RUNX1 isoform disequilibrium promotes the development of trisomy 21-associated myeloid leukemia.

Gain of chromosome 21 (Hsa21) is among the most frequent aneuploidies in leukemia. However, it remains unclear how partial or complete amplifications of Hsa21 promote leukemogenesis and why children with Down syndrome (DS) (ie, trisomy 21) are particularly at risk of leukemia development. Here, we propose that RUNX1 isoform disequilibrium with RUNX1A bias is key to DS-associated myeloid leukemia (ML-DS). Starting with Hsa21-focused CRISPR-CRISPR-associated protein 9 screens, we uncovered a strong and specific RUNX1 dependency in ML-DS cells. Expression of the RUNX1A isoform is elevated in patients with ML-DS, and mechanistic studies using murine ML-DS models and patient-derived xenografts revealed that excess RUNX1A synergizes with the pathognomonic Gata1s mutation during leukemogenesis by displacing RUNX1C from its endogenous binding sites and inducing oncogenic programs in complex with the MYC cofactor MAX. These effects were reversed by restoring the RUNX1A:RUNX1C equilibrium in patient-derived xenografts in vitro and in vivo. Moreover, pharmacological interference with MYC:MAX dimerization using MYCi361 exerted strong antileukemic effects. Thus, our study highlights the importance of alternative splicing in leukemogenesis, even on a background of aneuploidy, and paves the way for the development of specific and targeted therapies for ML-DS, as well as for other leukemias with Hsa21 aneuploidy or RUNX1 isoform disequilibrium.

Texture Transfer in Dielectric Layers via Nanocrystalline Networks: Insights from in Situ 4D-STEM.

Transition metal oxide dielectric layers have emerged as promising candidates for various relevant applications, such as supercapacitors or memory applications. However, the performance and reliability of these devices can critically depend on their microstructure, which can be strongly influenced by thermal processing and substrate-induced strain. To gain a more in-depth understanding of the microstructural changes, we conducted in situ transmission electron microscopy (TEM) studies of amorphous HfO2 dielectric layers grown on highly textured (111) substrates. Our results indicate that the minimum required phase transition temperature is 180 °C and that the developed crystallinity is affected by texture transfer. Using in situ TEM and 4D-STEM can provide valuable insights into the fundamental mechanisms underlying the microstructural evolution of dielectric layers and could pave the way for the development of more reliable and efficient devices for future applications.

The DNA methyltransferase inhibitor decitabine blunts the response to a high animal fat and protein diet in mice.

Increasing evidence hints that DNA hypermethylation may mediate the pathogenic response to cardiovascular risk factors. Here, we tested a corollary of that hypothesis, i.e., that the DNA methyltransferase inhibitor decitabine (Dec) ameliorates the metabolic profile of mice fed a moderately high-animal fat and protein diet (HAFPD), a proxy of cardiovascular risk-associated Western-type diet. HAFPD-fed mice were exposed to Dec or vehicle for eight weeks (8W set, 4-32/group). To assess any memory of past exposure to Dec, we surveyed a second mice set treated as 8W but HAFPD-fed for further eight weeks without any Dec (16W set, 4-20/group). In 8W, Dec markedly reduced HAFPD-induced body weight gain in females, but marginally in males. Characterization of females revealed that Dec augmented skeletal muscle lipid content, while decreasing liver fat content and increasing plasma non-esterified fatty acids, adipose insulin resistance, and -although marginally- whole blood acylcarnitines, compared to HAFPD alone. Skeletal muscle mitochondrial DNA copy number was higher in 8W mice exposed to HAFPD and Dec, or in 16W mice fed HAFPD only, relative to 8W mice fed HAFPD only, but Dec induced a transcriptional profile indicative of ameliorated mitochondrial function. Memory of past Dec exposure was tissue-specific and sensitive to both duration of exposure to HAFPD and age. In conclusion, Dec redirected HAFPD-induced lipid accumulation towards the skeletal muscle, likely due to augmented mitochondrial functionality and increased lipid demand. As caveat, Dec induced adipose insulin resistance. Our findings may help identifying strategies for prevention and treatment of lipid dysmetabolism.

Technical Note: mzML and imzML Libraries for Processing Mass Spectrometry Data with the High-Performance Programming Language Julia.

Julia combines the virtues of high-level and low-level programming languages: The code is human-readable, and the performance of the created binaries competes with machine-orientated compilers. Thus, Julia is popular in "Big Data" sciences. Reading mass spectrometry (MS) data with Julia was impossible until now due to missing libraries. Here, we present a Julia library for importing mass spectrometry (MS) data in HUPO standard mzML and imzML formats and demonstrate its function with direct and ambient ionization MS, liquid chromatography-MS, and MS imaging data on standard platforms (Windows, Linux, and Mac OS). The processing speed of Julia for reading imzML MS imaging files was up to 214 times faster than the comparable code in R. Julia can remove bottlenecks for computationally demanding tasks in large-scale MS-Omics and MS imaging data processing workflows and supports their agile development. In addition, time-critical and complex data evaluation tasks become possible, such as following the real-time monitoring of biological processes and pattern recognition in large MS imaging projects. Our mzML/imzML libraries and code examples are available under the terms of the MIT license from https://github.com/CINVESTAV-LABI/julia_mzML_imzML.

Multi-Stimuli Operando Transmission Electron Microscopy for Two-Terminal Oxide-Based Devices.

The integration of microelectromechanical systems (MEMS)-based chips for in situ transmission electron microscopy (TEM) has emerged as a highly promising technique in the study of nanoelectronic devices within their operational parameters. This innovative approach facilitates the comprehensive exploration of electrical properties resulting from the simultaneous exposure of these devices to a diverse range of stimuli. However, the control of each individual stimulus within the confined environment of an electron microscope is challenging. In this study, we present novel findings on the effect of a multi-stimuli application on the electrical performance of TEM lamella devices. To approximate the leakage current measurements of macroscale electronic devices in TEM lamellae, we have developed a postfocused ion beam (FIB) healing technique. This technique combines dedicated MEMS-based chips and in situ TEM gas cells, enabling biasing experiments under environmental conditions. Notably, our observations reveal a reoxidation process that leads to a decrease in leakage current for SrTiO3-based memristors and BaSrTiO3-based tunable capacitor devices following ion and electron bombardment in oxygen-rich environments. These findings represent a significant step toward the realization of multi-stimuli TEM experiments on metal-insulator-metal devices, offering the potential for further exploration and a deeper understanding of their intricate behavior.

Transduction of Single Nanomechanical Pillar Resonators by Scattering of Surface Acoustic Waves.

One of the challenges of nanoelectromechanical systems (NEMS) is the effective transduction of the tiny resonators. Vertical structures, such as nanomechanical pillar resonators, which are exploited in optomechanics, acoustic metamaterials, and nanomechanical sensing, are particularly challenging to transduce. Existing electromechanical transduction methods are ill-suited as they put constraints on the pillars' material and do not enable a transduction of freestanding pillars. Here, we present an electromechanical transduction method for single nanomechanical pillar resonators based on surface acoustic waves (SAWs). We demonstrate the transduction of freestanding nanomechanical platinum-carbon pillars in the first-order bending and compression mode. Since the principle of the transduction method is based on resonant scattering of a SAW by a nanomechanical resonator, our transduction method is independent of the pillar's material and not limited to pillar-shaped geometries. It represents a general method to transduce vertical mechanical resonators with nanoscale lateral dimensions.

Backcrossing Modulates the Metabolic Profiles of Anthocyanin-Pigmented 'Vitamaize' Lines Derived from Elite Maize Lines.

Vitamaize lines (VMLs) were created by backcrossing the pigmented aleurone trait into Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT) maize lines (CMLs). This study evaluates metabolic differences between the VMLs and their original CMLs. Direct infusion mass spectrometry (DIMS) analyses, carotenoid profiling, total anthocyanins content (TAC) determination, and biochemical evaluation of the quality protein maize (QPM) endosperm trait allowed a comprehensive chemical characterization of the maize lines. DIMS data indicate higher hexoses and trigonelline content for most VMLs; the carotenoid profile revealed a decrease in ß-cryptoxanthin to less than half of the original parent content for two VMLs but an augmentation for one VML. The pigmented aleurone VMLs did not inherit the complex QPM endosperm trait of the QPM CMLs. Except for anthocyanin accumulation, no other metabolites were consistently modified across all the backcross-generated maize lines with a pigmented aleurone trait. These findings suggest using genetic or metabolic markers rather than morphological or visual traits for future breeding programs.

The plant organellar primase-helicase directs template recognition and primosome assembly via its zinc finger domain.

BACKGROUND: The mechanisms and regulation for DNA replication in plant organelles are largely unknown, as few proteins involved in replisome assembly have been biochemically studied. A primase-helicase dubbed Twinkle (T7 gp4-like protein with intramitochondrial nucleoid localization) unwinds double-stranded DNA in metazoan mitochondria and plant organelles. Twinkle in plants is a bifunctional enzyme with an active primase module. This contrast with animal Twinkle in which the primase module is inactive. The organellar primase-helicase of Arabidopsis thaliana (AtTwinkle) harbors a primase module (AtPrimase) that consists of an RNA polymerase domain (RPD) and a Zn + + finger domain (ZFD). RESULTS: Herein, we investigate the mechanisms by which AtTwinkle recognizes its templating sequence and how primer synthesis and coupling to the organellar DNA polymerases occurs. Biochemical data show that the ZFD of the AtPrimase module is responsible for template recognition, and this recognition is achieved by residues N163, R166, and K168. The role of the ZFD in template recognition was also corroborated by swapping the RPDs of bacteriophage T7 primase and AtPrimase with their respective ZFDs. A chimeric primase harboring the ZFD of T7 primase and the RPD of AtPrimase synthesizes ribonucleotides from the T7 primase recognition sequence and conversely, a chimeric primase harboring the ZFD of AtPrimase and the RPD of T7 primase synthesizes ribonucleotides from the AtPrimase recognition sequence. A chimera harboring the RPDs of bacteriophage T7 and the ZBD of AtTwinkle efficiently synthesizes primers for the plant organellar DNA polymerase. CONCLUSIONS: We conclude that the ZFD is responsible for recognizing a single-stranded sequence and for primer hand-off into the organellar DNA polymerases active site. The primase activity of plant Twinkle is consistent with phylogeny-based reconstructions that concluded that Twinkle´s last eukaryotic common ancestor (LECA) was an enzyme with primase and helicase activities. In plants, the primase domain is active, whereas the primase activity was lost in metazoans. Our data supports the notion that AtTwinkle synthesizes primers at the lagging-strand of the organellar replication fork.

Guided analysis of ambient ionization mass spectrometry data with the MQ_Assistant.

RATIONALE: Ambient ionization mass spectrometry (AIMS) delivers realistic data from samples in their native state. In addition, AIMS methods reduce time and costs for sample preparation and have less environmental impact. However, AIMS data are often complex and require substantial processing before interpretation. METHODS: We developed an interactive R script for guided mass spectrometry (MS) data processing. The "MQ_Assistant" is based on MALDIquant, a popular R package for MS data processing. In each step, the user can try and preview the effect of chosen parameters before deciding on the values with the best result and proceeding to the next stage. The outcome of the MQ_Assistant is a feature matrix that can be further analyzed in R and statistics tools such as MetaboAnalyst. RESULTS: Using 360 AIMS example spectra, we demonstrate the step-by-step processing for creating a feature matrix. In addition, we show how to visualize the results of three biological replicates of a plant-microbe interaction between Arabidopsis and Trichoderma as a heatmap using R and upload them to MetaboAnalyst. The final parameter set can be saved for reuse in MALDIquant workflows of similar data. CONCLUSIONS: The MQ_Assistant helps novices and experienced users to develop workflows for (AI)MS data processing. The interactive procedure supports the quick finding of appropriate settings. These parameters can be exported and reused in future projects. The stepwise operation with visual feedback also suggests the use of the MQ_Assistant in education.

Target-Decoy MineR for determining the biological relevance of variables in noisy datasets.

MOTIVATION: Machine learning algorithms excavate important variables from big data. However, deciding on the relevance of identified variables is challenging. The addition of artificial noise, 'decoy' variables, to raw data, 'target' variables, enables calculating a false-positive rate and a biological relevance probability for each variable rank. These scores allow the setting of a cut-off for informative variables, depending on the required sensitivity/specificity of a scientific question. RESULTS: We tested the function of the Target-Decoy MineR (TDM) using synthetic data with different degrees of perturbation. Following, we applied the TDM to experimental Omics (metabolomics, transcriptomics and proteomics) results. The TDM graphs indicate the degree of difference between sample groups. Further, the TDM reports the contribution of each variable to correct classification, i.e. its biological relevance. AVAILABILITYAND IMPLEMENTATION: An implementation of the algorithm in R is freely available from https://bitbucket.org/cesaremov/targetdecoy_mining/. The Target-Decoy MineR is applicable to different types of quantitative data in tabular format. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Loss of Sensory Cup Quality: Physiological and Chemical Changes during Green Coffee Storage.

Coffee is one of the most valued consumer products. Surprisingly, there is limited scientific knowledge about the biochemical processes during the storage of green coffee that affects its sensory quality. This review analyzes the impact of the different variables involved in the green coffee storage on quality from a chemical point of view. Further, it highlights the relationship between the physiological processes of the grain, its viability, and shelf-life. Notably, the storage conditions and postharvest treatment affect both the longevity and the sensory quality of the coffee, probably due to the biological behavior of green coffee. Various studies found modifications in their chemical profiles involving carbohydrates, lipids, proteins/amino acids, and phenolic compounds. To make future studies more comparable, we recommend standardized protocols for evaluating and linking the sensory coffee quality with instrumental analysis methods and pre-defined settings for experimental storage conditions.

Novel UV filters from Pentacalia pulchella extracts with photoprotective properties and antioxidant activity.

Most of the plant species found in the high mountain ecosystems of the tropics is unique and exceptional, because they have developed complex adaptations to survive in extreme environmental conditions, such as high levels of UVR and low temperatures of these ecological environments. In an exploratory study carried out on some plants of this ecosystem, we found that one of the most promising species was the Pentacalia pulchella (Kunth) Cuatrec. (Asteraceae) an endemic plant of Colombia, which grows between 2500 and 3500 m.a.s.l. Therefore, the objective of this work was to evaluate the photoprotective, antioxidant, and chemical composition of extracts from the leaves of P. pulchella. Extracts showed good absorption coefficients in UVA-UVB, high content of total phenols, with antioxidant activity comparable to that obtained with butylhydroxytoluene (BHT). Finally, the formulation labeled "7" with 10% extract presented adequate sensory characteristics for topical use, good in vitro photoprotection values in the UVA-UVB range (SPF (Sun Protection Factor): 7.3 ± 0.9, UVAPF (Ultraviolet A Protection Factor): 5.3 ± 0.6, λc 376), and antioxidant activity. Results obtained allow us to suggest that the extract of P. pulchella has a high potential as a source of new natural solar filters.

Mass spectrometry imaging of thin-layer chromatography plates using laser desorption/low-temperature plasma ionisation.

Thin-layer chromatography (TLC) is a classic method for the separation and analysis of complex mixtures. Biological assays, chemical derivatisation and spectroscopy techniques are compatible with TLC and provide extra information about isolated compounds. However, coupling TLC to mass spectrometry is hampered by the difficulty to desorb the analytes from the silica surfaces. In this study, we used a multimodal ion source for laser desorption (LD) and low-temperature plasma (LTP) post-ionisation. Efficient desorption was reached by covering the TLC plates with activated carbon. Regions of interest can be analysed by spots, by lines or by area. We show the separation of methylxanthines from coffee, tea and cocoa preparations by TLC, with subsequent mass spectrometry imaging (MSI). Using a lateral resolution of 400 µm × 400 µm, allowed the acquisition of 21 895 spectra in 2.4 h (2.5 pixels per s). Further, we demonstrate the possibility of direct mass fragmentation studies and quantification. We mounted the system on an Open LabBot with a theoretical lateral resolution of 12.5 µm and performed the visualisation of ions of interest and the pixel-wise review of mass spectra with our free software RmsiGUI (). This non-proprietary and modular platform enables the cost-efficient adaption of the system and further development by the community.

Elucidating the Distribution of Plant Metabolites from Native Tissues with Laser Desorption Low-Temperature Plasma Mass Spectrometry Imaging.

Secondary metabolites of plants have important biological functions, which often depend on their localization in tissues. Ideally, a fresh untreated material should be directly analyzed to obtain a realistic view of the true sample chemistry. Therefore, there is a large interest for ambient mass-spectrometry-based imaging (MSI) methods. Our aim was to simplify this technology and to find an optimal combination of desorption/ionization principles for a fast ambient MSI of macroscopic plant samples. We coupled a 405 nm continuous wave (CW) ultraviolet (UV) diode laser to a three-dimensionally (3D) printed low-temperature plasma (LTP) probe. By moving the sample with a RepRap-based sampling stage, we could perform imaging of samples up to 16 × 16 cm2. We demonstrate the system performance by mapping mescaline in a San Pedro cactus ( Echinopsis pachanoi) cross section, tropane alkaloids in jimsonweed ( Datura stramonium) fruits and seeds, and nicotine in tobacco ( Nicotiana tabacum) seedlings. In all cases, the anatomical regions of enriched compound concentrations were correctly depicted. The modular design of the laser desorption (LD)-LTP MSI platform, which is mainly assembled from commercial and 3D-printed components, facilitates its adoption by other research groups. The use of the CW-UV laser for desorption enables fast imaging measurements. A complete tobacco seedling with an image size of 9.2 × 15.0 mm2 was analyzed at a pixel size of 100 × 100 µm2 (14 043 mass scans), in less than 2 h. Natural products can be measured directly from native tissues, which inspires a broad use of LD-LTP MSI in plant chemistry studies.

Trichoderma atroviride from Predator to Prey: Role of the Mitogen-Activated Protein Kinase Tmk3 in Fungal Chemical Defense against Fungivory by Drosophila melanogaster Larvae.

The response to injury represents an important strategy for animals and plants to survive mechanical damage and predation. Plants respond to injury by activating a defense response that includes the production of an important variety of compounds that help them withstand predator attack and recover from mechanical injury (MI). Similarly, the filamentous fungus Trichoderma atroviride responds to MI by strongly modifying its transcriptional profile and producing asexual reproduction structures (conidia). Here, we analyzed whether the response to MI in T. atroviride is related to a possible predator defense mechanism from a metabolic perspective. We found that the production of specific groups of secondary metabolites increases in response to MI but is reduced after fungivory by Drosophila melanogaster larvae. We further show that fungivory results in repression of the expression of genes putatively involved in the regulation of secondary metabolite production in T. atroviride Activation of secondary metabolite production appears to depend on the mitogen-activated protein kinase (MAPK) Tmk3. Interestingly, D. melanogaster larvae preferred to feed on a tmk3 gene replacement mutant rather than on the wild-type strain. Consumption of the mutant strain, however, resulted in increased larval mortality.IMPORTANCE Fungi, like other organisms, have natural predators, including fungivorous nematodes and arthropods that use them as an important food source. Thus, they require mechanisms to detect and respond to injury. Trichoderma atroviride responds to mycelial injury by rapidly regenerating its hyphae and developing asexual reproduction structures. Whether this injury response is associated with attack by fungivorous insects is unknown. Therefore, determining the possible conservation of a defense mechanism to predation in T. atroviride and plants and elucidating the mechanisms involved in the establishment of this response is of major interest. Here, we describe the chemical response of T. atroviride to mechanical injury and fungivory and the role of a MAPK pathway in the regulation of this response.

Impact of Solvent Structuring in Water/ tert-Butanol Mixtures on the Assembly of Silica Nanoparticles to Aerogels.

Soft matter structuring is a useful tool for the preparation of well-structured inorganic materials. Here, we report a strategy using a structured solvent based on binary mixtures as a directing agent for silica nanoparticles in aerogel elaboration. Binary mixtures involving water/ethanol and water/ tert-butanol have been respectively chosen as representatives of unstructured and structured solvents. The water/alcohol/TEOS systems were effectively characterized as surfactant-free microemulsions. The enhanced solvent structuring, however, disappears upon the reaction with TEOS, and assembly is directed by solvent structuring found in the binary mixtures. For the first time, the influence of solvent composition on the sol-gel reaction was investigated with respect to the reaction rate and the structuring behavior thanks to dynamic light scattering (DLS), small- and wide-angle X-ray scattering (SWAXS), and transmission electron microscopy (TEM) experiments. The silica nanoparticles aggregate in a different manner depending on the solvent composition, which allows the change in the morphology, the degree of interconnection, and the surface area of the resulting material. Silica nanoparticles with a very high surface area of up to 2000 m2/g can be obtained by this approach.

Open-label study to evaluate trifluridine/tipiracil safety, tolerability and pharmacokinetics in patients with advanced solid tumours and hepatic impairment.

AIMS: Trifluridine/tipiracil (FTD/TPI) prolongs survival in refractory metastatic colorectal cancer, but limited data exist on its use in patients with hepatic impairment. This Phase I, open-label, nonrandomized study investigated the safety, tolerability and pharmacokinetics of FTD/TPI in patients with advanced solid tumours (except breast cancer) and varying degrees of hepatic impairment, to provide dosing recommendations. METHODS: Patients aged ≥18 years with advanced solid tumours and normal hepatic function, or mild, moderate or severe hepatic impairment according to National Cancer Institute criteria, were planned to be enrolled. Patients received FTD/TPI 35 mg/m2 orally twice daily on days 1-5 and 8-12 of each 28-day cycle. RESULTS: Twenty-four patients were enrolled to the normal hepatic function (n = 8) and mild (n = 10) and moderate (n = 6) hepatic impairment cohorts. Overall, 12 patients (50.0%) had at least 1 adverse event leading to study discontinuation. In the moderate hepatic impairment cohort, 5 of 6 patients experienced grade ≥ 3 elevation in bilirubin. No patients with severe hepatic impairment were enrolled. FTD area under the curve at steady state decreased by 18% and 22% in the mild and moderate cohorts, respectively; however, no clear change was observed in TPI area under the curve. CONCLUSIONS: FTD/TPI can be safely administered in patients with normal hepatic function and mild hepatic impairment, with no initial dose adjustment. FTD/TPI is not recommended for use in patients with moderate hepatic impairment because of findings of grade 3 or 4 increased blood bilirubin. Therefore, FTD/TPI is not recommended for patients with moderate or severe hepatic impairment.

Vinylogous chain branching catalysed by a dedicated polyketide synthase module.

Bacteria use modular polyketide synthases (PKSs) to assemble complex polyketides, many of which are leads for the development of clinical drugs, in particular anti-infectives and anti-tumoral agents. Because these multifarious compounds are notoriously difficult to synthesize, they are usually produced by microbial fermentation. During the past two decades, an impressive body of knowledge on modular PKSs has been gathered that not only provides detailed insight into the biosynthetic pathways but also allows the rational engineering of enzymatic processing lines to yield structural analogues. Notably, a hallmark of all PKS modules studied so far is the head-to-tail fusion of acyl and malonyl building blocks, which leads to linear backbones. Yet, structural diversity is limited by this uniform assembly mode. Here we demonstrate a new type of PKS module from the endofungal bacterium Burkholderia rhizoxinica that catalyses a Michael-type acetyl addition to generate a branch in the carbon chain. In vitro reconstitution of the entire PKS module, X-ray structures of a ketosynthase-branching didomain and mutagenesis experiments revealed a crucial role of the ketosynthase domain in branching the carbon chain. We present a trapped intermediary state in which acyl carrier protein and ketosynthase are covalently linked by the branched polyketide and suggest a new mechanism for chain alkylation, which is functionally distinct from terpenoid-like ß-branching. For the rice seedling blight toxin rhizoxin, one of the strongest known anti-mitotic agents, the non-canonical polyketide modification is indispensable for phytotoxic and anti-tumoral activities. We propose that the formation of related pharmacophoric groups follows the same general scheme and infer a unifying vinylogous branching reaction for PKS modules with a ketosynthase-branching-acyl-carrier-protein architecture. This study unveils the structure and function of a new PKS module that broadens the biosynthetic scope of polyketide biosynthesis and sets the stage for rationally creating structural diversity.

A Mass Spectrometry-Based Study Shows that Volatiles Emitted by Arthrobacter agilis UMCV2 Increase the Content of Brassinosteroids in Medicago truncatula in Response to Iron Deficiency Stress.

Iron is an essential plant micronutrient. It is a component of numerous proteins and participates in cell redox reactions; iron deficiency results in a reduction in nutritional quality and crop yields. Volatiles from the rhizobacterium Arthrobacter agilis UMCV2 induce iron acquisition mechanisms in plants. However, it is not known whether microbial volatiles modulate other metabolic plant stress responses to reduce the negative effect of iron deficiency. Mass spectrometry has great potential to analyze metabolite alterations in plants exposed to biotic and abiotic factors. Direct liquid introduction-electrospray-mass spectrometry was used to study the metabolite profile in Medicago truncatula due to iron deficiency, and in response to microbial volatiles. The putatively identified compounds belonged to different classes, including pigments, terpenes, flavonoids, and brassinosteroids, which have been associated with defense responses against abiotic stress. Notably, the levels of these compounds increased in the presence of the rhizobacterium. In particular, the analysis of brassinolide by gas chromatography in tandem with mass spectrometry showed that the phytohormone increased ten times in plants grown under iron-deficient growth conditions and exposed to microbial volatiles. In this mass spectrometry-based study, we provide new evidence on the role of A. agilis UMCV2 in the modulation of certain compounds involved in stress tolerance in M. truncatula.

Mass Fingerprints of Tomatoes Fertilized with Different Nitrogen Sources Reveal Potential Biomarkers of Organic Farming.

Direct-injection electron spray ionization mass spectrometry (DIESI-MS) can be used to quantify the whole set of positive and negative ions in complex biological samples. A cherry tomato cultivar was grown inside a greenhouse in soil pots supplemented with different nitrogen sources. Organic cultivation increased fruit dry matter while conventional chemical fertilizers increased yield due to higher water content. While soluble sugars were unaltered, secondary metabolism of tomato fruit was highly sensitive to compost soil supplied to the roots. From a total of ~1647 DIESI-MS signals, 725 revealed significant differences between treatments. Heatmap biclustering showed that ionomic differences were robustly maintained in independent experiments carried out during three consecutive years. The ionomic fingerprints allowed reproducible sample classification, reflecting the effect of organic farming on tomato fruit quality. Specific biomarker ions could be identified for various nitrogen sources. We propose DIESI-MS as an up-front strategy for plant food characterization aiming to identify the ions with the most significant differences across genotypes or agronomic conditions.