A tomato NAC transcription factor, SlNAP1, directly regulates gibberellin-dependent fruit ripening.

In tomato (Solanum lycopersicum), the ripening of fruit is regulated by the selective expression of ripening-related genes, and this procedure is controlled by transcription factors (TFs). In the various plant-specific TF families, the no apical meristem (NAM), Arabidopsis thaliana activating factor 1/2 (ATAF1/2), and cup-shaped cotyledon 2 (CUC2; NAC) TF family stands out and plays a significant function in plant physiological activities, such as fruit ripening (FR). Despite the numerous genes of NAC found in the tomato genome, limited information is available on the effects of NAC members on FR, and there is also a lack of studies on their target genes. In this research, we focus on SlNAP1, which is a NAC TF that positively influences the FR of tomato. By employing CRISPR/Cas9 technology, compared with the wild type (WT), we generated slnap1 mutants and observed a delay in the ethylene production and color change of fruits. We employed the yeast one-hybrid (Y1H) and dual-luciferase reporter (DLR) assays to confirm that SlNAP1 directly binds to the promoters of two crucial genes involved in gibberellin (GA) degradation, namely SlGA2ox1 and SlGA2ox5, thus activating their expression. Furthermore, through a yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BIFC) and luciferase (LUC) assays, we established an interaction between SlNAP1 and SlGID1. Hence, our findings suggest that SlNAP1 regulates FR positively by activating the GA degradation genes directly. Additionally, the interaction between SlNAP1 and SlGID1 may play a role in SlNAP1-induced FR. Overall, our study provides important insights into the molecular mechanisms through which NAC TFs regulate tomato FR via the GA pathway.

Review on NMR as a tool to analyse natural products extract directly: Molecular structure elucidation and biological activity analysis.

INTRODUCTION: Natural products, the small organic molecules produced by plants, microbes and invertebrates, often present in the form of a mixture, this leads to the structural characterisation of natural extracts often requiring time-consuming multistep purification procedures. Nuclear magnetic resonance (NMR) technology is traditionally utilised as a tool for the structural elucidation of pure compounds. Contemporarily, an up-to-date trend in the application of NMR in natural product research is shifting to the direct NMR analysis of crude mixtures, to obtain molecular structure and biological activity information without performing cumbersome separation. OBJECTIVE: To review works of literature on the evolution, principle and progress of NMR technologies for analysing mixtures, we focus on the successful application of NMR technologies in direct analysis of natural product extracts. METHODOLOGY: Based on our research experience, academic tracking and extensive literature search, which involved, but not limited to, the use of various databases, like Web of Knowledge and PubMed. The keywords used, in various combinations, to retrieve recent literature on the successful application of NMR technologies to sheer natural product extracts, and excluded artificially natural product mixture and biofluid. RESULTS: NMR technologies for direct natural extracts analysis, including two-dimensional J-resolved spectroscopy (2D-JRES), pure shift NMR, diffusion-ordered NMR spectroscopy (DOSY), statistical correlation spectroscopy (STOCSY), concentration-ordered NMR spectroscopy (CORDY), saturation transfer difference (STD) and water-ligand observed via gradient spectroscopy (WaterLOGSY) were illustrated. CONCLUSIONS: By these methods, molecular structure and biological activity information will be directly obtained from NMR analysis of natural products extract, aiming to save experimental time and expenses.

The Role of Light-Regulated Auxin Signaling in Root Development.

The root is an important organ for obtaining nutrients and absorbing water and carbohydrates, and it depends on various endogenous and external environmental stimulations such as light, temperature, water, plant hormones, and metabolic constituents. Auxin, as an essential plant hormone, can mediate rooting under different light treatments. Therefore, this review focuses on summarizing the functions and mechanisms of light-regulated auxin signaling in root development. Some light-response components such as phytochromes (PHYs), cryptochromes (CRYs), phototropins (PHOTs), phytochrome-interacting factors (PIFs) and constitutive photo-morphorgenic 1 (COP1) regulate root development. Moreover, light mediates the primary root, lateral root, adventitious root, root hair, rhizoid, and seminal and crown root development via the auxin signaling transduction pathway. Additionally, the effect of light through the auxin signal on root negative phototropism, gravitropism, root greening and the root branching of plants is also illustrated. The review also summarizes diverse light target genes in response to auxin signaling during rooting. We conclude that the mechanism of light-mediated root development via auxin signaling is complex, and it mainly concerns in the differences in plant species, such as barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.), changes of transcript levels and endogenous IAA content. Hence, the effect of light-involved auxin signaling on root growth and development is definitely a hot issue to explore in the horticultural studies now and in the future.

Nitric oxide alleviates salt stress through protein S-nitrosylation and transcriptional regulation in tomato seedlings.

MAIN CONCLUSION: NO enhances the resistance of tomato seedlings to salt stress through protein S-nitrosylation and transcriptional regulation, which involves the regulation of MAPK signaling and carbohydrate metabolism. Nitric oxide (NO) regulates various physiological and biochemical processes and stress responses in plants. We found that S-nitrosoglutathione (GSNO) treatment significantly promoted the growth of tomato seedling under NaCl stress, indicating that NO plays a positive role in salt stress resistance. Moreover, GSNO pretreatment resulted in an increase of endogenous NO level, S-nitrosothiol (SNO) content, S-nitrosoglutathione reductase (GSNOR) activity and GSNOR expression under salt stress, implicating that S-nitrosylation might be involved in NO-alleviating salt stress. To further explore whether S-nitrosylation is a key molecular mechanism of NO-alleviating salt stress, the biotin-switch technique and liquid chromatography/mass spectrometry/mass spectrometry (LC-MS/MS) were conducted. A total of 1054 putative S-nitrosylated proteins have been identified, which were mainly enriched in chloroplast, cytoplasm and mitochondrion. Among them, 15 and 22 S-nitrosylated proteins were involved in mitogen-activated protein kinase (MAPK) signal transduction and carbohydrate metabolism, respectively. In MAPK signaling, various S-nitrosylated proteins, SAM1, SAM3, SAM, PP2C and SnRK, were down-regulated and MAPK, MAPKK and MAPKK5 were up-regulated at the transcriptional level by GSNO treatment under salt stress compared to NaCl treatment alone. The GSNO pretreatment could reduce ethylene production and ABA content under NaCl stress. In addition, the activities of enzyme identified in carbohydrate metabolism, their expression at the transcriptional level and the metabolite content were up-regulated by GSNO supplication under salt stress, resulting in the activation of glycolysis and tricarboxylic acid cycle (TCA) cycles. Thus, these results demonstrated that NO might beneficially regulate MAPK signaling at transcriptional levels and activate carbohydrate metabolism at the post-translational and transcriptional level, protecting seedlings from energy deficiency and salinity, thereby alleviating salt stress-induced damage in tomato seedlings. It provides initial insights into the regulatory mechanisms of NO in response to salt stress.

DNA methylation in tomato fruit ripening.

Fleshy fruit, the most economical and nutritional value unique to flowering plants, is an important part of our daily diet. Previous studies have shown that fruit ripening is regulated by transcription factors and the plant hormone ethylene, but recent research has also shown that epigenetics also plays an essential role, especially DNA methylation. DNA methylation is the process of transferring -CH3 to the fifth carbon of cytosine residues under the action of methyltransferase to form 5-methylcytosine (5-mC). So far, most works have been focused on tomato. Tomato ripening is dynamically regulated by DNA methylation and demethylation, but the understanding of this mechanism is still in its infancy. The dysfunction of a DNA demethylase, DEMETER-like DNA demethylases 2 (DML2), prevents the ripening of tomato fruits, but immature fruits ripen prematurely under the action of DNA methylation inhibitors. Additionally, studies have shown that the relationship between fruit quality and DNA methylation is not linear, but the specific molecular mechanism is still unclear. Here, we review the recent advances in the role of DNA methylation in tomato fruit ripening, the interaction of ripening transcription factors and DNA methylation, and its effects on quality. Then, a number of questions for future research of DNA methylation regulation in tomato fruit ripening is proposed.

Highly sensitive and multiplexed mass spectrometric immunoassay techniques and clinical applications.

Immunoassay is one of the most important clinical techniques for disease/pathological diagnosis. Mass spectrometry (MS) has been a popular and powerful readout technique for immunoassays, generating the mass spectrometric immunoassays (MSIAs) with unbeatable channels for multiplexed detection. The sensitivity of MSIAs has been greatly improved with the development of mass labels from element labels to small-molecular labels. MSIAs are also expended from the representative element MS-based methods to the laser-based organic MS and latest ambient MS, improving in both technology and methodology. Various MSIAs present high potential for clinical applications, including the biomarker screening, the immunohistochemistry, and the advanced single-cell analysis. Here, we give an overall review of the development of MSIAs in recent years, highlighting the latest improvement of mass labels and MS techniques for clinical immunoassays.

Towards high throughput and high information coverage: advanced single-cell mass spectrometric techniques.

Mass spectrometry (MS) is attractive for single-cell analysis because of its high sensitivity, rich information, and large dynamic ranges, especially for the single-cell metabolome and proteome analysis. Efforts have been made to deal with the throughput and information coverage problems in typical manual single-cell MS techniques. In this review, advanced techniques to improve the automation and throughput for single-cell sampling and single-cell metabolome and proteome MS detection have been discussed. Furthermore, representative MS-based strategies that can increase the in-depth cellular information coverage and achieve the more comprehensive single-cell multiomics information during high throughput detection have been highlighted, providing an ongoing perspective of the MS performance for the single-cell research.

Clinical grade lentiviral vector purification and quality control requirements.

Lentiviral vectors have been proven to be a powerful tool in gene therapies that includes the ability to perform long-term gene editing in both dividing and non-dividing cells. In order to meet the rising demand for clinical-grade lentiviral vectors for future clinical trials and requirements by regulatory agencies, new methods and technologies were developed, including the rapid optimization of production and purification processes. However, gaps still exist in achieving ideal yields and recovery rates in large-scale manufacturing process steps. The downstream purification process is a critical step required to obtain a sufficient quantity and high-quality lentiviral vectors products, which is challenged by the low stability of the lentiviral vector particles and large production volumes associated with the manufacturing process. This review summarizes the most recent and promising technologies and enhancements used in the large-scale purification process step of lentiviral vector manufacturing and aims to provide a significant contribution towards the achievement of providing sufficient quantity and quality of lentiviral vectors in scalable processes.

Strigolactone is involved in nitric oxide-enhanced the salt resistance in tomato seedlings.

Both strigolactones (SLs) and nitric oxide (NO) are regulatory signals with diverse roles during stress responses. At present, the interaction and mechanism of SLs and NO in tomato salt tolerance remain unclear. In the current study, tomato 'Micro-Tom' was used to study the roles and interactions of SLs and NO in salinity stress tolerance. The results show that 15 µM SLs synthetic analogs GR24 and 10 µM NO donor S-nitrosoglutathione (GSNO) promoted seedling growth under salt stress. TIS108 (an inhibitor of strigolactone synthesis) suppressed the positive roles of NO in tomato growth under salt stress, indicating that endogenous SLs might be involved in NO-induced salt response in tomato seedlings. Meanwhile, under salt stress, GSNO or GR24 treatment induced the increase of endogenous SLs content in tomato seedlings. Moreover, GR24 or GSNO treatment effectively increased the content of chlorophyll, carotenoids and ascorbic acid (ASA), and enhanced the activities of antioxidant enzymes (superoxide dismutase, peroxidase, catalase, and ascorbate peroxidase), glutathione reductase (GR) and cleavage dioxygenase (CCD) enzyme. Additionally, GSNO or GR24 treatment also up-regulated the expression of SLs synthesis genes (SlCCD7, SlCCD8, SlD27 and SlMAX1) and its signal transduction genes (SlD14 and SlMAX2) in tomato seedlings under salt stress. While, a strigolactone synthesis inhibitor TIS108 blocked the increase of endogenous SLs, chlorophyll, carotenoids and ASA content, and antioxidant enzyme, GR, CCD enzyme activity and SLs-related gene expression levels induced by GSNO. Thus, SLs may play an important role in NO-enhanced salinity tolerance in tomato seedlings by increasing photosynthetic pigment content, enhancing antioxidant capacity and improving endogenous SLs synthesis.

Maltose-functional metal-organic framework assisted laser desorption/ionization mass spectrometry for small biomolecule determination.

A series of functional metal-organic frameworks (MOFs) were facilely prepared through an one-pot procedure or post-synthetic modification strategy and used as matrices in laser desorption ionization mass spectrometry (LDI-MS). Compared with traditional organic matrices and other MOFs, maltose-functional MOF MIL-101-maltose demonstrated ultrahigh ionization efficiency, free matrix background, uniform crystallization, and good dispersibility. A simple, general, and efficient LDI-MS platform was developed for rapid detection of various small biomolecules using MIL-101-maltose as matrix, providing several advantages including low sample consumption of 500 nL, short analysis time of few seconds, strong salt tolerance (500 mM NaCl), and satisfactory reproducibility. The MIL-101-maltose matrix was used for serum glucose determination and successfully distinguished the diabetic patients from the healthy controls. This work provides a generic LDI-MS platform for fast determination of small biomolecules with high potential in clinical diagnosis and disease monitoring.

Ratiometric fluorescence sensing of formaldehyde in food samples based on bifunctional MOF.

A new fluorescence strategy was described for ratiometric sensing of formaldehyde (FA) with bifunctional MOF, which acted as a fluorescence reporter as well as biomimetic peroxidase. With the assistance of H2O2, NH2-MIL-101 (Fe) catalyzes the oxidation of non-luminescent substrate o-phenylenediamine (OPD) to produce fluorescent product (oxOPD) with the maximum emission at 570 nm. Besides, intrinsic fluorescence of MOF (λem = 445 nm) was quenched by oxOPD through inner filter effect (IFE). However, FA and OPD reacted to generate Schiff bases, which competitively consumed OPD inhibiting the generation of oxOPD. Under the excitation wavelength of 375 nm, a ratiometric strategy was designed to detect FA with the fluorescence intensity ratio at 445 nm and 570 nm (F445/F570) as readout signal. This strategy exhibited a wide linear range (0.1-50 µM) and low detection limit of 0.03 µM. This method was confirmed for FA detection in food samples. In addition to establishing a new method to detect FA, this work will open new applications of MOF in food safety.

Separation and determination of 3-hydroxyaspartate by online concentration capillary electrophoresis/laser-induced fluorescence with microwave-assisted derivatization.

A chiral analytical method was proposed based on capillary electrophoresis with laser-induced fluorescence detection coupled with microwave-assisted derivatization for the simultaneous baseline separation and sensitive detection of four stereoisomers of 3-hydroxyaspartate. The derivatization reaction of 3-hydroxyaspartate with 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole was greatly accelerated by microwave irradiation. Under the optimized conditions, the derivatization yield was increased by 20% and the derivatization time was shortened by 20 min when compared with those from conventional water bath heating. In addition, the sensitivity was improved by online sample concentration methods. The detection limit of l-threo-3-hydroxyaspartate obtained by large-volume sample stacking with polarity switching was 5.3 nmol/L, which was around 1000-fold lower than that of the capillary electrophoresis/laser-induced fluorescence without stacking. The excellent analytical performance in terms of linearity and precision was also achieved. Furthermore, the developed method was successfully applied to the determination of 3-hydroxyaspartate in the spiked urine, and satisfactory recoveries were obtained ranging from 90.5 to 107.0%.

Development and applications of deep eutectic solvent derived functional materials in chromatographic separation.

Deep eutectic solvents have received increasing attention over the past decade, and the green and versatile nature makes them important media for developing environmentally friendly and sustainable technologies. In addition to act as green alternatives to traditional organic solvents, deep eutectic solvents offer tremendous opportunities to produce different kinds of emerging functional materials. The present review highlights the recent development and applications of deep functional materials based on deep eutectic solvents as novel adsorbents for diverse analytes in complex matrices. The type, preparation, and unique properties of deep eutectic solvents, the synthesis of deep eutectic solvent derived materials, as well as their applications in chromatographic separation are described. We aim to demonstrate that deep eutectic solvents not only allow the design of eco-friendly extraction processes but also open straightforward access to advanced materials in sample preparation.

Glutathione-functionalized two-dimensional cobalt sulfide nanosheets for rapid and highly efficient enrichment of N-glycopeptides.

Protein glycosylation plays pivotal role in a variety of biological processes and has association with many diseases. The highly efficient glycopeptide enrichment is essential for the mass spectrometry-based glycoproteome research to reduce interference from non-glycopeptides. In this study, novel glutathione-functionalized two-dimensional cobalt sulfide nanosheets (Co-S@Au-GSH) were synthesized for rapid and highly effective enrichment of glycopeptides. By using this nanomaterial, 34 and 21 N-glycopeptides were effectively captured from human serum immunoglobulin G (IgG) and horseradish peroxidase (HRP) digests, respectively. In addition, the Co-S@Au-GSH showed remarkable performance in N-glycopeptide extraction with high selectivity (HRP: BSA = 1:500), low limit of detection (0.5 fmol/µL), high binding capacity (150 mg/g), good reusability, and great robustness. Moreover, it was successfully applied in complex serum samples, demonstrating its excellent enrichment performance. These results indicated that this nanomaterial has great potential in complicated practice samples in glycoproteome determination.

Determination of patulin in apple juice by amine-functionalized solid-phase extraction coupled with isotope dilution liquid chromatography tandem mass spectrometry.

BACKGROUND: Patulin is a mycotoxin that mainly contaminates apple juice, which is a typical high sugar matrix. Many different adsorbents have been utilized to develop a sample pretreatment method to minimize the matrix interference from apple juice. RESULTS: A simple and reliable extraction method for the determination of patulin in apple juice has been developed. The sample preparation involves a simple one-step cleanup procedure using amine-functionalized polymeric solid-phase extraction cartridges (Retain AX) that effectively remove interferences and facilitate the quantification. Isotope dilution liquid chromatography tandem mass spectrometry (ID-LC-MS/MS) was employed to minimize the matrix effect and ensure reliable results. The limit of detection was as low as 0.2 µg kg-1 , which was satisfactory with regard to current European, US, and Chinese legislation. Matrix-matched linearity (r2 = 0.9997) was established in the range of 1-400 µg kg-1 . Recovery was performed in samples spiked at three levels, and results were between 97.2% and 100.2%. CONCLUSION: The results indicated that, with one-step cleanup, the matrix effect was negligible and sensitivity was satisfactory. Our work provided a simple and reliable method for patulin detection in apple juice and is also very promising in routine quality control. © 2020 Society of Chemical Industry.

Multi-Dimensional Organic Mass Cytometry: Simultaneous Analysis of Proteins and Metabolites on Single Cells.

Mass cytometry is attracting significant attention for enabling spatiotemporal high-throughput single-cell analysis. As the first demonstration of the simultaneous detection of single-cell proteins and untargeted metabolites, a multi-dimensional organic mass-cytometry system was established by a simple microfluidic chip connected to a nanoelectrospray mass spectrometer, providing useful heterogeneous information about the cells. A series of mass probes with online-dissociated mass tags were developed, ensuring the semi-quantification of cell-surface proteins and the compatibility of endogenous metabolite detection at the single-cell level. Six cell surface antigens and ≈100 metabolites from three ovarian-cancer cell types and two breast-cancer cell types were successfully monitored and contributed to highly sensitive and specific cell typing. Doxorubicin-resistant cancer-cell analysis confirmed the applications in distinguishing rare cell phenotypes. The proposed system is simple, extensible, and promising for cell typing, drug-resistance analysis of tumor cells, and clinical diagnosis and therapy at the single-cell level.

High-Throughput Single-Cell Immunoassay in the Cellular Native Environment Using Online Desalting Dual-Spray Mass Spectrometry.

Single-cell mass spectrometry (MS) remains challenging in the analysis of cells in the native environment due to the severe ion suspension from nonvolatile salts. Synchronous desalting and ionization would be ideal to both ensure the native environment and remove the salt interference. Here, a novel dual-spray ionization technique combining electrospray and nanoelectrospray ionization (ESI-nESI) was developed, enabling highly efficient online desalting during the ionization process. In situ detection of cell surface proteins from the intact cells in phosphate buffer saline (PBS) was achieved by dual ESI-nESI MS with the help of an MS-based immunoassay using rhodamine-based mass tags. These mass tags were confirmed to be highly competitive during desalting, which improved the protein detection sensitivity to a single-cell level. Through the combination of the single-cell immunoassay with ESI-nESI MS, the important surface protein markers, cancer antigen 125, in two cancer cell lines (OVCAR-3 and MCF-7) suspended in the PBS buffers were screened in a high-throughput cytometric mode, along with some proposed cellular endogenous lipids. The ESI-nESI MS system is promising for multidimensional organic mass cytometric analysis in the cellular native environment for clinical use and many basic biology researches.

In Situ Laser Scattering Electrospray Ionization Mass Spectrometry and Its Application in the Mechanism Study of Photoinduced Direct C-H Arylation of Heteroarenes.

An in situ laser scattering electrospray ionization mass spectrometry (LS-ESI-MS) was developed, where the laser scattering was simply achieved through the laser radiation of the "media" modified on the capillary. The laser scattering extended the reaction window and powerfully promoted the reaction yield of the photoinduced organic reaction, which enables the trace intermediates to be efficiently tracked in real time. For instance, the key radical cation in the photoinduced direct C-H arylation of heteroarenes was captured inventively, which provided direct experimental evidence for the verification of the reaction mechanism. Together with the characterization of oxidative photocatalytic Ru(III) intermediate, the integral insight into the process of visible-light-mediated direct C-H arylation of heteroarenes was confirmed. This approach is facile, powerful, and promising in the mechanism study of organic reaction.

A novel online two-dimensional supercritical fluid chromatography/reversed phase liquid chromatography-mass spectrometry method for lipid profiling.

A novel online two-dimensional supercritical fluid chromatography/reversed-phase liquid chromatography-triple-quadrupole mass spectrometry (2D SFC/RPLC-QQQ MS) method based on a vacuum solvent evaporation interface was developed for lipid profiling in human plasma, in which lipid classes were separated by the first-dimension SFC and different lipid molecular species were further separated by the second-dimension RPLC. All separation condition parameters were carefully optimized, and their influence on the chromatographic behavior of lipids is discussed. Finally, the recoveries of 11 lipid standards were all more than 88% for the interface. Besides, the limit of detection for these lipid standards was on the order of nanograms per milliliter, and the relative standard deviations of the peak area and retention time ranged from 1.54% to 19.85% and from 0.00% to 0.10%, respectively. The final 2D SFC/RPLC-QQQ MS method allowed the identification of 370 endogenous lipid species from ten lipid classes, including diacylglycerol, triacylglycerol, ceramide, glucosylceramide, galactosylceramide, lactosylceramide, sphingomyelin, acylcarnitine, phosphatidylcholine, and lysophosphatidylethanolamine, in human plasma within 38 min, which was used for screening potential lipid biomarkers in breast cancer. The 2D SFC/RPLC-QQQ MS method is a potentially useful tool for in-depth studies focused on complex lipid metabolism and biomarker discovery. Graphical Abstract.

Recent progresses of derivatization approaches in the targeted lipidomics analysis by mass spectrometry.

Lipidomics plays an essential role in the development of an improved understanding of lipids metabolism and the identification of new biomarkers or therapeutic targets of related diseases. The strong analytical power of mass spectrometry and its rapid developments in the respect of instruments and techniques have significantly accelerated the emerging lipidomics and related application fields in biology, medicine, and pharmacy. The strategy of chemical derivatization can remarkably improve the shortcomings of mass spectrometric analytical technologies of shotgun lipidomics and liquid chromatography mass spectrometry, and in the past decade many related studies have been reported for fatty acids, glycerophospholipids, sphingomyelins, monoglycerides, diacylglycerols, long-chain bases, steroids, and so on. Therefore, this review will focus on new chemical derivatization approaches about the research progresses of shotgun-based and liquid chromatography mass spectrometry-based targeted lipidomics (from 2005 to July 2019, most of reports emerged in the past 5 years), and put forward the problems and prospects in this field. It is expected to be helpful for the design and synthesis of new derivatization reagents, especially the outstanding stable isotope labeling derivatization reagents, and the development and application of new chemical derivatization strategies and matched mass spectrometric analysis methods.