Spatio-Temporal Metabolite Profiling of the Barley Germination Process by MALDI MS Imaging

Spatial specificity of metabolism regulation of abscisic acid-imposed seed germination inhibition in Korean pine (Pinus koraiensis sieb et zucc)

Introduction

Abscisic acid (ABA) can negatively regulate seed germination, but the mechanisms of ABA-mediated metabolism modulation are not well understood. Moreover, it remains unclear whether metabolic pathways vary with the different tissue parts of the embryo, such as the radicle, hypocotyl and cotyledon.

Methods

In this report, we performed the first comprehensive metabolome analysis of the radicle and hypocotyl + cotyledon in Pinus koraiensis seeds in response to ABA treatment during germination.

Results and discussion

Metabolome profiling showed that following ABA treatment, 67 significantly differentially accumulated metabolites in the embryo were closely associated with pyrimidine metabolism, phenylalanine metabolism, cysteine and methionine metabolism, galactose metabolism, terpenoid backbone biosynthesis, and glutathione metabolism. Meanwhile, 62 metabolites in the hypocotyl + cotyledon were primarily involved in glycerophospholipid metabolism and glycolysis/gluconeogenesis. We can conclude that ABA may inhibit Korean pine seed germination primarily by disrupting the biosynthesis of certain plant hormones mediated by cysteine and methionine metabolism and terpenoid backbone biosynthesis, as well as reducing the reactive oxygen species scavenging ability regulated by glutathione metabolism and shikimate pathway in radicle. ABA may strongly disrupt the structure and function of cellular membranes due to alterations in glycerophospholipid metabolism, and weaken glycolysis/gluconeogenesis in the hypocotyl + cotyledon, both of which are major contributors to ABA-mediated inhibition of seed germination. These results highlight that the spatial modulation of metabolic pathways in Pinus koraiensis seeds underlies the germination response to ABA.

Sodium doping and trapped ion mobility spectrometry improve lipid detection for novel MALDI-MSI analysis of oats

Oat (Avena sativa L.) is an important cereal grain with a unique nutritional profile including a high proportion of lipids. Understanding lipid composition and distribution in oats is valuable for plant, food and nutritional research, and can be achieved using MALDI mass spectrometry imaging (MALDI-MSI). However, this approach presents several challenges for sample preparation (hardness of grains) and analysis (isobaric and isomeric properties of lipids). Here, oat sections were successfully mounted onto gelatin-coated indium tin oxide slides with minimal tearing. Poor detection of triacylglycerols was resolved by applying sodium chloride during mounting, increasing signal intensity. In combination with trapped ion mobility spectrometry (TIMS), lipid identification significantly improved, and we report the separation of several isobaric and isomeric lipids with visualisation of their "true" spatial distributions. This study describes a novel MALDI-TIMS-MSI analytical technique for oat lipids, which may be used to improve the discovery of biomarkers for grain quality.

Plant Life with and without Oxygen: A Metabolomics Approach

Oxygen deficiency is an environmental challenge which affects plant growth, the development and distribution in land and aquatic ecosystems, as well as crop yield losses worldwide. The capacity to exist in the conditions of deficiency or the complete lack of oxygen depends on a number of anatomic, developmental and molecular adaptations. The lack of molecular oxygen leads to an inhibition of aerobic respiration, which causes energy starvation and the acceleration of glycolysis passing into fermentations. We focus on systemic metabolic alterations revealed with the different approaches of metabolomics. Oxygen deprivation stimulates the accumulation of glucose, pyruvate and lactate, indicating the acceleration of the sugar metabolism, glycolysis and lactic fermentation, respectively. Among the Krebs-cycle metabolites, only the succinate level increases. Amino acids related to glycolysis, including the phosphoglycerate family (Ser and Gly), shikimate family (Phe, Tyr and Trp) and pyruvate family (Ala, Leu and Val), are greatly elevated. Members of the Asp family (Asn, Lys, Met, Thr and Ile), as well as the Glu family (Glu, Pro, Arg and GABA), accumulate as well. These metabolites are important members of the metabolic signature of oxygen deficiency in plants, linking glycolysis with an altered Krebs cycle and allowing alternative pathways of NAD(P)H reoxidation to avoid the excessive accumulation of toxic fermentation products (lactate, acetaldehyde, ethanol). Reoxygenation induces the downregulation of the levels of major anaerobically induced metabolites, including lactate, succinate and amino acids, especially members of the pyruvate family (Ala, Leu and Val), Tyr and Glu family (GABA and Glu) and Asp family (Asn, Met, Thr and Ile). The metabolic profiles during native and environmental hypoxia are rather similar, consisting in the accumulation of fermentation products, succinate, fumarate and amino acids, particularly Ala, Gly and GABA. The most intriguing fact is that metabolic alterations during oxidative stress are very much similar, with plant response to oxygen deprivation but not to reoxygenation.

Optimization of Mass Spectrometry Imaging for Drug Metabolism and Distribution Studies in the Zebrafish Larvae Model: A Case Study with the Opioid Antagonist Naloxone

Zebrafish (ZF; Danio rerio) larvae have emerged as a promising in vivo model in drug metabolism studies. Here, we set out to ready this model for integrated mass spectrometry imaging (MSI) to comprehensively study the spatial distribution of drugs and their metabolites inside ZF larvae. In our pilot study with the overall goal to improve MSI protocols for ZF larvae, we investigated the metabolism of the opioid antagonist naloxone. We confirmed that the metabolic modification of naloxone is in high accordance with metabolites detected in HepaRG cells, human biosamples, and other in vivo models. In particular, all three major human metabolites were detected at high abundance in the ZF larvae model. Next, the in vivo distribution of naloxone was investigated in three body sections of ZF larvae using LC-HRMS/MS showing that the opioid antagonist is mainly present in the head and body sections, as suspected from published human pharmacological data. Having optimized sample preparation procedures for MSI (i.e., embedding layer composition, cryosectioning, and matrix composition and spraying), we were able to record MS images of naloxone and its metabolites in ZF larvae, providing highly informative distributional images. In conclusion, we demonstrate that all major ADMET (absorption, distribution, metabolism, excretion, and toxicity) parameters, as part of in vivo pharmacokinetic studies, can be assessed in a simple and cost-effective ZF larvae model. Our established protocols for ZF larvae using naloxone are broadly applicable, particularly for MSI sample preparation, to various types of compounds, and they will help to predict and understand human metabolism and pharmacokinetics.

Species-specific dynamics of specialized metabolism in germinating sorghum grain revealed by temporal and tissue-resolved transcriptomics and metabolomics

Seed germination is crucial for plant productivity, and the biochemical changes during germination affect seedling survival, plant health and yield. While the general metabolism of germination is extensively studied, the role of specialized metabolism is less investigated. We therefore analyzed the metabolism of the defense compound dhurrin during sorghum (Sorghum bicolor) grain germination and early seedling development. Dhurrin is a cyanogenic glucoside, which is catabolized into different bioactive compounds at other stages of plant development, but its fate and role during germination is unknown. We dissected sorghum grain into three different tissues and investigated dhurrin biosynthesis and catabolism at the transcriptomic, metabolomic and biochemical level. We further analyzed transcriptional signature differences of cyanogenic glucoside metabolism between sorghum and barley (Hordeum vulgare), which produces similar specialized metabolites. We found that dhurrin is de novo biosynthesized and catabolized in the growing embryonic axis as well as the scutellum and aleurone layer, two tissues otherwise mainly acknowledged for their involvement in release and transport of general metabolites from the endosperm to the embryonic axis. In contrast, genes encoding cyanogenic glucoside biosynthesis in barley are exclusively expressed in the embryonic axis. Glutathione transferase enzymes (GSTs) are involved in dhurrin catabolism and the tissue-resolved analysis of GST expression identified new pathway candidate genes and conserved GSTs as potentially important in cereal germination. Our study demonstrates a highly dynamic tissue- and species-specific specialized metabolism during cereal grain germination, highlighting the importance of tissue-resolved analyses and identification of specific roles of specialized metabolites in fundamental plant processes.

MALDI MS Imaging of Cucumbers

There are many different methodologies in the literature for the preparation of plant material for subsequent MALDI MSI analysis. This chapter overviews preparation of cucumbers (Cucumis sativus L.), with emphasis on sample freezing, cryosectioning, and matrix deposition. This should act as a representative example of sample preparation for plant tissue, and due to wide sample variation (e.g., leaves, seeds, and fruit) and analytes of interest, method optimization will be required for different samples.

Genome-Wide Association Study of Salt Tolerance-Related Traits during Germination and Seedling Development in an Intermedium-Spike Barley Collection

Increased salinity is one of the major consequences of climatic change affecting global crop production. The early stages in the barley (Hordeum vulgare L.) life cycle are considered the most critical phases due to their contributions to final crop yield. Particularly, the germination and seedling development are sensitive to numerous environmental stresses, especially soil salinity. In this study, we aimed to identify SNP markers linked with germination and seedling development at 150 mM NaCl as a salinity treatment. We performed a genome-wide association study (GWAS) using a panel of 208 intermedium-spike barley (H. vulgare convar. intermedium (Körn.) Mansf.) accessions and their genotype data (i.e., 10,323 SNPs) using the genome reference sequence of “Morex”. The phenotypic results showed that the 150 mM NaCl salinity treatment significantly reduced all recorded germination and seedling-related traits compared to the control treatment. Furthermore, six accessions (HOR 11747, HOR 11718, HOR 11640, HOR 11256, HOR 11275 and HOR 11291) were identified as the most salinity tolerant from the intermedium-spike barley collection. GWAS analysis indicated that a total of 38 highly significantly associated SNP markers under control and/or salinity traits were identified. Of these, two SNP markers on chromosome (chr) 1H, two on chr 3H, and one on chr 4H were significantly linked to seedling fresh and dry weight under salinity stress treatment. In addition, two SNP markers on chr 7H were also significantly associated with seedling fresh and dry weight but under control condition. Under salinity stress, one SNP marker on chr 1H, 5H and 7H were detected for more than one phenotypic trait. We found that in most of the accessions exhibiting the highest salinity tolerance, most of the salinity-related QTLs were presented. These results form the basis for detailed studies, leading to improved salt tolerance breeding programs in barley.

Mutations in Rht-B1 Locus May Negatively Affect Frost Tolerance in Bread Wheat

The wheat semi-dwarfing genes Rht (Reduced height) are widely distributed among the contemporary wheat varieties. These genes also exert pleiotropic effects on plant tolerance towards various abiotic stressors. In this work, frost tolerance was studied in three near-isogenic lines of the facultative variety ‘April Bearded’ (AB), carrying the wild type allele Rht-B1a (tall phenotype), and the mutant alleles Rht-B1b (semi-dwarf) and Rht-B1c (dwarf), and was further compared with the tolerance of a typical winter type variety, ‘Mv Beres’. The level of freezing tolerance was decreasing in the order ‘Mv Beres’ > AB Rht-B1a > AB Rht-B1b > AB Rht-B1c. To explain the observed differences, cold acclimation-related processes were studied: the expression of six cold-related genes, the phenylpropanoid pathway, carbohydrates, amino acids, polyamines and compounds in the tricarboxylic acid cycle. To achieve this, a comprehensive approach was applied, involving targeted analyses and untargeted metabolomics screening with the help of gas chromatography/liquid chromatography—mass spectrometry setups. Several cold-related processes exhibited similar changes in these genotypes; indeed, the accumulation of eight putrescine and agmatine derivatives, 17 flavones and numerous oligosaccharides (max. degree of polymerization 18) was associated with the level of freezing tolerance in the ‘April Bearded’ lines. In summary, the mutant Rht alleles may further decrease the generally low frost tolerance of the Rht-B1a, and, based on the metabolomics study, the mechanisms of frost tolerance may differ for a typical winter variety and a facultative variety. Present results point to the complex nature of frost resistance.

Isolation and Characterisation of Hordatine-Rich Fractions from Brewer’s Spent Grain and Their Biological Activity on α-Glucosidase and Glycogen Phosphorylase α

Hordatines are a characteristic class of secondary metabolites found in barley which have been reported to be present in barley malt, beer and, recently, brewer´s spent grain (BSG). However, little is known about their biological activities such as antioxidative effects in beer or antifungal activity as their main task within the plants. We conducted an in vitro investigation of the activity of hordatines isolated from BSG towards enzymes of glucose metabolism. Hordatine-rich fractions from BSG were prepared by solid-liquid extraction (SLE) with 60% acetone followed by purification and fractionation. The fractions were characterised and investigated for their in vitro inhibitory potential on α-glucosidase and glycogen phosphorylase α (GPα). Both enzymes are relevant within the human glucose metabolism regarding the digestion of carbohydrates as well as the liberation of glucose from the liver. In total, 10 hordatine-rich fractions varying in the composition of different hordatines were separated and analysed by mass spectrometry. Hordatine A, B and C, as well as hydroxylated aglycons and many glycosides, were detected in the fractions. The total hordatine content was analysed by HPLC-DAD using a semi-quantitative approach and ranged from 60.7 ± 3.1 to 259.6 ± 6.1 µg p-coumaric acid equivalents/mg fraction. Regarding the biological activity of fractions, no inhibitory effect on GPα was observed, whereas an inhibitory effect on α-glucosidase was detected (IC50 values: 77.5 ± 6.5–194.1 ± 2.6 µg/mL). Overall, the results confirmed that hordatines are present in BSG in relatively high amounts and provided evidence that they are potent inhibitors of α-glucosidase. Further research is needed to confirm these results and identify the active hordatine structure.

Hordatines and Associated Precursors Dominate Metabolite Profiles of Barley (Hordeum vulgare L.) Seedlings: A Metabolomics Study of Five Cultivars

In the process of enhancing crop potential, metabolomics offers a unique opportunity to biochemically describe plant metabolism and to elucidate metabolite profiles that govern specific phenotypic characteristics. In this study we report an untargeted metabolomic profiling of shoots and roots of barley seedlings performed to reveal the chemical makeup therein at an early growth stage. The study was conducted on five cultivars of barley: ‘Overture’, ‘Cristalia’, ‘Deveron’, ‘LE7′ and ‘Genie’. Seedlings were grown for 16 days post germination under identical controlled conditions, and methanolic extracts were analysed on an ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC–HRMS) system. In addition, an unsupervised pattern identification technique, principal component analysis (PCA), was performed to process the generated multidimensional data. Following annotation of specific metabolites, several classes were revealed, among which phenolic acids represented the largest group in extracts from both shoot and root tissues. Interestingly, hordatines, barley-specific metabolites, were not found in the root tissue. In addition, metabolomic profiling revealed metabolites potentially associated with the plants’ natural protection system against potential pathogens. The study sheds light on the chemical composition of barley at a young developmental stage and the information gathered could be useful in plant research and biomarker-based breeding programs.

Mass spectrometry imaging of oligosaccharides following in situ enzymatic treatment of maize kernels

In recent years enzymatic treatment of maize has been utilized in the wet-milling process to increase the yield of extracted starch, proteins, and other constituents. One of the strategies to obtain this goal is to add enzymes that break down insoluble cell-wall polysaccharides which would otherwise entrap starch granules. Due to the high complexity of maize polysaccharides, this goal is not easily achieved and more knowledge about the substrate and enzyme performances is needed. To gather information of both enzyme performance and increase substrate understanding, a method was developed using mass spectrometry imaging (MSI) to analyze degradation products from polysaccharides following enzymatic treatment of the maize endosperm. Different enzymes were spotted onto cryosections of maize kernels which had been pre-treated with an amylase to remove starch. The cryosections were then incubated for 17 h. before mass spectrometry images were generated with a MALDI-MSI setup. The images showed varying degradation products for the different enzymes observed as pentose oligosaccharides differing with regards to sidechains and the number of linked pentoses. The method proved suitable for identifying the reaction products formed after reaction with different xylanases and arabinofuranosidases and for characterization of the complex arabinoxylan substrate in the maize kernel. HYPOTHESES: Mass spectrometry imaging can be a useful analytical tool for obtaining information of polysaccharide constituents and enzyme performance from maize samples.

Comparative Metabolomics Reveals Two Metabolic Modules Affecting Seed Germination in Rice (Oryza sativa)

The process of seed germination is crucial not only for the completion of the plant life cycle but also for agricultural production and food chemistry; however, the underlying metabolic regulation mechanism involved in this process is still far from being clearly revealed. In this study, one indica variety (Zhenshan 97, with rapid germination) and one japonica variety (Nipponbare, with slow germination) in rice were used for in-depth analysis of the metabolome at different germination stages (0, 3, 6, 9, 12, 24, 36, and 48 h after imbibition, HAI) and exploration of key metabolites/metabolic pathways. In total, 380 annotated metabolites were analyzed by using a high-performance liquid chromatography (HPLC)-based targeted method combined with a nontargeted metabolic profiling method. By using bioinformatics and statistical methods, the dynamic changes in metabolites during germination in the two varieties were compared. Through correlation analysis, coefficient of variation analysis and differential accumulation analysis, 74 candidate metabolites that may be closely related to seed germination were finally screened. Among these candidates, 29 members belong to the ornithine–asparagine–polyamine module and the shikimic acid–tyrosine–tryptamine–phenylalanine–flavonoid module. As the core member of the second module, shikimic acid’s function in the promotion of seed germination was confirmed by exogenous treatment. These results told that nitrogen flow and antioxidation/defense responses are potentially crucial for germinating seeds and seedlings. It deepens our understanding of the metabolic regulation mechanism of seed germination and points out the direction for our future research.

Detection and Verification of QTL for Salinity Tolerance at Germination and Seedling Stages Using Wild Barley Introgression Lines

Salinity is one of the major environmental factors that negatively affect crop development, particularly at the early growth stage of a plant and consequently the final yield. Therefore, a set of 50 wild barley (Hordeum vulgare ssp. spontaneum, Hsp) introgression lines (ILs) was used to detect QTL alleles improving germination and seedling growth under control, 75 mM, and 150 mM NaCl conditions. Large variation was observed for germination and seedling growth related traits that were highly heritable under salinity stress. In addition, highly significant differences were obtained for five salinity tolerance indices and between treatments as well. A total of 90 and 35 significant QTL were identified for ten investigated traits and for tolerance indices, respectively. The Hsp introgression alleles are involved in improving salinity tolerance at forty (43.9%) out of 90 QTL including introgression lines S42IL-109 (2H), S42IL-116 (4H), S42IL-132 (6H), S42IL-133 (7H), S42IL-148 (6H), and S42IL-176 (5H). Interestingly, seven exotic QTL alleles were successfully validated in the wild barley ILs including S42IL-127 (5H), 139 (7H), 125 (5H), 117 (4H), 118 (4H), 121 (4H), and 137 (7H). We conclude that the barley introgression lines contain numerous germination and seedling growth-improving novel QTL alleles, which are effective under salinity conditions.

Are all dietary fibers equal for patients with inflammatory bowel disease? A systematic review of randomized controlled trials

CONTEXT

Conflicting practice-based dietary recommendations are sometimes given to patients with inflammatory bowel disease (IBD); whereas intake of fiber should increase during remission, it should be avoided during relapse. Moreover, European countries set daily requirements of total fiber and do not specify any types.

OBJECTIVE

This systematic review appraised data from randomized clinical trials (RCTs) of the types of fibers beneficial for patients in the treatment of IBD to guide dietary fiber advice.

DATA SOURCES

The PubMED database was searched following PRISMA guidelines.

DATA EXTRACTION

RCTs evaluating the effects of any type of fiber on clinical and physiological outcomes in patients with IBD were assessed. Quality assessment of the selected full-text articles was conducted using the Cochrane Risk of Bias Tool.

DATA ANALYSIS

Eight studies were included reporting on 5 types of fibers. In 2 RCTs, germinated barley foodstuff (GBF) was shown to lower pro-inflammatory cytokines and clinical disease activity scores. Fructo-oligosaccharides (FOS) were demonstrated to lower IBD Questionnaire scores (lower well-being), in contrast to inulin, which decreased disease activity scores. An RCT could not find lower remission rates in the psyllium treatment group, while another RCT reported that administration led to less symptoms in patients. In RCTs, no concrete evidence was found that wheat bran improves disease course.

CONCLUSIONS

Although the evidence is sparse, GBF and inulin seem propitious and merit further exploration. Evidence on wheat bran and psyllium is still too limited. Adequately powered long-term human RCTs with objective outcomes are needed to improve dietary advice on types of fiber in IBD.

ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016

This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.

Phosphorus deprivation affects composition and spatial distribution of membrane lipids in legume nodules

In legumes, symbiotic nitrogen (N) fixation (SNF) occurs in specialized organs called nodules after successful interactions between legume hosts and rhizobia. In a nodule, N-fixing rhizobia are surrounded by symbiosome membranes, through which the exchange of nutrients and ammonium occurs between bacteria and the host legume. Phosphorus (P) is an essential macronutrient, and N2-fixing legumes have a higher requirement for P than legumes grown on mineral N. As in the previous studies, in P deficiency, barrel medic (Medicago truncatula) plants had impaired SNF activity, reduced growth, and accumulated less phosphate in leaves, roots, and nodules compared with the plants grown in P sufficient conditions. Membrane lipids in M. truncatula tissues were assessed using electrospray ionization-mass spectrometry. Galactolipids were found to increase in P deficiency, with declines in phospholipids (PL), especially in leaves. Lower PL losses were found in roots and nodules. Subsequently, matrix-assisted laser desorption/ionization-mass spectrometry imaging was used to spatially map the distribution of the positively charged phosphatidylcholine (PC) species in nodules in both P-replete and P-deficient conditions. Our results reveal heterogeneous distribution of several PC species in nodules, with homogeneous distribution of other PC classes. In P poor conditions, some PC species distributions were observed to change. The results suggest that specific PC species may be differentially important in diverse nodule zones and cell types, and that membrane lipid remodeling during P stress is not uniform across the nodule.

Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics

Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.

Fast visual exploration of mass spectrometry images with interactive dynamic spectral similarity pseudocoloring

Mass Spectrometry Imaging (MSI) is an established and still evolving technique for the spatial analysis of molecular co-location in biological samples. Nowadays, MSI is expanding into new domains such as clinical pathology. In order to increase the value of MSI data, software for visual analysis is required that is intuitive and technique independent. Here, we present QUIMBI (QUIck exploration tool for Multivariate BioImages) a new tool for the visual analysis of MSI data. QUIMBI is an interactive visual exploration tool that provides the user with a convenient and straightforward visual exploration of morphological and spectral features of MSI data. To improve the overall quality of MSI data by reducing non-tissue specific signals and to ensure optimal compatibility with QUIMBI, the tool is combined with the new pre-processing tool ProViM (Processing for Visualization and multivariate analysis of MSI Data), presented in this work. The features of the proposed visual analysis approach for MSI data analysis are demonstrated with two use cases. The results show that the use of ProViM and QUIMBI not only provides a new fast and intuitive visual analysis, but also allows the detection of new co-location patterns in MSI data that are difficult to find with other methods.

Plant Single-Cell Metabolomics-Challenges and Perspectives

Omics approaches for investigating biological systems were introduced in the mid-1990s and quickly consolidated to become a fundamental pillar of modern biology. The idea of measuring the whole complement of genes, transcripts, proteins, and metabolites has since become widespread and routinely adopted in the pursuit of an infinity of scientific questions. Incremental improvements over technical aspects such as sampling, sensitivity, cost, and throughput pushed even further the boundaries of what these techniques can achieve. In this context, single-cell genomics and transcriptomics quickly became a well-established tool to answer fundamental questions challenging to assess at a whole tissue level. Following a similar trend as the original development of these techniques, proteomics alternatives for single-cell exploration have become more accessible and reliable, whilst metabolomics lag behind the rest. This review summarizes state-of-the-art technologies for spatially resolved metabolomics analysis, as well as the challenges hindering the achievement of sensu stricto metabolome coverage at the single-cell level. Furthermore, we discuss several essential contributions to understanding plant single-cell metabolism, finishing with our opinion on near-future developments and relevant scientific questions that will hopefully be tackled by incorporating these new exciting technologies.

Metabolic Visualization Reveals the Distinct Distribution of Sugars and Amino Acids in Rice Koji

The compounds inside rice koji have been thoroughly investigated as an essential material in making many food-related products, including sake. However, these studies focused only on quantitative aspects, leaving features that can still be uncovered if seen from a new perspective. Visualization of the metabolites inside rice koji may as well be the new angle needed to retrieve more information regarding rice koji making. Here we utilized mass spectrometry imaging (MSI) to visualize the distribution of sugars, sugar alcohols, and amino acids inside rice koji. Imaging results revealed that several sugars alcohols and amino acids were shown to have characteristic distribution near the edges or surface of rice koji. Furthermore, the distribution appears to be correlated with the different structure of rice koji. This study is the first report of using MSI to visualize sugars, sugar alcohols, and amino acids in rice koji.

DOF, MYB and TCP transcription factors: Their possible roles on barley germination and seedling establishment

Seed germination is a multi-staged complex process during seed plant life cycle, and it is tightly regulated through a coordinated expression of diverse genes in diverse tissues. As regulatory molecules of gene expression, determination of transcription factors is crucial to understanding molecular basis and regulatory network of germination process and seedling establishment. However, limited data on the contributions of these transcription factors to the germination of crop barley (Hordeum vulgare L.) are available. Here, we investigated the expression profiles of selected transcription factors from different families (DOF, MYB and TCP) with qRT-PCR analysis in various tissues including coleoptiles, leaves and roots following the germination. Analysis of MYB and DOF gene expression profiles indicated that there were differing expressions in different aged tissues, HvMYB5 and HvDOF2 being the most outstanding one in the oldest tissue, 15-day-old root. On the other hand, investigated TCP genes were lowly expressed compared to selected MYB and DOF genes, except HvTCP3, where the highest expression was observed in 15-day-old root tissue. The obtained expression profiles illustrate the importance of potential regulatory roles of transcription factors in early developmental stages of barley germination and seedling establishment.

Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging of Metabolites during Sorghum Germination

Dhurrin is the most abundant cyanogenic glucoside found in sorghum (Sorghum bicolor) where it plays a key role in chemical defense by releasing toxic hydrogen cyanide upon tissue disruption. Besides this well-established function, there is strong evidence that dhurrin plays additional roles, e.g. as a transport and storage form of nitrogen, released via endogenous recycling pathways. However, knowledge about how, when and why dhurrin is endogenously metabolized is limited. We combined targeted metabolite profiling with matrix-assisted laser desorption/ionization-mass spectrometry imaging to investigate accumulation of dhurrin, its recycling products and key general metabolites in four different sorghum lines during 72 h of grain imbibition, germination and early seedling development, as well as the spatial distribution of these metabolites in two of the lines. Little or no dhurrin or recycling products were present in the dry grain, but their de novo biosynthesis started immediately after water uptake. Dhurrin accumulation increased rapidly within the first 24 h in parallel with an increase in free amino acids, a key event in seed germination. The trajectories and final concentrations of dhurrin, the recycling products and free amino acids reached within the experimental period were dependent on genotype. Matrix-assisted laser desorption/ionization-mass spectrometry imaging demonstrated that dhurrin primarily accumulated in the germinating embryo, confirming its function in protecting the emerging tissue against herbivory. The dhurrin recycling products, however, were mainly located in the scutellum and/or pericarp/seed coat region, suggesting unknown key functions in germination.

Application of Mass Spectrometry Imaging for Visualizing Food Components

Consuming food is essential for survival, maintaining health, and triggering positive emotions like pleasure. One of the factors that drive us toward such behavior is the presence of various compounds in foods. There are many methods to analyze these molecules in foods; however, it is difficult to analyze the spatial distribution of these compounds using conventional techniques, such as mass spectrometry combined with high-performance liquid chromatography or gas chromatography. Mass spectrometry imaging (MSI) is a two-dimensional ionization technology that enables detection of compounds in tissue sections without extraction, purification, separation, or labeling. There are many methods for ionization of analytes, including secondary ion mass spectrometry, matrix-assisted laser desorption/ionization, and desorption electrospray ionization. Such MSI technologies can provide spatial information on the location of a specific analyte in food. The number of studies utilizing MSI technologies in food science has been increasing in the past decade. This review provides an overview of some of the recent applications of MSI in food science and related fields. In the future, MSI will become one of the most promising technologies for visualizing the distribution of food components and for identifying food-related factors by their molecular weights to improve quality, quality assurance, food safety, nutritional analysis, and to locate administered food factors.

Genome-Wide Association Study of Salinity Tolerance During Germination in Barley (Hordeum vulgare L.)

Barley seeds need to be able to germinate and establish seedlings in saline soils in Mediterranean-type climates. Despite being a major cereal crop, barley has few reported quantitative trait loci (QTL) and candidate genes underlying salt tolerance at the germination stage. Breeding programs targeting salinity tolerance at germination require an understanding of genetic loci and alleles in the current germplasm. In this study, we investigated seed-germination-related traits under control and salt stress conditions in 350 diverse barley accessions. A genome-wide association study, using ~24,000 genetic markers, was undertaken to detect marker-trait associations (MTA) and the underlying candidate genes for salinity tolerance during germination. We detected 19 loci containing 52 significant salt-tolerance-associated markers across all chromosomes, and 4 genes belonging to 4 family functions underlying the predicted MTAs. Our results provide new genetic resources and information to improve salt tolerance at germination in future barley varieties via genomic and marker-assisted selection and to open up avenues for further functional characterization of the identified candidate genes.

Mass Spectrometry Imaging of the Spatial and Temporal Localization of Alkaloids in Nightshades

Alkaloids are common secondary metabolites found also in plants of the large family of Solanaceae, and they contribute frequently to the economic importance of these plants as food, spices, drugs, or pharmaceuticals. Matrix-assisted laser desorption/ionization mass spectrometry imaging was applied to visualize the spatial localization of the main steroidal alkaloids in diverse plant tissues of Lycopersicon esculentum, Solanum nigrum, and Solanum dulcamara. Among others, the basic aglycons, tomatidenol, tomatidine, solasodine, and soladulcine, along with their corresponding glycoalkaloids, were identified with distinct distributions within plant tissue structures and plant parts and with respect to the degree of ripeness. The alkaloids are identified by their mass and fragmentation pattern. Multivariate unsupervised principal compound analysis and the k-means clustering analysis were calculated on the basis of all peaks, automatically picked from all selected regions, with total ion count normalization resulting in characterization of the tissues and organs with respect to their chemical similarity. It can therefore be concluded that the tissue-specific localizations of alkaloids in nightshades depend upon the ripeness status and the developmental stage of the plants.

Spatio-Temporal Metabolite and Elemental Profiling of Salt Stressed Barley Seeds During Initial Stages of Germination by MALDI-MSI and µ-XRF Spectrometry

Seed germination is the essential first step in crop establishment, and can be severely affected by salinity stress which can inhibit essential metabolic processes during the germination process. Salt stress during seed germination can trigger lipid-dependent signalling cascades that activate plant adaptation processes, lead to changes in membrane fluidity to help resist the stress, and cause secondary metabolite responses due to increased oxidative stress. In germinating barley (Hordeum vulgare), knowledge of the changes in spatial distribution of lipids and other small molecules at a cellular level in response to salt stress is limited. In this study, mass spectrometry imaging (MSI), liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF-MS), inductively coupled plasma mass spectrometry (ICP-MS), and X-ray fluorescence (XRF) were used to determine the spatial distribution of metabolites, lipids and a range of elements, such as K+ and Na+, in seeds of two barley genotypes with contrasting germination phenology (Australian barley varieties Mundah and Keel). We detected and tentatively identified more than 200 lipid species belonging to seven major lipid classes (fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, prenol lipids, sterol lipids, and polyketides) that differed in their spatial distribution based on genotype (Mundah or Keel), time post-imbibition (0 to 72 h), or treatment (control or salt). We found a tentative flavonoid was discriminant in post-imbibed Mundah embryos under saline conditions, and a delayed flavonoid response in Keel relative to Mundah. We further employed MSI-MS/MS and LC-QToF-MS/MS to explore the identity of the discriminant flavonoid and study the temporal pattern in five additional barley genotypes. ICP-MS was used to quantify the elemental composition of both Mundah and Keel seeds, showing a significant increase in Na+ in salt treated samples. Spatial mapping of elements using µ-XRF localized the elements within the seeds. This study integrates data obtained from three mass spectrometry platforms together with µ-XRF to yield information on the localization of lipids, metabolites and elements improving our understanding of the germination process under salt stress at a molecular level.

rMSIKeyIon: An Ion Filtering R Package for Untargeted Analysis of Metabolomic LDI-MS Images

Many MALDI-MS imaging experiments make a case versus control studies of different tissue regions in order to highlight significant compounds affected by the variables of study. This is a challenge because the tissue samples to be compared come from different biological entities, and therefore they exhibit high variability. Moreover, the statistical tests available cannot properly compare ion concentrations in two regions of interest (ROIs) within or between images. The high correlation between the ion concentrations due to the existence of different morphological regions in the tissue means that the common statistical tests used in metabolomics experiments cannot be applied. Another difficulty with the reliability of statistical tests is the elevated number of undetected MS ions in a high percentage of pixels. In this study, we report a procedure for discovering the most important ions in the comparison of a pair of ROIs within or between tissue sections. These ROIs were identified by an unsupervised segmentation process, using the popular k-means algorithm. Our ion filtering algorithm aims to find the up or down-regulated ions between two ROIs by using a combination of three parameters: (a) the percentage of pixels in which a particular ion is not detected, (b) the Mann–Whitney U ion concentration test, and (c) the ion concentration fold-change. The undetected MS signals (null peaks) are discarded from the histogram before the calculation of (b) and (c) parameters. With this methodology, we found the important ions between the different segments of a mouse brain tissue sagittal section and determined some lipid compounds (mainly triacylglycerols and phosphatidylcholines) in the liver of mice exposed to thirdhand smoke.

Detection and visualization of communities in mass spectrometry imaging data

Background

The spatial distribution and colocalization of functionally related metabolites is analysed in order to investigate the spatial (and functional) aspects of molecular networks. We propose to consider community detection for the analysis of m/z-images to group molecules with correlative spatial distribution into communities so they hint at functional networks or pathway activity. To detect communities, we investigate a spectral approach by optimizing the modularity measure. We present an analysis pipeline and an online interactive visualization tool to facilitate explorative analysis of the results. The approach is illustrated with synthetical benchmark data and two real world data sets (barley seed and glioblastoma section).

Results

For the barley sample data set, our approach is able to reproduce the findings of a previous work that identified groups of molecules with distributions that correlate with anatomical structures of the barley seed. The analysis of glioblastoma section data revealed that some molecular compositions are locally focused, indicating the existence of a meaningful separation in at least two areas. This result is in line with the prior histological knowledge. In addition to confirming prior findings, the resulting graph structures revealed new subcommunities of m/z-images (i.e. metabolites) with more detailed distribution patterns. Another result of our work is the development of an interactive webtool called GRINE (Analysis of GRaph mapped Image Data NEtworks).

Conclusions

The proposed method was successfully applied to identify molecular communities of laterally co-localized molecules. For both application examples, the detected communities showed inherent substructures that could easily be investigated with the proposed visualization tool. This shows the potential of this approach as a complementary addition to pixel clustering methods.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2890-6) contains supplementary material, which is available to authorized users.

A substitute variety for agronomically and medicinally important Serenoa repens (saw palmetto)

Serenoa repens (saw palmetto) berries are one of the most consumed medicinal herbs in the United States and the wild green variety is used in the initial therapy of benign prostatic hyperplasia (BPH), globally. Use of saw palmetto is approved by the German Commission E, and several clinical trials are underway for evaluation of its efficacy. Exploitation of its habitats and over foraging imperil this plant, which only grows in the wild. This is the first study, to propose the use of the S. repens forma glauca (silver variety) as a qualitative substitute for the wild variety, to support its conservation. We compared tissue microstructures and lipid and water distribution through spatial imaging and examined metabolite distribution of three tissue domains and whole berries. This combined approach of 3D imaging and metabolomics provides a new strategy for studying phenotypic traits and metabolite synthesis of closely related plant varieties.

Metabolic and gene expression hallmarks of seed germination uncovered by sodium butyrate in Medicago truncatula

Because high-quality seeds are essential for successful crop production in challenging environments, understanding the molecular bases of seed vigour will lead to advances in seed technology. Histone deacetylase inhibitors, promoting histone hyperacetylation, are used as tools to explore aspects still uncovered of the abiotic stress response in plants. The aim of this work was to investigate novel signatures of seed germination in Medicago truncatula, using the histone deacetylase inhibitor sodium butyrate (NaB) as stress agent. NaB-treated and untreated seeds collected at 2 and 8 hr of imbibition and at the radicle protrusion stage underwent molecular phenotyping and nontargeted metabolome profiling. Quantitative enrichment analysis revealed the influence of NaB on seed nucleotide, amino acid, lipid, and carbohydrate metabolism. Up-regulation of antioxidant and polyamine biosynthesis genes occurred in response to NaB. DNA damage evidenced in NaB-treated seeds correlated with up-regulation of base-excision repair genes. Changes in N¹ -methyladenosine and N¹ -methylguanine were associated with up-regulation of MtALKBH1 (alkylation repair homolog) gene. N² ,N² -dimethylguanosine and 5-methylcytidine, tRNA modifications involved in the post-transcriptional regulation of DNA damage response, were also accumulated in NaB-treated seeds at the radicle protrusion stage. The observed changes in seed metabolism can provide novel potential metabolic hallmarks of germination.

Mass Spectrometry Imaging (MSI) for Plant Metabolomics

Mass spectrometry imaging (MSI) is a developing technique to measure the spatiotemporal distribution of many biomolecules in tissues. Over the preceding decade MSI has been adopted by plant biologists and applied in a broad range of areas including: primary metabolism, natural products, plant defense, plant responses to abiotic and biotic stress, plant lipids, and the developing field of spatial metabolomics. This methods chapter covers preparation of plant tissues for matrix-assisted laser desorption ionization (MALDI)-MSI, including sample embedding and freezing, sectioning, mounting, and matrix deposition using both sublimation and spray deposition prior to MSI analysis.

Mass Spectrometry Based Imaging of Labile Glucosides in Plants

Mass spectrometry based imaging is a powerful tool to investigate the spatial distribution of a broad range of metabolites across a variety of sample types. The recent developments in instrumentation and computing capabilities have increased the mass range, sensitivity and resolution and rendered sample preparation the limiting step for further improvements. Sample preparation involves sectioning and mounting followed by selection and application of matrix. In plant tissues, labile small molecules and specialized metabolites are subject to degradation upon mechanical disruption of plant tissues. In this study, the benefits of cryo-sectioning, stabilization of fragile tissues and optimal application of the matrix to improve the results from MALDI mass spectrometry imaging (MSI) is investigated with hydroxynitrile glucosides as the main experimental system. Denatured albumin proved an excellent agent for stabilizing fragile tissues such as Lotus japonicus leaves. In stem cross sections of Manihot esculenta, maintaining the samples frozen throughout the sectioning process and preparation of the samples by freeze drying enhanced the obtained signal intensity by twofold to fourfold. Deposition of the matrix by sublimation improved the spatial information obtained compared to spray. The imaging demonstrated that the cyanogenic glucosides (CNglcs) were localized in the vascular tissues in old stems of M. esculenta and in the periderm and vascular tissues of tubers. In MALDI mass spectrometry, the imaged compounds are solely identified by their m/z ratio. L. japonicus MG20 and the mutant cyd1 that is devoid of hydroxynitrile glucosides were used as negative controls to verify the assignment of the observed masses to linamarin, lotaustralin, and linamarin acid.

High-mass-resolution MALDI mass spectrometry imaging reveals detailed spatial distribution of metabolites and lipids in roots of barley seedlings in response to salinity stress

INTRODUCTION

Mass spectrometry imaging (MSI) is a technology that enables the visualization of the spatial distribution of hundreds to thousands of metabolites in the same tissue section simultaneously. Roots are below-ground plant organs that anchor plants to the soil, take up water and nutrients, and sense and respond to external stresses. Physiological responses to salinity are multifaceted and have predominantly been studied using whole plant tissues that cannot resolve plant salinity responses spatially.

OBJECTIVES

This study aimed to use a comprehensive approach to study the spatial distribution and profiles of metabolites, and to quantify the changes in the elemental content in young developing barley seminal roots before and after salinity stress.

METHODS

Here, we used a combination of liquid chromatography-mass spectrometry (LC-MS), inductively coupled plasma mass spectrometry (ICP-MS), and matrix-assisted laser desorption/ionization (MALDI-MSI) platforms to profile and analyze the spatial distribution of ions, metabolites and lipids across three anatomically different barley root zones before and after a short-term salinity stress (150 mM NaCl).

RESULTS

We localized, visualized and discriminated compounds in fine detail along longitudinal root sections and compared ion, metabolite, and lipid composition before and after salt stress. Large changes in the phosphatidylcholine (PC) profiles were observed as a response to salt stress with PC 34:n showing an overall reduction in salt treated roots. ICP-MS analysis quantified changes in the elemental content of roots with increases of Na⁺ and decreases of K⁺ content.

CONCLUSION

Our results established the suitability of combining three mass spectrometry platforms to analyze and map ionic and metabolic responses to salinity stress in plant roots and to elucidate tolerance mechanisms in response to abiotic stress, such as salinity stress.

Automated Morphological and Morphometric Analysis of Mass Spectrometry Imaging Data: Application to Biomarker Discovery

Mass spectrometry imaging datasets are mostly analyzed in terms of average intensity in regions of interest. However, biological tissues have different morphologies with several sizes, shapes, and structures. The important biological information, contained in this highly heterogeneous cellular organization, could be hidden by analyzing the average intensities. Finding an analytical process of morphology would help to find such information, describe tissue model, and support identification of biomarkers. This study describes an informatics approach for the extraction and identification of mass spectrometry image features and its application to sample analysis and modeling. For the proof of concept, two different tissue types (healthy kidney and CT-26 xenograft tumor tissues) were imaged and analyzed. A mouse kidney model and tumor model were generated using morphometric - number of objects and total surface - information. The morphometric information was used to identify m/z that have a heterogeneous distribution. It seems to be a worthwhile pursuit as clonal heterogeneity in a tumor is of clinical relevance. This study provides a new approach to find biomarker or support tissue classification with more information. Graphical Abstract ᅟ.

Towards Better Understanding of Pea Seed Dormancy Using Laser Desorption/Ionization Mass Spectrometry

Seed coats of six pea genotypes contrasting in dormancy were studied by laser desorption/ionization mass spectrometry (LDI-MS). Multivariate statistical analysis discriminated dormant and non-dormant seeds in mature dry state. Separation between dormant and non-dormant types was observed despite important markers of particular dormant genotypes differ from each other. Normalized signals of long-chain hydroxylated fatty acids (HLFA) in dormant JI64 genotype seed coats were significantly higher than in other genotypes. These compounds seem to be important markers likely influencing JI64 seed imbibition and germination. HLFA importance was supported by study of recombinant inbred lines (JI64xJI92) contrasting in dormancy but similar in other seed properties. Furthemore HLFA distribution in seed coat was studied by mass spectrometry imaging. HLFA contents in strophiole and hilum are significantly lower compared to other parts indicating their role in water uptake. Results from LDI-MS experiments are useful in understanding (physical) dormancy (first phases of germination) mechanism and properties related to food processing technologies (e.g., seed treatment by cooking).

Down-regulation of the sucrose transporters HvSUT1 and HvSUT2 affects sucrose homeostasis along its delivery path in barley grains

Sucrose transport and partitioning are crucial for seed filling. While many plasma-membrane-localised sucrose transporters (SUT1 family members) have been analysed in seeds, the functions of vacuolar SUT2 members are still obscure. In barley grains, expression of HvSUT1 and HvSUT2 overlap temporally and spatially, suggesting concerted functions to regulate sucrose homeostasis. Using HvSUT2-RNAi plants, we found that grains were also deficient in HvSUT1 expression and seemingly sucrose-limited during mid-to-late grain filling. Transgenic endosperms accumulated less starch and dry weight, although overall sucrose and hexose contents were higher. Comprehensive transcript and metabolite profiling revealed that genes related to glycolysis, the tricarboxylic acid cycle, starch and amino acid synthesis, grain maturation, and abscisic acid signalling were down-regulated together with most glycolytic intermediates and amino acids. Sucrose was increased along the sucrose delivery route in the nucellar projection, the endosperm transfer cells, and the starchy endosperm, indicating that suppressed transporter activity diminished sucrose efflux from vacuoles, which generated sugar deficiency in the cytoplasm. Thus, endosperm vacuoles may buffer sucrose concentrations to regulate homeostasis at grain filling. Transcriptional changes revealed that limited endosperm sucrose initiated sugar starvation responses, such as sugar recycling from starch, hemicelluloses and celluloses together with vacuolar protein degradation, thereby supporting formation of nucleotide sugars. Barley endosperm cells can thus suppress certain pathways to retrieve resources to maintain essential cell functions.