility of applying machine learning to quantify the patterns and extent of insect damage to plant specimens is appealing. The contributions of machine learning to the plant sciences, especially for automated species identification from images of digitized herbarium specimens, is showing great promise (Schuettpelz et al., [37]; Wäldchen and Mäder, [47]). [Extracted from the article]

Inquiry- and course-based research pedagogies have demonstrated effectiveness for preparing undergraduate biology students with authentic scientific skills and competencies, yet many students lack the experience to engage successfully in open-ended research activities without sufficient scaffolding and structure. Further, curricula for student-centered laboratory activities are lacking for several biological disciplines, including plant biology and botany. In this article, I describe a semester-long structured-inquiry research curriculum developed for a plant biology course taught to second-year biology students that integrates key elements of inquiry and discovery while providing a structured approach to gaining research skills. In the research project, students collect leaves from woody dicot plants across a range of environments that are characterized by different mean annual temperatures, and investigate the relationship between various leaf characteristics and temperature. Curricular materials are provided to teach skills in scientific paper reading, field data collection, data processing including microscopy and image analysis, quantitative data analysis in R, biological inference, and scientific writing. This comprehensive, ready-to-implement curriculum is suitable for plant biology, botany, and plant ecology courses and is particularly valuable for students with no prior research experience. [ABSTRACT FROM AUTHOR]

The Society for Integrative and Comparative Biology (SICB) should, in theory, be a home for scientists working across the entire Tree of Life. In practice, SICB has remained principally a society that supports integrative zoological research. Here we highlight a broad collection of what we consider to the best in integrative and comparative plant biology, gathered together for a special symposium at the 2019 SICB meeting. This symposium and special issue mark the initiation of a new Division of Botany within SICB, which we hope will usher in a new era of SICB where botanists and zoologists engage, collaborate, and celebrate together in this especially creative period of integrative and comparative biology. [ABSTRACT FROM AUTHOR]

The article offers information related to the biology and applications of Endophytic Insect-Pathogenic Fungi. Topics include occurrence of interactions which lead to the demise of plant insect pests; the nature of plant–insect–fungus relationships; and overview of EIPF by reviewing the knowledge about their evolution, ecology, and mechanisms of insect and plant colonization.

Eucommia ulmoides Oliver, a single species of Eucommia genus belonging to the Eucommiaceae family, is an endemic in China and has been used in traditional Chinese medicine for nearly two thousand years. Records from different historical periods highlight E. ulmoides and its officinal botanical parts, usefulness in adaptation to disease and its central role in Chinese medicine theory. There are also historical collection documents for minorities in China. Tearing the leaves, bark and fruit produces strands of latex; a description of E. ulmoides's morphological features is recorded in this paper. This review summarizes 204 natural compounds isolated from this plant, which are divided into seven categories: lignans, iridoids, flavonoids, phenols, steroids, terpenes and others. These components possess wide-ranging pharmacological efficacies, such as antihypertensive, antihyperglycemic, antihyperlipidemia, anti-oxidative, anti-osteoporosis, antitumor, immunomodulatory and neuroprotective activities. This review aims to provide a reference for extensive researches of E. ulmoides crude drugs, especially for quality control, biosynthesis and structure modification of active ingredients and pharmacological mechanism. [ABSTRACT FROM AUTHOR]

Metric data are usually assessed on a continuous scale with good precision, but sometimes agricultural researchers cannot obtain precise measurements of a variable. Values of such a variable cannot then be expressed as real numbers (e.g., 1.51 or 2.56), but often can be represented by intervals into which the values fall (e.g., from 1 to 2 or from 2 to 3). In this situation, statisticians talk about censoring and censored data, as opposed to missing data, where no information is available at all. Traditionally, in agriculture and biology, three methods have been used to analyse such data: (a) when intervals are narrow, some form of imputation (e.g., mid‐point imputation) is used to replace the interval and traditional methods for continuous data are employed (such as analyses of variance [ANOVA] and regression); (b) for time‐to‐event data, the cumulative proportions of individuals that experienced the event of interest are analysed, instead of the individual observed times‐to‐event; (c) when intervals are wide and many individuals are collected, non‐parametric methods of data analysis are favoured, where counts are considered instead of the individual observed value for each sample element. In this paper, we show that these methods may be suboptimal: The first one does not respect the process of data collection, the second leads to unreliable standard errors (SEs), while the third does not make full use of all the available information. As an alternative, methods of survival analysis for censored data can be useful, leading to reliable inferences and sound hypotheses testing. These methods are illustrated using three examples from plant and crop sciences. [ABSTRACT FROM AUTHOR]

This Virtual Issue "The biology of wood", highlights the central role of wood biology in basic plant science, as well as critical ecological, environmental, economic and societal issues. It seems as though the plastid and mitochondrial carbon metabolism pathway genes show a coordinated expression with their nuclear gene counterparts, and with specific stages of wood development. The functional characterization of a poplar Class I KNOX gene, I KNAT2/6b i , concluded that this gene is important for the regulation of cell differentiation, in part through its influence on the expression of NAC transcription factors (Zhao I et al i ., [14], in this issue of I New Phytologist i , pp. 1531-1543). Integration of these data showed an enrichment of specific epigenetic markers with genes expressed during wood formation, and together represent an important advancement in our global understanding of gene regulation during wood formation. [Extracted from the article]

Aquatic plants fulfil a wide range of ecological roles, and make a substantial contribution to the structure, function and service provision of aquatic ecosystems. Given their well-documented importance in aquatic ecosystems, research into aquatic plants continues to blossom. The 14th International Symposium on Aquatic Plants, held in Edinburgh in September 2015, brought together 120 delegates from 28 countries and six continents. This special issue of Hydrobiologia includes a select number of papers on aspects of aquatic plants, covering a wide range of species, systems and issues. In this paper, we present an overview of current trends and future directions in aquatic plant research in the early twenty first century. Our understanding of aquatic plant biology, the range of scientific issues being addressed and the range of techniques available to researchers have all arguably never been greater; however, substantial challenges exist to the conservation and management of both aquatic plants and the ecosystems in which they are found. The range of countries and continents represented by conference delegates and authors of papers in the special issue illustrates the global relevance of aquatic plant research in the early twenty first century but also the many challenges that this burgeoning scientific discipline must address. [ABSTRACT FROM AUTHOR]

Summary: Ubiquitination is mediated by an enzymatic cascade that results in the modification of substrate proteins, redefining their fate. This post‐translational modification is involved in most cellular processes, yet its analysis faces manifold obstacles due to its complex and ubiquitous nature. Reconstitution of the ubiquitination cascade in bacterial systems circumvents several of these problems and was shown to faithfully recapitulate the process. Here, we present UbiGate − a synthetic biology toolbox, together with an inducible bacterial expression system – to enable the straightforward reconstitution of the ubiquitination cascades of different organisms in Escherichia coli by ‘Golden Gate’ cloning. This inclusive toolbox uses a hierarchical modular cloning system to assemble complex DNA molecules encoding the multiple genetic elements of the ubiquitination cascade in a predefined order, to generate polycistronic operons for expression. We demonstrate the efficiency of UbiGate in generating a variety of expression elements to reconstitute autoubiquitination by different E3 ligases and the modification of their substrates, as well as its usefulness for dissecting the process in a time‐ and cost‐effective manner. [ABSTRACT FROM AUTHOR]

Aim Refugia under past climates have been important in structuring current patterns in diversity, while refugia under anthropogenic climate change will likely be important in retaining this diversity and shaping new patterns. However, few studies have examined the congruence of past, present and future refugia, or the spatiotemporal connectivity of these refugia. Our aim was to test the extent of overlap of refugia under Last Glacial Maximum ( LGM), present (2015) and likely future climates (2100), for Tasmania's palaeoendemic flora. We then aimed to identify areas of high spatiotemporal refugia connectivity, as priority areas for conservation and management. Location Tasmania, Australia. Methods We developed and applied a new community-level approach to identifying refugia, based on generalized dissimilarity modelling of compositional turnover and a set of reference sites with known biodiversity value. Using these projections of palaeoendemic plant refugia for past, present and future climates, we developed and applied a second approach to quantify the level of connectivity of these refugia over space and time. Results Although there was large overlap (85%) between current and future climates in the distribution of the highest value palaeoendemic refugia, the small congruence of these areas with refugia at the LGM resulted in only a small area ( c. 9 km2) of persistent high value refugia over all three time periods. Despite this, our spatiotemporal analysis identified several areas of high connectivity in refugial environments for Tasmania's palaeoendemic flora over time. Main conclusions The community-level approaches we demonstrate here to quantify refugia and their spatiotemporal connectivity have the potential to advance our understanding of biodiversity dynamics, particularly for taxonomic groups that are species-rich, poorly studied or comprised of many rare species, where species-level approaches are less suitable. [ABSTRACT FROM AUTHOR]

The article offers information about a botanical research on the ecology and evolution of mutualism.

Pyrolae herba is the dried whole plant of Pyrola calliantha H. Andres or Pyrola decorata H. Andres (Pyrolaceae). Pyrolae herba has a long history of medicinal use in China. In ancient times, it was often used to treat pain in tendons and bones, swollen sore, cough, expectoration, bleeding, and other diseases. and was commonly used in ancient times to treat pain in the tendons and bones, swollen sore, cough, expectoration, bleeding and other diseases. This paper summarizes the botany, traditional uses, phytochemistry, pharmacology, quality control and toxicology of Pyrolae herba , with a view to providing reference for further development and research. The relevant information on Pyrolae herba was collected from the scientific databases including PubMed, CNKI, ScienceDirect, Wiley, Springer, Web of Science, Google Scholar, Baidu Scholar, Pharmacopoeia of the People's Republic of China and Flora Republicae Popularis Sinicae, etc. At present, more than 70 compounds have been identified from Pyrolae herba , including flavonoids, phenolic glycosides, quinones, terpenoids, volatile oils and other compounds. Pharmacological studies have shown that Pyrolae herba has a variety of pharmacological activities, such as anti-inflammatory, anti-bacterial, anti-viral, anti-tumor, anti-oxidation, reducing blood lipids, protective on cardiovascular and cerebrovascular, promoting osteoblast proliferation, and so on. It is used clinically in modern times to treat rheumatic arthritis, rheumatoid arthritis, bone hyperplasia, sciatica, cervical spondylosis, lumbar spondylosis, acute and chronic bronchitis, mammary gland hyperplasia, tumor, hypertension, coronary heart disease and bleeding diseases. Pyrolae herba is rich in chemical constituents, diverse in pharmacological activities and abundant in resources, which is widely used in clinics from traditional to modern. However, there is a lack of research on the relationship between chemical constituents and pharmacodynamics of Pyrolae herba. In addition, the existing clinical applications suggest that Pyrolae herba has a certain therapeutic potential in the treatment of hemorrhagic diseases, but there is a lack of information on experimental studies. It is worthwhile to further investigate the Pyrolae herba in depth in the hope of making discoveries and breakthroughs. [Display omitted] • Systematically sorted out the clinical application of Pyrolae herba. • Put forward a promising research direction for Pyrolae herba. • The hemostatic effect of Pyrolae herba has been widely used in clinical medicine in traditional Chinese medicine. [ABSTRACT FROM AUTHOR]

Xanthomonas albilineans, the causal agent of sugarcane leaf scald, is a bacterial plant pathogen that is mainly spread by infected cuttings and contaminated harvesting tools. However, some strains of this pathogen are known to be spread by aerial means and are able to colonize the phyllosphere of sugarcane before entering the host plant and causing disease. The objective of this study was to identify the molecular factors involved in the survival or growth of X. albilineans on sugarcane leaves. We developed a bioassay to test for the attachment of X. albilineans on sugarcane leaves using tissue-cultured plantlets grown in vitro. Six mutants of strain XaFL07-1 affected in surface polysaccharide production completely lost their capacity to survive on the sugarcane leaf surface. These mutants produced more biofilm in vitro and accumulated more cellular poly-β-hydroxybutyrate than the wild-type strain. A mutant affected in the production of small molecules (including potential biosurfactants) synthesized by non-ribosomal peptide synthetases ( NRPSs) attached to the sugarcane leaves as well as the wild-type strain. Surprisingly, the attachment of bacteria on sugarcane leaves varied among mutants of the rpf gene cluster involved in bacterial quorum sensing. Therefore, quorum sensing may affect polysaccharide production, or both polysaccharides and quorum sensing may be involved in the survival or growth of X. albilineans on sugarcane leaves. [ABSTRACT FROM AUTHOR]

An analytical procedure allowing multi-elemental analyses and isotope ratio measurements of eight of these (B, Cd, Cu, Fe, Pb, Sr, Tl and Zn) in matrices relevant for bio-monitoring using a single high-pressure acid digestion was developed. Method blanks, separation efficiency of matrix elements, repeatability and reproducibility were evaluated using sets of preparation blanks, certified reference materials and duplicate samples prepared and analyzed over a period of several months. The method was used to assess the natural variability of concentrations and isotopic compositions in bio-indicators (tree leaves, needles and mushrooms, over 240 samples) collected mainly from a confined area in North-East Sweden. Ranges found from leaves and needles were compared with data obtained for limited numbers of samples collected in Spain, Italy, France, United Kingdom and Iceland. [ABSTRACT FROM AUTHOR]

The native palm flora of Singapore can be described as a microcosm of the palm flora of the Malay Peninsula. With 20 genera, Singapore has close to twothirds of the genera found in the contiguous palm flora that is formed between Peninsular Malaysia (131,598 km2) and Singapore (716.1 km2). [ABSTRACT FROM AUTHOR]

Background and Aims Arabinogalactan protein 31 (AGP31) is a remarkable plant cell-wall protein displaying a multi-domain organization unique in Arabidopsis thaliana: it comprises a predicted signal peptide (SP), a short AGP domain of seven amino acids, a His-stretch, a Pro-rich domain and a PAC (PRP-AGP containing Cys) domain. AGP31 displays different O-glycosylation patterns with arabinogalactans on the AGP domain and Hyp-O-Gal/Ara-rich motifs on the Pro-rich domain. AGP31 has been identified as an abundant protein in cell walls of etiolated hypocotyls, but its function has not been investigated thus far. Literature data suggest that AGP31 may interact with cell-wall components. The purpose of the present study was to identify AGP31 partners to gain new insight into its function in cell walls. Methods Nitrocellulose membranes were prepared by spotting different polysaccharides, which were either obtained commercially or extracted from cell walls of Arabidopsis thaliana and Brachypodium distachyon. After validation of the arrays, in vitro interaction assays were carried out by probing the membranes with purified native AGP31 or recombinant PAC-V5-6xHis. In addition, dynamic light scattering (DLS) analyses were carried out on an AGP31 purified fraction. Key Results It was demonstrated that AGP31 interacts through its PAC domain with galactans that are branches of rhamnogalacturonan I. This is the first experimental evidence that a PAC domain, also found as an entire protein or a domain of AGP31 homologues, can bind carbohydrates. AGP31 was also found to bind methylesterified polygalacturonic acid, possibly through its His-stretch. Finally, AGP31 was able to interact with itself in vitro through its PAC domain. DLS data showed that AGP31 forms aggregates in solution, corroborating the hypothesis of an auto-assembly. Conclusions These results allow the proposal of a model of interactions of AGP31 with different cell-wall components, in which AGP31 participates in complex supra-molecular scaffolds. Such scaffolds could contribute to the strengthening of cell walls of quickly growing organs such as etiolated hypocotyls. [ABSTRACT FROM PUBLISHER]

Background (1,3)-β-Glucan callose is a cell wall polymer that is involved in several fundamental biological processes, ranging from plant development to the response to abiotic and biotic stresses. Despite its importance in maintaining plant integrity and plant defence, knowledge about the regulation of callose biosynthesis at its diverse sites of action within the plant is still limited. The moderately sized family of GSL (GLUCAN SYNTHASE-LIKE) genes is predicted to encode callose synthases with a specific biological function and subcellular localization. Phosphorylation and directed translocation of callose synthases seem to be key post-translational mechanisms of enzymatic regulation, whereas transcriptional control of GSL genes might only have a minor function in response to biotic or abiotic stresses. Scope and Conclusions Among the different sites of callose biosynthesis within the plant, particular attention has been focused on the formation of callose in response to pathogen attack. Here, callose is deposited between the plasma membrane and the cell wall to act as a physical barrier to stop or slow invading pathogens. Arabidopsis (Arabidopsis thaliana) is one of the best-studied models not only for general plant defence responses but also for the regulation of pathogen-induced callose biosynthesis. Callose synthase GSL5 (GLUCAN SYNTHASE–LIKE5) has been shown to be responsible for stress-induced callose deposition. Within the last decade of research into stress-induced callose, growing evidence has been found that the timing of callose deposition in the multilayered system of plant defence responses could be the key parameter for optimal effectiveness. This timing seems to be achieved through co-ordinated transport and formation of the callose synthase complex. [ABSTRACT FROM PUBLISHER]

Background The epidermal cells of the seed coat of certain species accumulate polysaccharides during seed development for cell wall reinforcement or release on imbibition to form mucilage. Seed-coat epidermal cells show natural variation in their structure and mucilage production, which could explain the diverse ecophysiological roles proposed for the latter. Arabidopsis mucilage mutants have proved to be an important tool for the identification of genes involved in the production of seed-coat polysaccharides. Scope This review documents genes that have been characterized as playing a role in the differentiation of the epidermal cells of the arabidopsis seed coat, the natural variability in polysaccharide features of these cells and the physiological roles attributed to seed mucilage. Conclusions Seed-coat epidermal cells are an excellent model for the study of polysaccharide metabolism and properties. Intra- and interspecies natural variation in the differentiation of these epidermal cells is an under-exploited resource for such studies and promises to play an important part in improving our knowledge of polysaccharide production and ecophysiological function. [ABSTRACT FROM PUBLISHER]

Background and Aims Penium margaritaceum is a unicellular charophycean green alga with a unique bi-directional polar expansion mechanism that occurs at the central isthmus zone prior to cell division. This entails the focused deposition of cell-wall polymers coordinated by the activities of components of the endomembrane system and cytoskeletal networks. The goal of this study was to elucidate the structural organization of the cortical cytoskeletal network during the cell cycle and identify its specific functional roles during key cell-wall developmental events: pre-division expansion and cell division. Methods Microtubules and actin filaments were labelled during various cell cycle phases with an anti-tubulin antibody and rhodamine phalloidin, respectively. Chemically induced disruption of the cytoskeleton was used to elucidate specific functional roles of microtubules and actin during cell expansion and division. Correlation of cytoskeletal dynamics with cell-wall development included live cell labelling with wall polymer-specific antibodies and electron microscopy. Key Results The cortical cytoplasm of Penium is highlighted by a band of microtubules found at the cell isthmus, i.e. the site of pre-division wall expansion. This band, along with an associated, transient band of actin filaments, probably acts to direct the deposition of new wall material and to mark the plane of the future cell division. Two additional bands of microtubules, which we identify as satellite bands, arise from the isthmus microtubular band at the onset of expansion and displace toward the poles during expansion, ultimately marking the isthmus of future daughter cells. Treatment with microtubule and actin perturbation agents reversibly stops cell division. Conclusions The cortical cytoplasm of Penium contains distinct bands of microtubules and actin filaments that persist through the cell cycle. One of these bands, termed the isthmus microtubule band, or IMB, marks the site of both pre-division wall expansion and the zone where a cross wall will form during cytokinesis. This suggests that prior to the evolution of land plants, a dynamic, cortical cytoskeletal array similar to a pre-prophase band had evolved in the charophytes. However, an interesting variation on the cortical band theme is present in Penium, where two satellite microtubule bands are produced at the onset of cell expansion, each of which is destined to become an IMB in the two daughter cells after cytokinesis. These unique cytoskeletal components demonstrate the close temporal control and highly coordinated cytoskeletal dynamics of cellular development in Penium. [ABSTRACT FROM PUBLISHER]

The Food and Agriculture Organization (FAO) predicts that food production must rise 70% over the next 40 years to meet the demands of a growing population that is expected to reach nine billion by the year 2050. Many facets of basic plant science promoted by the Botanical Society of America are important for agriculture; however, more explicit connections are needed to bridge the gap between basic and applied plant research. This special issue, Speaking of Food: Connecting Basic and Applied Plant Science, was conceived to showcase productive overlaps of basic and applied research to address the challenges posed by feeding billions of people and to stimulate more research, fresh connections, and new paradigms. Contributions to this special issue thus illustrate some interactive areas of study in plant science--historical and modem plant-human interaction, crop and weed origins and evolution, and the effects of natural and artificial selection on crops and their wild relatives. These papers provide examples of how research integrating the basic and applied aspects of plant science benefits the pursuit of knowledge and the translation of that knowledge into actions toward sustainable production of crops and conservation of diversity in a changing climate. [ABSTRACT FROM AUTHOR]

Dear colleagues, I Plant Species Biology i is published jointly with two international journals, namely, I Ecological Research i and I Population Ecology i . Our readers can choose the journals they want to read from this portal page, and manuscript authors can select the most suitable journals for their submissions by comparing the journal scopes, objectives, and recent papers. The three journal editors can also recommend authors to transfer their manuscripts to another of the three journals if the submitted manuscript better matches their scopes and targets. [Extracted from the article]

The article discusses that Plants continuously adjust their body plans to adapt to the local environment by forming new organs in different developmental contexts. Underground, lateral roots initiate from designated cells in the pericycle of the main root. Aboveground, plants generate shoot-borne roots, bypassing the embryonic root-shoot lineage separation.

Cover Caption: This special issue commemorates the 70th anniversary of JIPB. In this special issue, we invited experts to review the latest advances in plant science. We sincerely thank everyone who has supported the development of JIPB over the past 70 years, including our editorial board, authors, staff, and reviewers, and we look forward to continuing to publish cutting‐edge plant biology in the future. We also thank the Institute of Botany, CAS, and the Botanical Society of China for their longstanding support. [ABSTRACT FROM AUTHOR]