Development of a method for comprehensive and quantitative analysis of plant hormones by highly sensitive nanoflow liquid chromatography-electrospray ionization-ion trap mass spectrometry

Genome-wide epigenetic dynamics of tea leaves under mechanical wounding stress during oolong tea postharvest processing

Understanding the epigenetic responses to mechanical wounding stress during the postharvest processing of oolong tea provides insight into the reprogramming of the tea genome and its impact on tea quality. Here, we characterized the 5mC DNA methylation and chromatin accessibility landscapes of tea leaves subjected to mechanical wounding stress during the postharvest processing of oolong tea. Analysis of the differentially methylated regions and preferentially accessible promoters revealed many overrepresented TF-binding motifs, highlighting sets of TFs that are likely important for the quality of oolong tea. Within these sets, we constructed a chromatin accessibility-mediated gene regulatory network specific to mechanical wounding stress. In combination with the results of the TF-centred yeast one-hybrid assay, we identified potential binding sites of CsMYC2 and constructed a gene regulatory network centred on CsMYC2, clarifying the potential regulatory role of CsMYC2 in the postharvest processing of oolong tea. Interestingly, highly accessible chromatin and hypomethylated cytosine were found to coexist in the promoter region of the indole biosynthesis gene (tryptophan synthase β-subunit, CsTSB) under wounding stress, which indicates that these two important epigenetic regulatory mechanisms are jointly involved in regulating the synthesis of indole during the postharvest processing of oolong tea. These findings improve our understanding of the epigenetic regulatory mechanisms involved in quality formation during the postharvest processing of oolong tea.

Network analysis of metabolomics, transcriptome and hormones reveals propionic acid-mediated novel survival strategy against drought in wheat

Propionic acid (PA), a low-molecular-weight organic acid, is crucial to plant life metabolism. However, the regulatory mechanism of PA-mediated drought resistance in wheat remains largely unknown. Herein, we reported on a regulatory network of PA-mediated drought resistance in wheat using integrated transcriptome and metabolomics analysis and verified genes associated with drought resistance. Compared to the water-treated group, the application of PA alleviated the damage of drought by increasing plant water content, antioxidant enzyme activities and decreasing the malondialdehyde level (MDA). Transcriptome and metabolomics analysis revealed that PA triggered upregulation of key genes and metabolites, including TaBCAT, TaALDH6A1, TaALDH7A1, TaCHI, TaFLS, chrysin, and galangin, which were involved in valine, leucine and isoleucine degradation or flavonoid biosynthesis, respectively. In addition, the expression of genes encoding auxin-related transcription factors (TFs) strikingly increased, such as auxin/indoleacetic acid (AUX/IAA) and auxin response factor (ARF). Moreover, PA activated abscisic acid (ABA) and indole-3-acetic acid (IAA) signalling pathways. Taken together, our findings suggest that PA promotes energy metabolism and antioxidant activities to confer wheat drought resistance by introducing comprehensive and systemic effects of valine, leucine and isoleucine degradation flavonoid biosynthesis. Furthermore, activated AUX/IAA and ARF TFs might serve vital roles in drought resistance via modulating IAA signalling. This study provides novel insights into PA-mediated crop resistance and the improvement of the agroecological environment.

SET DOMAIN GROUP 711-mediated H3K27me3 methylation of cytokinin metabolism genes regulates organ size in rice

Organ size shapes plant architecture during rice (Oryza sativa) growth and development, affecting key factors influencing yield, such as plant height, leaf size, and seed size. Here, we report that the rice Enhancer of Zeste [E(z)] homolog SET DOMAIN GROUP 711 (OsSDG711) regulates organ size in rice. Knockout of OsSDG711 produced shorter plants with smaller leaves, thinner stems, and smaller grains. We demonstrate that OsSDG711 affects organ size by reducing cell length and width and increasing cell number in leaves, stems, and grains. The result of chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) using an antitrimethylation of histone H3 lysine 27 (H3K27me3) antibody showed that the levels of H3K27me3 associated with cytokinin oxidase/dehydrogenase genes (OsCKXs) were lower in the OsSDG711 knockout line Ossdg711. ChIP-qPCR assays indicated that OsSDG711 regulates the expression of OsCKX genes through H3K27me3 histone modification. Importantly, we show that OsSDG711 directly binds to the promoters of these OsCKX genes. Furthermore, we measured significantly lower cytokinin contents in Ossdg711 plants than in wild-type plants. Overall, our results reveal an epigenetic mechanism based on OsSDG711-mediated modulation of H3K27me3 levels to regulate the expression of genes involved in the cytokinin metabolism pathway and control organ development in rice. OsSDG711 may be an untapped epigenetic resource for ideal plant type improvement.

The G protein-coupled receptor COLD1 promotes chilling tolerance in maize during germination

The geographic range and yield of the staple crop maize (Zea mays L.) are both strongly limited by low-temperature conditions. One of the most economical and effective measures for improvement of maize production is chilling tolerance enhancement. In this study, a chilling-tolerance gene in maize, ZmCOLD1, was cloned and characterized. This gene encodes a G protein-coupled receptor that is localized to the plasma membrane and the endoplasmic reticulum. A single nucleotide polymorphism (SNP) in ZmCOLD1, SNP2738, was found to confer chilling tolerance and to have promoted maize adaptations during speciation from teosinte. Overexpression of the excellent haplotype ZmCOLD1Hap11 significantly enhanced chilling tolerance, whereas knocking down ZmCOLD1 increased sensitivity to low temperatures during the germination and seedling stages. ZmCOLD1 was associated with an influx of extracellular Ca2+, increases in abscisic acid content, and decreases in gibberellic acid and indole-3-acetic acid content under low temperatures during the germination stage. ZmCOLD1 interacted with the G protein α subunit ZmCT2 at the plasma membrane, and ZmCT2 interacted with ZmLanCL in the nucleus. These proteins are components of the chilling tolerance signaling pathway in maize that are triggered by abscisic acid and photosynthesis. These results offer novel strategies for improvement of chilling tolerance in key crop species.

Gene editing of ZmGA20ox3 improves plant architecture and drought tolerance in maize

KEY MESSAGE

Editing ZmGA20ox3 can achieve the effect similar to applying Cycocel, which can reduce maize plant height and enhance stress resistance. Drought stress, a major plant abiotic stress, is capable of suppressing crop yield performance severely. However, the trade-off between crop drought tolerance and yield performance turns out to be significantly challenging in drought-resistant crop breeding. Several phytohormones [e.g., gibberellin (GA)] have been reported to play a certain role in plant drought response, which also take on critical significance in plant growth and development. In this study, the loss-of-function mutations of GA biosynthesis enzyme ZmGA20ox3 were produced using the CRISPR-Cas9 system in maize. As indicated by the result of 2-year field trials, the above-mentioned mutants displayed semi-dwarfing phenotype with the decrease of GA1, and almost no yield loss was generated compared with wild-type (WT) plants. Interestingly, as revealed by the transcriptome analysis, differential expressed genes (DEGs) were notably enriched in abiotic stress progresses, and biochemical tests indicated the significantly increased ABA, JA, and DIMBOA levels in mutants, suggesting that ZmGA20ox3 may take on vital significance in stress response in maize. The in-depth analysis suggested that the loss function of ZmGA20ox3 can enhance drought tolerance in maize seedling, reduce Anthesis-Silking Interval (ASI) delay while decreasing the yield loss significantly in the field under drought conditions. The results of this study supported that regulating ZmGA20ox3 can improve plant height while enhancing drought resistance in maize, thus serving as a novel method for drought-resistant genetic improvement in maize.

Can plant hormonomics be built on simple analysis? A review

The field of plant hormonomics focuses on the qualitative and quantitative analysis of the hormone complement in plant samples, akin to other omics sciences. Plant hormones, alongside primary and secondary metabolites, govern vital processes throughout a plant's lifecycle. While active hormones have received significant attention, studying all related compounds provides valuable insights into internal processes. Conventional single-class plant hormone analysis employs thorough sample purification, short analysis and triple quadrupole tandem mass spectrometry. Conversely, comprehensive hormonomics analysis necessitates minimal purification, robust and efficient separation and better-performing mass spectrometry instruments. This review summarizes the current status of plant hormone analysis methods, focusing on sample preparation, advances in chromatographic separation and mass spectrometric detection, including a discussion on internal standard selection and the potential of derivatization. Moreover, current approaches for assessing the spatiotemporal distribution are evaluated. The review touches on the legitimacy of the term plant hormonomics by exploring the current status of methods and outlining possible future trends.

(Z)-3-Hexenol integrates drought and cold stress signaling by activating abscisic acid glucosylation in tea plants

Cold and drought stresses severely limit crop production and can occur simultaneously. Although some transcription factors and hormones have been characterized in plants subjected each stress, the role of metabolites, especially volatiles, in response to cold and drought stress exposure is rarely studied due to lack of suitable models. Here, we established a model for studying the role of volatiles in tea (Camellia sinensis) plants experiencing cold and drought stresses simultaneously. Using this model, we showed that volatiles induced by cold stress promote drought tolerance in tea plants by mediating reactive oxygen species and stomatal conductance. Needle trap microextraction combined with GC-MS identified the volatiles involved in the crosstalk and showed that cold-induced (Z)-3-hexenol improved the drought tolerance of tea plants. In addition, silencing C. sinensis alcohol dehydrogenase 2 (CsADH2) led to reduced (Z)-3-hexenol production and significantly reduced drought tolerance in response to simultaneous cold and drought stress. Transcriptome and metabolite analyses, together with plant hormone comparison and abscisic acid (ABA) biosynthesis pathway inhibition experiments, further confirmed the roles of ABA in (Z)-3-hexenol-induced drought tolerance of tea plants. (Z)-3-Hexenol application and gene silencing results supported the hypothesis that (Z)-3-hexenol plays a role in the integration of cold and drought tolerance by stimulating the dual-function glucosyltransferase UGT85A53, thereby altering ABA homeostasis in tea plants. Overall, we present a model for studying the roles of metabolites in plants under multiple stresses and reveal the roles of volatiles in integrating cold and drought stresses in plants.

Hyphal Growth and Conidia Germination Are Induced by Phytohormones in the Root Colonizing and Plant Growth Promoting Fungus Metarhizium guizhouense

Beneficial associations are very important for plants and soil-dwelling microorganisms in different ecological niches, where communication by chemical signals is relevant. Among the chemical signals, the release of phytohormones by plants is important to establish beneficial associations with fungi, and a recently described association is that of the entomopathogenic ascomycete fungus Metarhizium with plants. Here, we evaluated the effect of four different phytohormones, synthetic strigolactone (GR24), sorgolactone (SorL), 3-indolacetic acid (IAA) and gibberellic acid (GA3), on the fungus Metarhizium guizhouense strain HA11-2, where the germination rate and hyphal elongation were determined at three different times. All phytohormones had a positive effect on germination, with GA3 showing the greatest effect, and for hyphal length, on average, the group treated with synthetic strigolactone GR24 showed greater average hyphal length at 10 h of induction. This work expands the knowledge of the effect of phytohormones on the fungus M. guizhouense, as possible chemical signals for the rapid establishment of the fungus-plant association.

Metabolic profiles of 2-oxindole-3-acetyl-amino acid conjugates differ in various plant species

Auxins are a group of phytohormones that play a key role in plant growth and development, mainly presented by the major member of the family - indole-3-acetic acid (IAA). The levels of free IAA are regulated, in addition to de novo biosynthesis, by irreversible oxidative catabolism and reversible conjugation with sugars and amino acids. These conjugates, which serve as inactive storage forms of auxin and/or degradation intermediates, can also be oxidized to form 2-oxindole-3-acetyl-1-O-ß-d-glucose (oxIAA-glc) and oxIAA-amino acids (oxIAA-AAs). Until now, only oxIAA conjugates with aspartate and glutamate have been identified in plants. However, detailed information on the endogenous levels of these and other putative oxIAA-amino acid conjugates in various plant species and their spatial distribution is still not well understood but is finally getting more attention. Herein, we identified and characterized two novel naturally occurring auxin metabolites in plants, namely oxIAA-leucine (oxIAA-Leu) and oxIAA-phenylalanine (oxIAA-Phe). Subsequently, a new liquid chromatography-tandem mass spectrometry method was developed for the determination of a wide range of IAA metabolites. Using this methodology, the quantitative determination of IAA metabolites including newly characterized oxIAA conjugates in roots, shoots and cotyledons of four selected plant models - Arabidopsis thaliana, pea (Pisum sativum L.), wheat (Triticum aestivum L.) and maize (Zea mays L.) was performed to compare auxin metabolite profiles. The distribution of various groups of auxin metabolites differed notably among the studied species as well as their sections. For example, oxIAA-AA conjugates were the major metabolites found in pea, while oxIAA-glc dominated in Arabidopsis. We further compared IAA metabolite levels in plants harvested at different growth stages to monitor the dynamics of IAA metabolite profiles during early seedling development. In general, our results show a great diversity of auxin inactivation pathways among angiosperm plants. We believe that our findings will greatly contribute to a better understanding of IAA homeostasis.

Dual-template hydrophilic imprinted resin as an adsorbent for highly selective simultaneous extraction and determination of multiple trace plant growth regulators in red wine samples

In recent years, numerous plant growth regulators have been found in foods and have a toxicity to human health, so its simultaneous multiple monitoring is urgently. For the first time, a rapid, accurate, and high-selective method was established to extract and determine multiple plant growth regulators simultaneously in red wines using a new dual-template hydrophilic molecularly imprinted resin (DHMIR) as an adsorbent of pipette tip solid-phase extraction coupled with HPLC. The as-prepared DHMIR combined the advantages of the hydrophilicity of hydrophilic resin and multi-imprinted recognition of dual-template molecular imprinting, overcoming the poor imprinted recognition ability of traditional imprinting materials in water and low extraction efficiency to multiple targets. Under the optimized conditions, the proposed method exhibited high sensitivity (2.29-3.94 ng mL^-1) and recoveries (80.9-109.0 %) using only 15 mg DHMIR. This study provides an effective strategy for rapid, accurate, low-cost, and high-selective determination of the multiple analytes in food samples.

Interactive effects of polystyrene microplastics and Pb on growth and phytochemicals in mung bean (Vigna radiata L.)

Interaction of different pollutants can aggravate hazards to biotic components in agroecosystems. Microplastics (MPs) are especially needed to be focused on because of their increasing use in life around the globe. We investigated the interactive impacts of polystyrene microplastics (PS-MP) and lead (Pb) on mung bean (Vigna radiata L.). Toxicity of MPs and Pb directly impeded V. radiata attributes. In combination i.e., M2P2 (40 µM Pb + 4.0 mg L-1 MPs) predominantly reduced the shoot root fresh and dry weights. \ Pb and PS-MP impaired the Rubisco activity and chlorophyll contents. The dose dependent relationship (M2P2) discomposed indole 3-acetic acid by 59.02%. Individual treatments P2 (40 µM Pb) and M2 (4.0 mg L^-1 MPs) respectively instigated a decline (44.07% and 27.12%) in IBA, while ABA was elevated. M2 significantly enhanced the contents of Alanine (Ala), Arginine (Arg), Proline (Pro), and glycine (Gly) by 64.11%, 63%, and 54% compared to control. Lysine (Lys) and Valine (Val) presented a converse relationship with other amino acids. Except for control, a gradual decline in yield parameters were observed in individual and combined applications of PS-MP. Proximate composition of carbohydrates, lipids and proteins also reflected a clear decrease in these compounds after combined application of Pb and MPs. Although, individual doses caused a decline in these compounds but effect of combined doses Pb and PS-MP was highly significant. Our results demonstrated the toxicity effect of Pb and MP in V. radiata attributes that is mainly linked with cumulative physiological and metabolic perturbations. These collective negative impacts of different doses of MPs and Pb on V. radiata would certainly pose serious implications for humans.

Jasmonic acid enhances osmotic stress responses by MYC2-mediated inhibition of protein phosphatase 2C1 and response regulators 26 transcription factor in tomato

The jasmonic acid (JA) signaling pathway is involved in the plant response to drought stress. JA and other hormones synergistically regulate the drought response in plants. However, the molecular mechanism underlying this synergism remains poorly defined. In the present study, transcriptome analyses of guard cells and quantitative PCR experiments revealed that MYC2 negatively regulated the negative regulator of ABA signaling, SlPP2C1, and the type-B response regulator in the cytokinin pathway, SlRR26, and this negative regulation was direct. SlRR26 overexpression reduced drought tolerance in transgenic tomatoes, whereas slrr26^cr lines were more tolerant to drought. SlRR26 negatively modulated reactive oxygen species levels in stomata and stomatal closure through RobhB. Moreover, SlRR26 overexpression counteracted JA-mediated stomatal closure, suggesting that SlRR26 played a negative role in the JA-mediated drought response. These findings suggest that MYC2 plays a key role in JA-regulated stomatal closure under drought stress by inhibiting SlPP2C1 and SlRR26.

Toxicity effects of nanoplastics on soybean (Glycine max L.): Mechanisms and transcriptomic analysis

Microplastic (MP) pollution has become a major concern in recent years. In agricultural production, MPs can not only affect the growth of crops but also affect yield. Compared with micron-sized MPs, nanoplastics (NPs) may be more harmful to plants. However, the effects of NPs on plant growth and development have attracted relatively little attention. As such, research has currently plateaued at the level of morphology and physiology, and the molecular mechanisms are still unclear. In this study, soybeans (Glycine max L.) were treated with polystyrene nanoplastics (PS-NPs) to observe phenotypic changes and measure the effects of PS-NPs on diverse aspects of soybeans. Compared to the control group, the soybean stem and root lengths were inhibited by 11.78% and 12.58%, respectively. The reactive oxygen species content and the antioxidant enzyme activities changed significantly (p < 0.05). The accumulation of manganese (Mn) and magnesium (Mg) in the roots revealed that root transmembrane transport was affected by PS-NPs stress. The content of salicylic acid 2-O-β-glucoside was inhibited whereas the accumulation of l-tryptophan, the precursor of auxin synthesis, was significantly increased (p < 0.05) in leaves. Transcriptomic analysis showed that PS-NPs could affect soybean DNA repair, membrane protein transport, and hormone synthesis and response. This study revealed the toxicity of NPs to soybeans and that NPs affected a variety of biological processes through transcriptome and hormone metabolome analysis, which provides a theoretical basis to further study the molecular mechanism of the effects on plants.

Solid Phase Microextraction-Multicapillary Column-Ion Mobility Spectrometry (SPME-MCC-IMS) for Detection of Methyl Salicylate in Tomato Leaves

Methyl salicylate (MeSA) is a plant-signaling molecule that plays an essential role in the regulation of plant responses to biotic and abiotic pathogens. In this work, solid phase microextraction (SPME) and a multicapillary column (MCC) are coupled to ion mobility spectrometry (IMS) to detect MeSA in tomato leaves. The SPME-MCC-IMS method provides two-dimensional (2D) separation by both MCC and IMS, based on the retention and drift times. The effect of the IMS polarity on the separation efficiency of MCCs was also investigated. In the positive polarity, ionization of MeSA resulted in [MeSA + H]⁺ formation while, in the negative, deprotonated ions, [MeSA - H]^-, and the O₂^- adduct ion, [MeSA + O₂]^-, were formed. In the real sample analysis, the negative polarity operation resulted in the suppression of many matrix molecules and thus in the reduction of interferences. Four different SPME fibers were used for head space analysis, and four MCC columns were investigated. In the negative polarity, complete separation was achieved for all of the MCCs columns. The limits of detection (LODs) of 0.1 μg mL^-1 and linear range of 0.25-12 μg mL^-1 were obtained for the measurement of MeSA in a standard solution (H₂O/CH₃OH, 50:50) by the SPME-IMS method with a 5 min extraction time using an SPME with a PDMS fiber, in the negative mode of IMS. The MeSA contents of fresh tomato leaves were determined as 1.5-9.8 μg g^-1, 24-96 h after inoculation by tomato mosaic ringspot virus (ToRSV).

SlMYC2 mediates stomatal movement in response to drought stress by repressing SlCHS1 expression

Drought stress limits plant development and reproduction. Multiple mechanisms in plants are activated to respond to stress. The MYC2 transcription factor is a core regulator of the jasmonate (JA) pathway and plays a vital role in the crosstalk between abscisic acid (ABA) and JA. In this study, we found that SlMYC2 responded to drought stress and regulated stomatal aperture in tomato (Solanum lycopersicum). Overexpression of SlMYC2 repressed SlCHS1 expression and decreased the flavonol content, increased the reactive oxygen species (ROS) content in guard cells and promoted the accumulation of JA and ABA in leaves. Additionally, silencing the SlCHS1 gene produced a phenotype that was similar to that of the MYC2-overexpressing (MYC2-OE) strain, especially in terms of stomatal dynamics and ROS levels. Finally, we confirmed that SlMYC2 directly repressed the expression of SlCHS1. Our study revealed that SlMYC2 drove stomatal closure by modulating the accumulation of flavonol and the JA and ABA contents, helping us decipher the mechanism of stomatal movement under drought stress.

Partially functional NARROW LEAF1 balances leaf photosynthesis and plant architecture for greater rice yield

NARROW LEAF1 (NAL1) is an elite gene in rice (Oryza sativa), given its close connection to leaf photosynthesis, hybrid vigor, and yield-related agronomic traits; however, the underlying mechanism by which this gene affects these traits remains elusive. In this study, we systematically measured leaf photosynthetic parameters, leaf anatomical parameters, architectural parameters, and agronomic traits in indica cultivar 9311, in 9311 with the native NAL1 replaced by the Nipponbare NAL1 (9311-NIL), and in 9311 with the NAL1 fully mutated (9311-nal1). Leaf length, width, and spikelet number gradually increased from lowest to highest in 9311-nal1, 9311, and 9311-NIL. In contrast, the leaf photosynthetic rate on a leaf area basis, leaf thickness, and panicle number gradually decreased from highest to lowest in 9311-nal1, 9311, and 9311-NIL. RNA-seq analysis showed that NAL1 negatively regulates the expression of photosynthesis-related genes; NAL1 also influenced expression of many genes related to phytohormone signaling, as also shown by different leaf contents of 3-Indoleacetic acid, jasmonic acid, Gibberellin A3, and isopentenyladenine among these genotypes. Furthermore, field experiments with different planting densities showed that 9311 had a larger biomass and yield advantage under low planting density compared to either 9311-NIL or 9311-nall. This study shows both direct and indirect effects of NAL1 on leaf photosynthesis; furthermore, we show that a partially functional NAL1 allele helps maintain a balanced leaf photosynthesis and plant architecture for increased biomass and grain yield in the field.

Comparative Proteomics Combined with Morphophysiological Analysis Revealed Chilling Response Patterns in Two Contrasting Maize Genotypes

Maize yield is significantly influenced by low temperature, particularly chilling stress at the maize seedling stage. Various physiological approaches have been established to resist chilling stress; however, the detailed proteins change patterns underlying the maize chilling stress response at the seedling stage remain unknown, preventing the development of breeding-based methods to resist chilling stress in maize. Thus, we performed comprehensive physiological, comparative proteomics and specific phytohormone abscisic acid (ABA) assay on different maize inbred lines (tolerant-line KR701 and sensitive-line hei8834) at different seedling stages (the first leaf stage and third leaf stage) under chilling stress. The results revealed several signalling proteins and pathways in response to chilling stress at the maize seedling stage. Meanwhile, we found ABA pathway was important for chilling resistance of tolerant-line KR701 at the first leaf stage. Related chilling-responsive proteins were further catalogued and analysed, providing a resource for further investigation and maize breeding.

Nano liquid chromatography, an updated review

Low flow chromatography has a rich history of innovation but has yet to reach widespread implementation in bioanalytical applications. Improvements in pump technology, microfluidic connections, and nano-electrospray sources for mass spectrometry have laid the groundwork for broader application, and innovation in this space has accelerated in recent years. This article reviews the instrumentation used for nano-flow liquid chromatography , the types of columns employed, and strategies for multi-dimensionality of separations, which is key to the future state of the technique to the high-throughput needs of modern bioanalysis. An update of the current applications where nano-LC is widely used, such as proteomics and metabolomics, is discussed. But the trend towards biopharmaceutical development of increasingly complex, targeted, and potent therapeutics for the safe treatment of disease drives the need for ultimate selectivity and sensitivity of our analytical platforms for targeted quantitation in a regulated space. The selectivity needs are best addressed by mass spectrometric detection, especially at high resolutions, and exquisite sensitivity is provided by nano-electrospray ionization as the technology continues to evolve into an accessible, robust, and easy to use platform.

The Effect of Low Temperature Stress on the Leaves and MicroRNA Expression of Potato Seedlings

In recent years, with the wanton destruction of the ecological environment by humans and the frequent occurrence of extreme bad weather, many places that should have been warm and blooming in spring have instead experienced the phenomenon of the “April blizzard,” which has seriously affected China's crops, especially spring potato production in most areas. Potato cultivars, especially potato seedlings, are sensitive to frost, and low temperature frost has become one of the most important abiotic stresses affecting potato production. Potato cold tolerance is regulated by a complex gene network. Although some low temperature resistant microRNAs have been identified, little is known about the role of miRNAs in response to low temperature stress in potato. Therefore, the objective of this study is to clarify the influence of low temperature stress on the miRNA expression of potato by comparing the expression differences of miRNA in potato which was treated with different low temperatures. For the study, 307 known miRNAs belonging to 73 small RNA families and 211 novel miRNAs were obtained. When the temperature decreased, the number of both known and novel miRNA decreased, and the minimum temperature was −2°C. Most of the miRNAs respond to low temperature, drought, and disease stress; some conserved miRNAs were first found to respond to low temperature stress in potato, such as stu-miR530, stu-miR156d, and stu-miR167b. The Gene Ontology, Kyoto Encyclopedia of Genes, and Genomes pathway enrichment analysis of 442 different expression miRNAs target genes indicated that there existed diversified low temperature responsive pathways, but Abscisic Acid was found likely to play a central coordinating role in response to low temperature stress in many metabolism pathways. Quantitative real-time PCR assays indicated that the related targets were negatively regulated by the tested different expression miRNAs during low temperature stress. The results indicated that miRNAs may play an important coordination role in response to low temperature stress in many metabolic pathways by regulating abscisic acid and gibberellin, which provided insight into the roles of miRNAs during low temperature stress and would be helpful for alleviating low temperature stress and promoting low temperature resistant breeding in potatoes.

The potential health risks and environmental pollution associated with the application of plant growth regulators in vegetable production in several suburban areas of Hanoi, Vietnam

Plant growth regulators (PGRs) play a pivotal role in increasing vegetable productivity, but they have many drawbacks that can include health and safe concerns of consumers. In this study, the plant growth regulators (PGRs) contents of 111 Brassica juncea (L.) Czern. samples collected from six main suburban areas of Hanoi, Vietnam, were determined by liquid chromatography-electrospray tandem mass spectrometry. Results showed the presence of PGRs residues in 83 analyzed samples (74.77%). Eight PGRs, including Indole-3-acetic acid (IAA), Indole-3-butyric acid (IBA), Indole-3-carboxylic acid (ICA), 3-Indolepropionic acid (IPA), Gibberellin A₃ (GA₃), Gibberellin A₄ (GA₄), Gibberellin A₇ (GA₇) and Trans-zeatin (tZ), were found in B. juncea with the average residues dropped in the range of 0.04 and 0.65 mg kg^-1. GA₄ was considered as the most popular PGR applying in vegetable production in the investigated areas. Notably, the concentrations of gibberellins were higher than the regulations in vegetables and fruits in Europe, USA and Japan. This might be the potential health risks to consumers and environmental pollution, which necessary to be controlled with consideration of residue regulations.

Polystyrene microplastics disturb the redox homeostasis, carbohydrate metabolism and phytohormone regulatory network in barley

As emerging contaminants, microplastics (mPS, <5 mm) have been reported to adversely affect the plant growth; however, the mechanisms of mPS-induced growth limitation are rarely known. Here, it was found that the plastic particles were absorbed and accumulated in barley plants, which limited the development of rootlets. The mPS-treated plants had significantly higher concentrations of H₂O₂ and O₂^- in roots than the control. The mPS significantly increased the activities of dehydroascorbate reductase, glutathione reductase, ADP-Glucose pyrophosphorylase, fructokinase and phosphofructokinase, while decreased the activities of cell wall peroxidase, vacuolar invertase, sucrose synthase, phosphoglucomutase, glucose-6-phosphate dehydrogenase and phosphoglucoisomerase in roots. The changes in activities of carbohydrate and ROS metabolism enzymes in leaves showed a different trend from that in roots. The mPS plants possessed a higher trans-zeatin concentration while lower concentrations of indole-3-acetic acid, indole-3-butyric acid and dihydrozeatin than the control plants in leaves. However, the phytohormone changes in roots were distinct from those in leaves under mPS. In addition, significant correlations between enzyme activities and phytohormone concentrations were found. It was suggested that the phytohormone regulatory network plays key roles in regulating the activities of key enzymes involved in carbohydrate and ROS metabolisms in response to mPS in barley.

Transcription-associated metabolomic adjustments in maize occur during combined drought and cold stress

Although simultaneous drought and cold stress occurs, especially in northwestern and eastern regions of China, and is an important factor limiting agricultural productivity, there are few studies focusing on plant responses to a combination of drought and cold stress. Here, by partially overlapping drought and cold stresses, we characterized the acclimation of maize (Zea mays B73) to these two stresses using physiological measurements, as well as comparative transcriptomics combined with metabolomics and hormonal analyses during the stress treatments and recovery stages. The combined drought and cold stress and drought stress alone were accompanied by a decline in photosynthetic capacity and enhanced transcriptional response, and subsequent recovery of these following removal from stress, whereas cold stress alone was accompanied by irreversible damage to photosynthetic capacity and chloroplast structure. The stress combination induced transcription-associated metabolomic alterations, in which raffinose, trehalose-6-phosphate, and proline accumulated, and monosaccharide abundance increased. Concomitantly, the increased abscisic acid (ABA) content and upregulated ABA signaling pathway may have provided the transcriptional regulation for the metabolic changes. In a parallel experiment, ABA treatments prior to exposure of the plants to cold stress primed the plants to survive the cold stress, thus confirming a key role for the endogenous ABA activated by the drought pretreatment in acclimation of the plants to cold. We present a model showing that the plant response to the combined stress is multi-faceted and reveal an ABA-dependent maize acclimation mechanism to the stress combination.

Simultaneous determination of multiple phytohormones in tomato by ionic liquid-functionalized carbon fibers-based solid-phase microextraction coupled with liquid chromatography-mass spectrometry

Phytohormones are interrelated by synergistic or antagonistic crosstalk and play important roles in the regulation of plant growth and development. In order to understand the interaction between phytohormones in the plant physiological network, it is necessary to determine trace levels of multiple phytohormones simultaneously in a complex matrix. Here, we synthesized ionic liquids containing different functional groups and modified the surface of carbon fibers with them. Based on these carbon fibers-ionic liquid (CFs-IL) materials, a solid phase microextraction method was developed to enable the simultaneous extraction of phytohormones. The adsorption specificity of multiple phytohormones was studied by identifying the hydrophobic, electrostatic, and π-π interactions, as well as hydrogen bonds, which favor simultaneous extraction of the relevant acidic, alkaline and neutral phytohormones by improving compatibility. The proposed method, coupled with liquid chromatography-tandem mass spectrometry, was applied to the simultaneous determination of 13 acidic, alkaline and neutral phytohormones in tomato. The limits of quantification were found to be in the range of 0.32-54.05 ng mL^-1 and 4.6-185.8 pg mL^-1, respectively, when measured by QQQ and Q-TOF. All of the relative recoveries were in the range of 94.40-113.37% with RSDs ≤15.36% (n = 3) for spiked tomato samples. This method is expected to be widely applied to multiple phytohormones analysis for in-depth researches concerning the physiological networks of plants.

Supramolecular solvent-based high-throughput sample treatment for monitoring phytohormones in plant tissues

Quantification of endogenous hormones in plants is essential to understand their growth, development and response to biotic and abiotic stresses. However, it is challenging to develop high-throughput sample treatments from complex plant tissues containing low amounts of structurally unrelated and labile phytohormones while delivering clean and analyte-enriched extracts. In this paper we propose the use of supramolecular solvents (SUPRASs) made up or inverted hexagonal nanostructures of alkanols to address this challenge. The strategy was applied, as a proof of concept, to the quantification of stress-related phytohormones belonging to different categories (abscisic acid, salicylic acid, jasmonic acid, methyl jasmonate and 3-indoleacetic acid) in melon and pepper leaves. Sample treatment consisted in a single extraction-cleanup step involving the use of a low volume of SUPRAS (244 μL), the stirring (5 min) and centrifugation (15 min) of the sample at room temperature, and the direct analysis of the extract by liquid chromatography tandem mass spectrometry (LC-MS/MS). This high-throughput sample treatment method delivered excellent results for the target phytohormones regarding absolute recoveries (80-92%), method quantification limits (0.05-2 ng g^-1), reproducibility (1-7%) and matrix effects (+13 to -31%), in both melon and pepper leaves, compared to reported methods based on repetitive solvent extraction, purification and solvent evaporation steps. The method was successfully applied to determine target hormones in melon and pepper plants for the evaluation of the effect of thermal stress. It was found that their concentration increased in the ranges 1.2-1.9 and 1.3-3.8 times in melon and pepper leaves, respectively, compared with control samples.

Improved Solid-Phase Extraction for Simple, Sensitive, and Efficient Determination of Trace Plant Growth Regulators in Cherry Tomatoes by High-Performance Liquid Chromatography

The overuse of plant growth regulators (PGRs) in agricultural products has gradually increased in recent years, resulting in hazardous effects on food safety and human health. For the first time, a sensitive, accurate, and low-cost analytical method involving improved solid-phase extraction coupled with high-performance liquid chromatography was developed to determine trace PGRs in cherry tomatoes. Thereafter, the extraction mechanism and conditions were elucidated. Under optimized conditions, good linearity (0.04-400 ng g^-1; r ≥ 0.9996) and lower limits of detection (0.005-0.006 ng g^-1) were observed. The recoveries were 81.4-90.1%, with relative standard deviations of ≤6.7% (three levels). Finally, the developed method was successfully used to detect trace PGRs in cherry tomatoes. The results illustrated that this sensitive method shows great potential for application to monitor trace PGRs in agricultural products and, thus, provide technical support for food safety and public health.

Rice OsBT1 regulates seed dormancy through the glycometabolism pathway

Seed dormancy and germination in rice (Oryza sativa L.) are complex and important agronomic traits that involve a number of physiological processes and energy. A mutant named h470 selected from a⁶⁰Co-radiated indica cultivar N22 population had weakened dormancy that was insensitive to Gibberellin (GA) and Abscisic acid (ABA). The levels of GA₄ and ABA were higher in h470 than in wild-type (WT) plants. The gene controlling seed dormancy in h470 was cloned by mut-map and transgenesis and confirmed to encode an ADP-glucose transporter protein. A 1 bp deletion in Os02g0202400 (OsBT1) caused the weaker seed dormancy in h470. Metabolomics analyses showed that most sugar components were higher in h470 seeds than the wild type. The mutation in h470 affected glycometabolism.

An Analytical System for Single-Cell Metabolomics of Typical Mammalian Cells Based on Highly Sensitive Nano-Liquid Chromatography Tandem Mass Spectrometry

The rapid development of next-generation sequencing techniques has enabled single-cell genomic and transcriptomic analyses, which have revealed the importance of heterogeneity in biological systems. However, analytical methods to accurately identify and quantify comprehensive metabolites from single mammalian cells with a typical diameter of 10-20 μm are still in the process of development. The aim of this study was to develop a single-cell metabolomic analytical system based on highly sensitive nano-liquid chromatography tandem mass spectrometry (nano-LC-MS/MS) with multiple reaction monitoring. A packed nano-LC column (3-μm particle-size pentafluorophenylpropyl Discovery HSF5 of dimensions 100 μm i.d.×180 mm) was prepared using a slurry technique. The optimized nano-LC-MS/MS method showed 3-132-fold (average value, 26-fold) greater sensitivity than semimicro-LC-MS/MS, and the detection limits for several hydrophilic metabolites, including amino acids and nucleic acid related metabolites were in the sub-fmol range. By combining live single-cell sampling and nano-LC-MS/MS, we successfully detected 18 relatively abundant hydrophilic metabolites (16 amino acids and 2 nucleic acid related metabolites) from single HeLa cells (n=22). Based on single-cell metabolic profiles, the 22 HeLa cells were classified into three distinct subclasses, suggesting differences in metabolic function in cultured HeLa cell populations. Our single-cell metabolomic analytical system represents a potentially useful tool for in-depth studies focused on cell metabolism and heterogeneity.

In-Line Sample Processing System with an Immobilized Trypsin-Packed Fused-Silica Capillary Tube for the Proteomic Analysis of a Small Number of Mammalian Cells

Omics analysis at single-cell resolution has helped to demonstrate the shaping of cellular heterogeneity on the basis of the expression of various molecules. However, in-depth proteomic analysis of low-quantity samples has remained challenging because of difficulties associated with the measurement of large numbers of proteins by shotgun proteomics using nanoflow liquid chromatography tandem mass spectrometry (nano-LC/MS/MS). To meet such a demand, we developed a method called in-line sample preparation for efficient cellular proteomics (ISPEC) in which cells were captured, directly lysed, and digested with immobilized trypsin within fused-silica capillaries. ISPEC minimized sample loss during the sample preparation processes with a relatively small number of mammalian cells (<1000 cells) and improved the stability and efficiency of digestion by immobilized trypsin, compared to a conventional preparation method. Using our optimized ISPEC method with nano-LC/MS/MS analysis, we identified 1351, 351, and 60 proteins from 100 cells, 10 cells, and single cells, respectively. The linear response of the signal intensity of each peptide to the introduced cell number indicates the quantitative recovery of the proteome from a very small number of cells. Thus, our ISPEC strategy facilitates quantitative proteomic analysis of small cell populations.

Recent developments and emerging trends of mass spectrometric methods in plant hormone analysis: a review

Plant hormones are naturally occurring small molecule compounds which are present at trace amounts in plant. They play a pivotal role in the regulation of plant growth. The biological activity of plant hormones depends on their concentrations in the plant, thus, accurate determination of plant hormone is paramount. However, the complex plant matrix, wide polarity range and low concentration of plant hormones are the main hindrances to effective analyses of plant hormone even when state-of-the-art analytical techniques are employed. These factors substantially influence the accuracy of analytical results. So far, significant progress has been realized in the analysis of plant hormones, particularly in sample pretreatment techniques and mass spectrometric methods. This review describes the classic extraction and modern microextraction techniques used to analyze plant hormone. Advancements in solid phase microextraction (SPME) methods have been driven by the ever-increasing requirement for dynamic and in vivo identification of the spatial distribution of plant hormones in real-life plant samples, which would contribute greatly to the burgeoning field of plant hormone investigation. In this review, we describe advances in various aspects of mass spectrometry methods. Many fragmentation patterns are analyzed to provide the theoretical basis for the establishment of a mass spectral database for the analysis of plant hormones. We hope to provide a technical guide for further discovery of new plant hormones. More than 140 research studies on plant hormone published in the past decade are reviewed, with a particular emphasis on the recent advances in mass spectrometry and sample pretreatment techniques in the analysis of plant hormone. The potential progress for further research in plant hormones analysis is also highlighted.

A multi-channel localized surface plasmon resonance system for absorptiometric determination of abscisic acid by using gold nanoparticles functionalized with a polyadenine-tailed aptamer

A multi-channel localized surface plasmon resonance system is described for absorptiometric determination of abscisic acid (ABA). The system is making use of gold nanoparticles and consists of a broadband light source, a multi-channel alignment device, and a fiber spectrometer. The method is based on the specific interaction between an ABA-binding aptamer and ABA. This induces the growth of gold nanoparticles (AuNPs) functionalized with a polyadenine-tailed aptamer that act as optical probes. Different concentrations of ABA give rise to varied morphologies of grown AuNPs. This causes a change of absorption spectra which is recorded by the system. ABA can be quantified by measurement of the peak wavelength shifts of grown AuNPs. Under optimized conditions, this method shows a linear relationship in the 1 nM to 10 μM ABA concentration range. The detection limit is 0.51 nM. The sensitivity of the ABA assay is strongly improved compared to the method based on salt-induced AuNP aggregation. This is attributed to the use of a poly-A-tailed aptamer and the catalytic ability of AuNPs. In the actual application, the ABA concentration of ABA in fresh leaves of rice is measured with the maximum relative error of 8.03% in comparison with the ELISA method. Graphical abstractSchematic representation of an absorptiometric approach for determination of abscisic acid based on the growth of polyA-tailed aptamer-AuNPs probes and a multi-channel localized surface plasmon resonance system.

Uptake of pharmaceuticals acts as an abiotic stress and triggers variation of jasmonates in Malabar spinach (Basella alba. L)

In recent years, pharmaceuticals have received increasing attentions because of their potential risks to the environment, but researches focusing on their impacts on defense system of living plants are still lacking. As an important class of phytohormones, jasmonates play crucial roles in plant defense system against environmental stress. In order to investigate the effect of pharmaceuticals uptake on endogenous jasmonates, an in vivo solid phase microextraction (SPME) method was established to simultaneously detect and monitor both pharmaceuticals and jasmonates in living plants. The proposed method exhibited wide linear ranges, high sensitivity (limits of detection ranging 0.0043-0.035 ng g^-1 for pharmaceuticals and 0.091-0.22 ng g^-1 for jasmonates, respectively), and satisfactory reproducibility (relative standard deviation of intrafiber ranging 4.2%-8.6% and interfiber ranging 5.2%-8.2%, respectively). Subsequently, this method was successfully applied to track the concentrations of each pharmaceutical and corresponding jasmonates in living Malabar spinach plants (Basella alba. L) exposed to three common pharmaceuticals (i.e. gemfibrozil, mefenamic acid and tolfenamic acid) over 15 days. In result, all pharmaceuticals appeared to trigger intensive biosynthesis of jasmonic acid (JA) (3.1-9.4 times of control) while reduced the concentration of methyl jasmonate (MeJA) (18.3%-38.1% of control). We inferred that uptake of pharmaceuticals acted as an abiotic stress and stimulated the plant defense response because of the variation of jasmonates. To the best of our knowledge, this is the first study applying SPME to detect and track both pharmaceuticals and phytohormones in living plants, which not only provided a glimpse to the adverse effect of pharmaceuticals on plants as well as the regulation of endogenous jasmonates, but also set a promising template for future in vivo analysis of xenobiotics and plant endogenous substances.

Determination of Major Phytohormones in Fourteen Different Seaweeds Utilizing SPE–LC–MS/MS

Analysis of plant growth regulators (PGRs) should be approached by considering their extremely low concentrations and serious interfering effects that result from the matrix of various plant tissues. In the current research, the separation and simultaneous determination of different classes of phytohormones in 14 seaweeds collected from Turkey seashores were achieved by using solid-phase extraction (SPE) followed by a rapid and sensitive liquid chromatography tandem mass detection method. OASIS HLB (Hydrophilic-Lipophilic Balance) cartridges were successfully used for SPE process to eliminate the matrix effect and enhance the PGRs including zeatin, benzyl amino purine, indole-3-acetic acid, abscisic acid and gibberellic acid within partially different polarities. Based on the optimized experimental conditions, the method presented excellent performance related to linearity (r, 0.9996–0.9999) within the ranges of 0.5–500 ng/mL, relative standard deviation values ((1.43–2.01) for intraday and (2.36–3.50) for interday)), the limit of detection (0.01–0.84 μg/L) and the limit of quantification (0.02–2.76 μg/L). The obtained results confirm that the SPE–liquid chromatography/tandem mass spectrometry method performed is highly effective and convenient for routine analyses of trace amounts of the tested phytohormones in seaweeds and any other plant samples as well.

A classification of liquid chromatography mass spectrometry techniques for evaluation of chemical composition and quality control of traditional medicines

Natural products (NPs) and traditional medicines (TMs) are used for treatment of various diseases and also to develop new drugs. However, identification of drug leads within the immense biodiversity of living organisms is a challenging task that requires considerable time, labor, and computational resources as well as the application of modern analytical instruments. LC-MS platforms are widely used for both drug discovery and quality control of TMs and food supplements. Moreover, a large dataset generated during LC-MS analysis contains valuable information that could be extracted and handled by means of various data mining and statistical tools. Novel sophisticated LC-MS based approaches are being introduced every year. Therefore, this review is prepared for the scientists specialized in pharmacognosy and analytical chemistry of NPs as well as working in related areas, in order to navigate them in the world of diverse LC-MS based techniques and strategies currently employed for NP discovery and dereplication, quality control, pattern recognition and sample comparison, and also in targeted and untargeted metabolomic studies. The suggested classification system includes the following LC-MS based procedures: elemental composition determination, isotopic fine structure analysis, mass defect filtering, de novo identification, clustering of the compounds in Molecular Networking (MN), diagnostic fragment ion (or neutral loss) filtering, manual dereplication using MS/MS data, database-assisted peak annotation, annotation of spectral trees, MS fingerprinting, feature extraction, bucketing of LC-MS data, peak profiling, predicted metabolite screening, targeted quantification of biomarkers, quantitative analysis of multi-component system, construction of chemical fingerprints, multi-targeted and untargeted metabolite profiling.

Dispersive Matrix Solid-Phase Extraction Method Coupled with High Performance Liquid Chromatography-Tandem Mass Spectrometry for Ultrasensitive Quantification of Endogenous Brassinosteroids in Minute Plants and Its Application for Geographical Distribution Study

An ultrasensitive analysis method for quantification of endogenous brassinosteroids in fresh minute plants was developed based on dispersive matrix solid-phase extraction coupled with high performance liquid chromatography-tandem mass spectrometry. During the dispersive matrix solid-phase extraction, plant samples were first ground with solid sorbent (dispersant) in one microcentrifuge tube and then centrifuged after adding extraction solvent and cleanup materials (another type of sorbent). Three protocols based on dispersive matrix solid-phase extraction were compared and discussed for plant samples with different matrix complexity. The choice of any protocol was a compromise of increasing purification efficiency and decreasing sample loss. Under optimized conditions, the limits of detection were 1.38-6.75 pg mL^-1 for five brassinosteroids in the oilseed rape samples. The intraday and interday precisions were in the range of 0.8%-9.8% and 4.6%-17.3%, respectively. The proposed method was successfully applied to detection of endogenous brassinosteroids in milligram oilseed rape (2.0 mg) and submilligram Arabidopsis thaliana seedlings (0.5 mg). Finally, the geographical distribution of five endogenous brassinosteroids of Brassica napus L. oilseed rape in different provinces of origin in the Yangtze River basin was described.

Trace analysis of multi-class phytohormones in Oryza sativa using different scan modes in high-resolution Orbitrap mass spectrometry: method validation, concentration levels, and screening in multiple accessions

Phytohormones are signaling and regulating metabolites involved in numerous plant processes, including growth, development, and responses to stress. Currently, the focus is on the analysis of multiple phytohormones in order to characterize crosstalk and hormone signaling networks. In this paper, representative phytohormones of the major classes are simultaneously determined in rice tissues by a generic solid-liquid extraction, followed by liquid chromatography and electrospray ionization high-resolution tandem mass spectrometry using a Q-Exactive™ instrument. After a thorough optimization of the sample preparation, the analytical method was fully validated toward the ultra-trace quantification of six a priori selected plant hormones using three scan modes of the quadrupole-Orbitrap instrument: full-scan high-resolution mass spectrometry, targeted single ion monitoring (t-SIM), and t-SIM followed by data-dependent tandem mass spectrometry. Overall, a similar quantitative performance was noticed for the different scan modes. The analytical method was successfully applied to measure basal phytohormone levels in six different rice accessions, comprising Oryza sativa ssp. japonica, indica, and Oryza glaberrima. Hormone concentrations were higher in shoots than in roots or at least similar. Except for a lower level of salicylic acid in shoots of O. glaberrima versus O. sativa, no other differences in hormone levels could be noticed that were dependent of the (sub)species assignment of the analyzed accessions. Making use of the benefits of full-scan high-resolution mass spectrometry, a first post-run suspect screening was performed, suggesting - based on accurate mass measurements and isotopic patterns - the possible presence of about 50 additional plant hormones in the rice tissues. Graphical abstract ᅟ.

A review of nanoscale LC-ESI for metabolomics and its potential to enhance the metabolome coverage

Liquid chromatography-electrospray ionisation-mass spectrometry (LC-ESI-MS) platforms are widely used to perform high throughput untargeted profiling of biological samples for metabolomics-based approaches. However, these LC-ESI platforms usually favour the detection of metabolites present at relatively high concentrations because of analytical limitations such as ion suppression, thus reducing overall sensitivity. To counter this issue of sensitivity, the latest in terms of analytical platforms can be adopted to enable a greater portion of the metabolome to be analysed in a single analytical run. Here, nanoflow liquid chromatography-nanoelectrospray ionisation (nLC-nESI), which has previously been utilised successfully in proteomics, is explored for use in metabolomic and exposomic research. As a discovery based field, the markedly increased sensitivity of these nLC-nESI platforms offer the potential to uncover the roles played by low abundant signalling metabolites (e.g. steroids, eicosanoids) in health and disease studies, and would also enable an improvement in the detection of xenobiotics present at trace levels in biological matrices to better characterise the chemical exposome. This review aims to give an insight into the advantages associated with nLC-nESI for metabolomics-based approaches. Initially we detail the source of improved sensitivity prior to reviewing the available approaches to achieving nanoflow rates and nanospray ionisation for metabolomics. The robustness of nLC-nESI platforms was then assessed using the literature available from a metabolomic viewpoint. We also discuss the challenging point of sample preparation which needs to be addressed to fully enjoy the benefits of these nLC-nESI platforms. Finally, we assess metabolomic analysis utilising nano scale platforms and look ahead to the future of metabolomics using these new highly sensitive platforms.

Insights into the Structural Requirements of Potent Brassinosteroids as Vegetable Growth Promoters Using Second-Internode Elongation as Biological Activity: CoMFA and CoMSIA Studies

In the present study, we have employed the ligand-based drug design technique, 3D-QSAR, through a comparative molecular field analysis (CoMFA) and a comparative molecular similarity indices analysis (CoMSIA) to determine the key factors for the plant growth promoting activity of brassinosteroids reported in literature, using the bean second-internode bioassay measured on two groups of compounds with different molar concentrations. This is the first 3D-QSAR study using the second internode elongation as biological activity. These results provide useful ideas for the design of new molecules, which could be explored in the future to identify novel vegetable growth promoters with similar or greater biological activity than natural brassinosteroids. The reliability of this study was supported by the robust statistical parameters obtained from CoMFA (Model A, r²_pred = 0.751; Model B, r²_pred = 0.770) and CoMSIA (Model A, r²_pred = 0.946; Model B, r²_pred = 0.923) analysis.

Localized surface plasmon resonance-based abscisic acid biosensor using aptamer-functionalized gold nanoparticles

Abscisic acid (ABA) plays an important role in abiotic stress response and physiological signal transduction resisting to the adverse environment. Therefore, it is very essential for the quantitative detection of abscisic acid (ABA) due to its indispensable role in plant physiological activities. Herein, a new detection method based on localized surface plasmon resonance (LSPR) using aptamer-functionalized gold nanoparticles (AuNPs) is developed without using expensive instrument and antibody. In the presence of ABA, ABA specifically bind with their aptamers to form the ABA-aptamer complexes with G-quadruplex-like structure and lose the ability to stabilize AuNPs against NaCl-induced aggregation. Meanwhile, the changes of the LSPR spectra of AuNP solution occur and therefore the detection of ABA achieved. Under optimized conditions, this method showed a good linear range covering from 5×10-7 M to 5×10-5 M with a detection limit of 0.33 μM. In practice, the usage of this novel method has been demonstrated by its application to detect ABA from fresh leaves of rice with the relative error of 6.59%-7.93% compared with ELISA bioassay. The experimental results confirmed that this LSPR-based biosensor is simple, selective and sensitive for the detection of ABA. The proposed LSPR method could offer a new analytical platform for the detection of other plant hormones by changing the corresponding aptamer.

Simultaneous Analysis of Two Phytohormones in Chili and Wheat Using HPLC Using Novel Calixarene as SPE Sorbent

In this paper, a high-performance liquid chromatography with ultraviolet (HPLC-UV) detection method, using tetraazacalix[2]arene[2]triazine-modified silica gel (NCS) as solid-phase extraction (SPE) sorbent, was developed for extracting and purifying the two phytohormones (indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA)) in chili and wheat samples from different organs of chili and wheat. The limits of detection were about 0.02 and 0.04 μg/mL, and the limits of quantification were 0.04 and 0.20 μg/mL for IAA and IBA, respectively. The intraday and interday RSDs (n = 6) of peak areas and retention times were in the range of 0.76-1.20%. In addition, overall recoveries through the extraction and NCS-SPE purification ranged from 78.4% to 86.8% for IAA and IBA were obtained. Compared with the commercial SPE sorbents, NCS featured excellent selectivity to retain IAA and IBA in the sample matrices. In addition, the results more clearly indicated that high IAA and IBA content existed in roots and leaves of wheat and chili; in other organs of the plants, the concentration of the two phytohormones is lower. The results from theoretical computation were consistent with the retention behaviors of IAA and IBA on NCS. The proposed NCS-SPE-HPLC method is highly effective for trace analysis of the two phytohormones in plant samples.

Technical Challenges in Mass Spectrometry-Based Metabolomics

Metabolomics is a strategy for analysis, and quantification of the complete collection of metabolites present in biological samples. Metabolomics is an emerging area of scientific research because there are many application areas including clinical, agricultural, and medical researches for the biomarker discovery and the metabolic system analysis by employing widely targeted analysis of a few hundred preselected metabolites from 10-100 biological samples. Further improvement in technologies of mass spectrometry in terms of experimental design for larger scale analysis, computational methods for tandem mass spectrometry-based elucidation of metabolites, and specific instrumentation for advanced bioanalysis will enable more comprehensive metabolome analysis for exploring the hidden secrets of metabolism.

Hormonal profiling: Development of a simple method to extract and quantify phytohormones in complex matrices by UHPLC-MS/MS

Plant growth regulators (PGRs) are very different chemical compounds that play essential roles in plant development and the regulation of physiological processes. They exert their functions by a mechanism called cross-talk (involving either synergistic or antagonistic actions) thus; it is for great interest to study as many PGRs as possible to obtain accurate information about plant status. Much effort has been applied to develop methods capable of analyze large numbers of these compounds but frequently excluding some chemical families or important PGRs within each family. In addition, most of the methods are specially designed for matrices easy to work with. Therefore, we wanted to develop a method which achieved the requirements lacking in the literature and also being fast and reliable. Here we present a simple, fast and robust method for the extraction and quantification of 20 different PGRs using UHPLC-MS/MS optimized in complex matrices.

Mass spectrometry as a quantitative tool in plant metabolomics

Metabolomics is a research field used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include the analysis of a wide range of chemical species with very diverse physico-chemical properties, and therefore powerful analytical tools are required for the separation, characterization and quantification of this vast compound diversity present in plant matrices. In this review, challenges in the use of mass spectrometry (MS) as a quantitative tool in plant metabolomics experiments are discussed, and important criteria for the development and validation of MS-based analytical methods provided.This article is part of the themed issue 'Quantitative mass spectrometry'.

Progress and development of analytical methods for gibberellins

Gibberellins, as a group of phytohormones, exhibit a wide variety of bio-functions within plant growth and development, which have been used to increase crop yields. Many analytical procedures, therefore, have been developed for the determination of the types and levels of endogenous and exogenous gibberellins. As plant tissues contain gibberellins in trace amounts (usually at the level of nanogram per gram fresh weight or even lower), the sample pre-treatment steps (extraction, pre-concentration, and purification) for gibberellins are reviewed in details. The primary focus of this comprehensive review is on the various analytical methods designed to meet the requirements for gibberellins analyses in complex matrices with particular emphasis on high-throughput analytical methods, such as gas chromatography, liquid chromatography, and capillary electrophoresis, mostly combined with mass spectrometry. The advantages and drawbacks of the each described analytical method are discussed. The overall aim of this review is to provide a comprehensive and critical view on the different analytical methods nowadays employed to analyze gibberellins in complex sample matrices and their foreseeable trends.