Applications in Plant Sciences

The plant sciences are now facing an unprecedented time in our history in which technology is advancing at a rapid pace, creating a wide variety of novel opportunities for our field. Applications in Plant Sciences is a new source for sharing exciting and innovative applications of new technologies that have the potential to propel plant research forward into the future.

Proteomics, the systematic analysis of (differentially) expressed proteins, is a tool for the identification of proteins involved in cellular processes. Proteomics has already been used for many different applications in plant sciences, including the study of proteins of biosynthetic pathways leading to secondary metabolites. In secondary metabolism, many enzymes are involved, often working in close collaboration to catalyse cascades of reactions. Besides the enzymes, transport and regulatory proteins are also involved, which makes the proteome an essential topic for studying metabolic pathways. Proteomics technology is based on high-throughput techniques for the separation and identification of proteins, allowing an integral study of many proteins at the same time. For the separation of protein mixtures the most powerful technique available is two-dimensional polyacrylamide gel electrophoresis: after separation, proteins can be subsequently identified by mass spectrometry (MS). The increasing amount of genome sequence data has to be followed by deciphering the function of the genes and proteins. Studying differential expression by proteomics is a complementary tool for functional analysis. In this review practical aspects and applications of proteomics in plant sciences, with particular emphasis on secondary metabolism, are discussed. Copyright © 2000 John Wiley & Sons, Ltd.

Nanocarriers, engineered nanoparticles designed to deliver fertilizers, pesticides, and genetic materials, are emerging as essential tools in modern agriculture. This chapter explores nanocarrier types, mechanisms, and applications in plant science. Key systems such as liposomes, polymeric, metallic, and silica nanoparticles enable targeted delivery, enhancing nutrient uptake, pest control, and stress resilience. By ensuring precise agrochemical release, nanocarriers reduce wastage, contamination, and application frequency, supporting sustainable farming. They also facilitate genetic transformation and gene editing for stress-tolerant, non-transgenic crops. However, challenges in cost, regulation, and environmental impact remain. With ongoing research, nanocarriers show promise in advancing food security and sustainable agriculture.

CHAPTER 1Essentially, bioinformatics methodologies for omics constitute a crossover between bottom-up hypothesis-driven and top-down data-driven approaches, which is indispensable to integrate the acquisition, analysis and management of multiple omics data with genome-scale statistical and mathematical modelling and simulation (57).During recent decades, bioinformatics developed a score of methods for sequence analysis, in terms of sequence assembly, genome annotation, comparative genomics, genetics and population genomics, computational evolutionary biology; for expression analysis, in terms of gene expression, protein expression, metabolite profiling; for structural bioinformatics, in terms of genome 3D chromatin modelling, RNA secondary structure prediction, protein structure prediction, homology modelling; for network and system biology, in terms of biological network analysis, gene co-expression analysis, molecular interaction networks; and for data management, in terms of database and web service development, data curation, data visualization, workflow management, and so on. Perspective of crop omicsA global food crisis can soon develop, given the rapid growth of the world population and the lagging pace of yield increase for major crops, including rice, maize, wheat, and sorghum.Domestication, design, and development of genetically improved, stressresilient, and environmental adapted crops have become the research priority.The crop omics perspective necessitates the convergence of low-cost genome sequencing with improved computational power and high-throughput molecular phenotyping technologies to accelerate the identification of genes and/or loci underlying important agronomic traits relevant to food production and quality (58).As the basis of crop omics, the first essential step is assembly and decoding of the reference genomes.This was a challenge for NGS based methodologies as the size and dynamic nature of the plant genome are complicated and diversified (59,60).Plants

Designing and developing sensors for molecular oxygen (O2) has turned into a large, interdisciplinary field of research, with significant progress seen in the past decades. Until the early 1980s, the field of O2 sensing was dominated by polarographic electrode sensors, among which the most popular Clark-type electrode found wide application in plant science. Nevertheless, the great demand for more sophisticated, intracellularly applicable O2 sensors for real-time measurements in plants cannot be satisfied by the predominant techniques. Thus, optical sensors applying an O2-specific reduction of luminescent probes or dyes provide novel, promising tools and open new perspectives on the cellular or even subcellular level of O2 measurements. This chapter aims to give a comprehensive overview on the variety of methods and systems available in the field of O2 sensing with respect to application in plant tissue. Different types of the earlier polarographic electrode technique as well as emerging alternatives will be discussed, including fluorescent proteins as potential, genetically encoded intracellular O2 sensors. Due to the tremendous variety of materials and formats, the young field of optical O2 sensing will receive particular attention directing the focus towards the progress that has been made in developing new probes and dyes. Moreover, the current state of fluorescence measurements will be explored, particularly novel, plant-specific measurement modalities that mask plant autofluorescence. For the potential user, important practical aspects are also presented, revealing the limitations of the existing methods and further encouraging more interdisciplinary research in O2 sensing.KeywordsGreen Fluorescent ProteinOptical SensorYellow Fluorescent ProteinPlant ScienceSensor FilmThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

BackgroundSplit-root systems (SRS) have many applications in plant sciences, but their implementation, depending on the experimental design, can be difficult and time-consuming. Additionally, the system is not exempt from limitations, since the time required for the establishment of the SRS imposes a limit to how early in plant development experiments can be performed. Here, we optimized and explained in detail a method for establishing a SRS in young Arabidopsis thaliana seedlings, both in vitro and in soil.ResultsWe found that the partial de-rooting minimized the recovery time compared to total de-rooting, thus allowing the establishment of the split-root system in younger plants. Analysis of changes in the Arabidopsis leaf proteome following the de-rooting procedure highlighted the distinct metabolic alterations that totally and partially de-rooted plants undergo during the healing process. This system was also validated for its use in drought experiments, as it offers a way to apply water-soluble compounds to plants subjected to drought stress. By growing plants in a split-root system with both halves being water-deprived, it is possible to apply the required compound to one half of the root system, which can be cut from the main plant once the compound has been absorbed, thus minimizing rehydration and maintaining drought conditions.ConclusionsPartial de-rooting is the suggested method for obtaining split-root systems in small plants like Arabidopsis thaliana, as growth parameters, survival rate, and proteomic analysis suggest that is a less stressful procedure than total de-rooting, leading to a final rosette area much closer to that of uncut plants. Additionally, we provide evidence that split root-systems can be used in drought experiments where water-soluble compounds are applied with minimal effects of rehydration.

Covering: up to the end of 2013 New mass spectrometry imaging (MSI) techniques are gaining importance in the analysis of plant metabolite distributions, and significant technological improvements have been introduced in the past decade. This review provides an introduction to the different MSI techniques and their applications in plant science. The most common methods for sample preparation are described, and the review also features a comprehensive table of published studies in MSI of plant material. A number of significant works are highlighted for their contributions to advance the understanding of plant biology through applications of plant metabolite imaging. Particular attention is given to the possibility for imaging of surface metabolites since this is highly dependent on the methods and techniques which are applied in imaging studies.

PremiseThe objective of this study was to optimize an existing DNA extraction protocol for recalcitrant plant taxa to obtain high‐quality DNA from preserved herbarium tissue suitable for downstream PCR applications.Methods and ResultsLeaf tissue from 30 diverse plant species was obtained from the U.S. National Arboretum Herbarium. Our previous DNA extraction protocol (Gouker et al., 2020, Applications in Plant Sciences 8: e11403) was improved by use of 10X Tris‐EDTA buffer, addition of polyvinylpolypyrrolidone, and omission of sample heating during homogenization, and resulted in total DNA yields ranging from 60–2460 ng. Optimized PCR amplification using universal plant primers for the ITS‐p3/u4 region and the P6 loop of the trnL (UAA) chloroplast intron was successful for most specimens.ConclusionsThis protocol, which is simple, fast, and uses standard laboratory‐grade chemicals, yields DNA from herbarium specimens that is comparable in quality to that from commercially available kits, and is of sufficient quality and quantity for other applications.

New imaging methodologies with high contrast and molecular specificity allow researchers to analyze dynamic processes in plant cells at multiple scales, from single protein and RNA molecules to organelles and cells, to whole organs and tissues. These techniques produce informative images and quantitative data on molecular dynamics to address questions that cannot be answered by conventional biochemical assays. Here, we review selected microscopy techniques, focusing on their basic principles and applications in plant science, discussing the pros and cons of each technique, and introducing methods for quantitative analysis. This review thus provides guidance for plant scientists in selecting the most appropriate techniques to decipher structures and dynamic processes at different levels, from protein dynamics to morphogenesis.

Super-resolution Microscopy in Plant Cell Imaging.

With the rapid advancement of sequencing technologies and bioinformatics, coupled with significant progress in sequencing efficiency and reduced costs, substantial breakthroughs have been achieved in plant functional genomics, evolutionary genetics, and molecular breeding. However, as research deepens, accumulating evidence demonstrates that reference genomes derived from a single individual fail to adequately represent the genetic diversity of entire species. This limitation has catalyzed the emergence of the pan-genome concept. Pan-genome research now stands at the forefront of plant genomics, serving as a pivotal area of focus. Its application in plant studies has unveiled extensive genetic variations, identified numerous novel genes, and significantly enhanced our understanding of genetic diversity within relevant species. This review comprehensively summarizes recent progress in plant pan-genome research, construction methodologies, current applications in plant science, and key achievements. Finally, we outline future research directions, aiming to provide a reference for theoretical and applied pan-genome studies while offering novel perspectives for deciphering the genetic basis of plant breeding, evolutionary domestication, and phenotypic diversity.

Advanced materials for intracellular delivery of plant cells: Strategies, mechanisms and applications

ABSTRACTModern infrared (IR) spectroscopy and imaging has a wide range of applications in health and plant sciences. Initially, it was extensively used for the study of proteins, nucleotides, lipids and carbohydrates. With time, its use has extended to disease assessment to discriminate healthy and diseased samples on the basis of chemical changes. The application of an advanced focal plane array detector, which is able to scan a large area of samples in a short time, helps in investigating specific changes that could be correlated with different environmental stresses. An IR microscope connected with a synchrotron light source further enhances the lateral spatial resolution at diffraction limit because of the compact beam size. For example, synchrotron-based IR spectroscopy imaging in combination with multivariate statistical analysis has been proven to be a powerful non-destructive analytical tool to probe changes in plant cell wall composition/structure in response to biological processes and environmental stresses. New development of nano-Fourier transform infrared spectroscopy (FTIR) combined with scattering type scanning near-field optical microscopy breaks the diffraction limitation, which opens the new area of applications. This review focuses on a new area of diagnostic research as well as development of IR spectroscopy and imaging for biological specimens including compositional changes in plant cell wall.

Stable carbon isotope ratios (δ(13) C) of terrestrial plants are employed across a diverse range of applications in environmental and plant sciences; however, the kind of information that is desired from the δ(13) C signal often differs. At the extremes, it ranges between purely environmental and purely biological. Here, we review environmental drivers of variation in carbon isotope discrimination (Δ) in terrestrial plants, and the biological processes that can either damp or amplify the response. For C3 plants, where Δ is primarily controlled by the ratio of intercellular to ambient CO2 concentrations (ci /ca ), coordination between stomatal conductance and photosynthesis and leaf area adjustment tends to constrain the potential environmentally driven range of Δ. For C4 plants, variation in bundle-sheath leakiness to CO2 can either damp or amplify the effects of ci /ca on Δ. For plants with crassulacean acid metabolism (CAM), Δ varies over a relatively large range as a function of the proportion of daytime to night-time CO2 fixation. This range can be substantially broadened by environmental effects on Δ when carbon uptake takes place primarily during the day. The effective use of Δ across its full range of applications will require a holistic view of the interplay between environmental control and physiological modulation of the environmental signal.

Estimation of leaf chlorophyll content with polarization measurements: Degree of linear polarization