Gene-specific translation regulation mediated by the hormone-signaling molecule EIN2.

The central role of translation in modulating gene activity has long been recognized, yet the systematic exploration of quantitative changes in translation at a genome-wide scale in response to a specific stimulus has only recently become technically feasible. Using the well-characterized signaling pathway of the phytohormone ethylene and plant-optimized genome-wide ribosome footprinting, we have uncovered a molecular mechanism linking this hormone's perception to the activation of a gene-specific translational control mechanism. Characterization of one of the targets of this translation regulatory machinery, the ethylene signaling component EBF2, indicates that the signaling molecule EIN2 and the nonsense-mediated decay proteins UPFs play a central role in this ethylene-induced translational response. Furthermore, the 3'UTR of EBF2 is sufficient to confer translational regulation and required for the proper activation of ethylene responses. These findings represent a mechanistic paradigm of gene-specific regulation of translation in response to a key growth regulator.

Arabidopsis as a model for translational research.

Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage lab and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.

Tandem C2 domains mediate dynamic organelle targeting of a DOCK family guanine nucleotide exchange factor.

Multicellular organisms use dedicator of cytokinesis (DOCK) family guanine nucleotide exchange factors (GEFs) to activate Rac/Rho-of-plants small GTPases and coordinate cell shape change. In developing tissues, DOCK signals integrate cell-cell interactions with cytoskeleton remodeling, and the GEFs cluster reversibly at specific organelle surfaces to orchestrate cytoskeletal reorganization. The domain organizations among DOCK orthologs are diverse, and the mechanisms of localization control are poorly understood. Here, we use combinations of transgene complementation and live-cell imaging assays to uncover an evolutionarily conserved and essential localization determinant in the DOCK-GEF named SPIKE1. The SPIKE1-DHR3 domain is sufficient for organelle association in vivo, and displays a complicated lipid-binding selectivity for both phospholipid head groups and fatty acid chain saturation. SPIKE1-DHR3 is predicted to adopt a C2-domain structure and functions as part of a tandem C2 array that enables reversible clustering at the cell apex. This work provides mechanistic insight into how DOCK GEFs sense compositional and biophysical membrane properties at the interface of two organelle systems.

A rapid and scalable approach to build synthetic repetitive hormone-responsive promoters.

Advancement of DNA-synthesis technologies has greatly facilitated the development of synthetic biology tools. However, high-complexity DNA sequences containing tandems of short repeats are still notoriously difficult to produce synthetically, with commercial DNA synthesis companies usually rejecting orders that exceed specific sequence complexity thresholds. To overcome this limitation, we developed a simple, single-tube reaction method that enables the generation of DNA sequences containing multiple repetitive elements. Our strategy involves commercial synthesis and PCR amplification of padded sequences that contain the repeats of interest, along with random intervening sequence stuffers that include type IIS restriction enzyme sites. GoldenBraid molecular cloning technology is then employed to remove the stuffers, rejoin the repeats together in a predefined order, and subclone the tandem(s) in a vector using a single-tube digestion-ligation reaction. In our hands, this new approach is much simpler, more versatile and efficient than previously developed solutions to this problem. As a proof of concept, two different phytohormone-responsive, synthetic, repetitive proximal promoters were generated and tested in planta in the context of transcriptional reporters. Analysis of transgenic lines carrying the synthetic ethylene-responsive promoter 10x2EBS-S10 fused to the GUS reporter gene uncovered several developmentally regulated ethylene response maxima, indicating the utility of this reporter for monitoring the involvement of ethylene in a variety of physiologically relevant processes. These encouraging results suggest that this reporter system can be leveraged to investigate the ethylene response to biotic and abiotic factors with high spatial and temporal resolution.

Developing customized fuel models for shrub and bracken communities in Galicia (NW Spain).

Geospatial fire behaviour and fire hazard simulators, fire effects models and smoke emission software commonly use standard fuel models in order to simplify data collection and the inclusion of complex fuel scenarios. These fuel models are often mapped using remotely sensed data. However, given the great complexity of fuelbeds, with properties that vary widely in both time and space, the use of these standard fuel models can greatly limit accurate fuel mapping. This affects fuel hazard assessment, fuel reduction treatment plans, fire management decision-making and evaluation of the environmental impact of wildfire. In this study, we developed unique customized fire behaviour fuel models for shrub and bracken communities, by using k-medoids clustering analysis based on both fuel structural characteristics and potential fire behaviour. We used an original database of 722 destructive sample plots in nine different shrub and bracken communities covering the entire distribution area in Galicia (NW Spain), one of the regions in Europe most affected by forest fires. Measurements of cover, height and fuel fractions loads differentiated by size and vegetative state (live or dead) were used to estimate the potential rate of fire spread with five different models including fireline intensity, heat per unit area and the flame length for each sampling site and considering extreme environmental conditions. The optimal number of clusters was established by combining practical knowledge about the shrubland communities under study and their associated fire behaviour, with maximization of the mean value of the silhouette variable and minimization of the within-cluster sum of squares. The structural characteristics of the medoids derived from the analysis were associated with each of the proposed customized fuel models. Finally, a simple dichotomous classification based only on shrub height was developed to enable construction of spatially explicit fuel model maps based on remotely sensed data. Thus, the methodology applied allows generation of a more realistic representation of fuel distribution in the landscape, based on fuel structure measurements of natural regional ecosystems rather than on the use of standard models. We believe that the proposed methodology is generally applicable to communities composed of other shrub and fern species in different biogeographical regions.

An Improved Recombineering Toolset for Plants.

Gene functional studies often rely on the expression of a gene of interest as transcriptional and translational fusions with specialized tags. Ideally, this is done in the native chromosomal contexts to avoid potential misexpression artifacts. Although recent improvements in genome editing have made it possible to directly modify the target genes in their native chromosomal locations, classical transgenesis is still the preferred experimental approach chosen in most gene tagging studies because of its time efficiency and accessibility. We have developed a recombineering-based tagging system that brings together the convenience of the classical transgenic approaches and the high degree of confidence in the results obtained by direct chromosomal tagging using genome-editing strategies. These simple, scalable, customizable recombineering toolsets and protocols allow a variety of genetic modifications to be generated. In addition, we developed a highly efficient recombinase-mediated cassette exchange system to facilitate the transfer of the desired sequences from a bacterial artificial chromosome clone to a transformation-compatible binary vector, expanding the use of the recombineering approaches beyond Arabidopsis (Arabidopsis thaliana). We demonstrated the utility of this system by generating more than 250 whole-gene translational fusions and 123 Arabidopsis transgenic lines corresponding to 62 auxin-related genes and characterizing the translational reporter expression patterns for 14 auxin biosynthesis genes.

Straightforward Synthesis of Bis[(trifluoromethyl)sulfonyl]ethylated Isocoumarins from 2-Ethynylbenzoates.

Herein, we report a facile isocoumarin and isoquinolone preparation by taking advantage of an initial bis(triflyl)ethylation [triflyl = (trifluoromethyl)sulfonyl] reaction, followed by heterocyclization, which contrasts with our previous results on cyclobutene formation. The efficiency of the catalyst- and irradiation-free heterocyclization/bis(triflyl)ethylation sequence showed exquisite dependence on the electronic nature of the substituents at the 2-ethynylbenzoate(benzamide) precursors. Molecular docking of model bis(triflyl)ethylated isocoumarins on human acetylcholinesterase (hAChE) revealed promising biological activities through selective coordination on both the catalytic active site and peripheral active site.

Deciphering the Chameleonic Chemistry of Allenols: Breaking the Taboo of a Onetime Esoteric Functionality.

The allene functionality has participated in one of the most exciting voyages in organic chemistry, from chemical curiosities to a recurring building block in modern organic chemistry. In the last decades, a special kind of allene, namely, allenol, has emerged. Allenols, formed by an allene moiety and a hydroxyl functional group with diverse connectivity, have become common building blocks for the synthesis of a wide range of structures and frequent motif in naturally occurring systems. The synergistic effect of the allene and hydroxyl functional groups enables allenols to be considered as a unique and sole functionality exhibiting a special reactivity. This Review summarizes the most significant contributions to the chemistry of allenols that appeared during the past decade, with emphasis on their synthesis, reactivity, and occurrence in natural products.

TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development.

Plants have evolved a tremendous ability to respond to environmental changes by adapting their growth and development. The interaction between hormonal and developmental signals is a critical mechanism in the generation of this enormous plasticity. A good example is the response to the hormone ethylene that depends on tissue type, developmental stage, and environmental conditions. By characterizing the Arabidopsis wei8 mutant, we have found that a small family of genes mediates tissue-specific responses to ethylene. Biochemical studies revealed that WEI8 encodes a long-anticipated tryptophan aminotransferase, TAA1, in the essential, yet genetically uncharacterized, indole-3-pyruvic acid (IPA) branch of the auxin biosynthetic pathway. Analysis of TAA1 and its paralogues revealed a link between local auxin production, tissue-specific ethylene effects, and organ development. Thus, the IPA route of auxin production is key to generating robust auxin gradients in response to environmental and developmental cues.

Thigh ultrasound monitoring identifies muscle atrophy in mechanically ventilated pediatric patients.

Over the last decade, ultrasonography has taken on an increasingly important role in the daily management of critically patients and has recently been proposed as a means of measuring muscle volume and architecture. This study had two main aims: to monitor for the onset of muscle atrophy in mechanically ventilated pediatric patients during stays in a pediatric intensive care unit based on quadriceps femoris muscle thickness measurements and to study whether demographic and clinical variables have an impact on muscle loss in critically children. The study followed a prospective, observational, single-center design. The sample included all children admitted to our pediatric intensive care unit (PICU) who required mechanical ventilation for more than 48 h. Two trained clinicians measured the thickness of the quadriceps using a 12-MHz linear ultrasound transducer within 24 h of initiating invasive mechanical ventilation and again at 72 h, 1 week, and weekly thereafter until extubation. For the entire cohort, quadriceps femoris muscle thickness decreased by 4.67% on average (IQR = -13.4 to -0.59) between the first two assessments and 13% by the time of the final measurement (IQR = -24 to -0.5%) or 1.57%/day (p < 0.001). Approximately half of all the children (23/41; 56%) experienced muscle atrophy (defined a priori as a decrease in thickness of 10% or more). Bivariate analyses revealed that increasing age, being a child (vs. infant), cumulative energy and protein deficit, highest C-reactive protein value, exposure to neuromuscular blockers, and a longer stay in the PICU were all predictive of a greater decrease in thickness. In a multivariate model, exposure to neuromuscular blockers was linked with greater muscle loss.       Conclusion: In mechanically ventilated children, point-of-care ultrasonography can identify skeletal muscle atrophy. Muscle atrophy of limbs is strongly associated with the use of neuromuscular blockers. Ultrasound-based monitoring of the quadriceps femoris is a clinically useful tool for assessing muscle mass that can provide information on nutritional status and guide rehabilitation. What is Known: • ICU-acquired muscle atrophy is common and has a deleterious effect on adult outcomes. The prevalence and severity of muscular atrophy in critically ill children, however, are poorly understood. • Point-of-care ultrasonography has been put forward as an accurate, reliable method for monitoring variations in muscle mass.. What is New: • The quadriceps femoris muscle tends to suffer an intense loss of thickness early on in most critically ill children. • Quadriceps femoris ultrasound monitoring is a helpful tool for measuring muscle thickness and could lead to the development of novel therapies for critically ill children.

Coexistence of Two Spin Frustration Pathways in the Quantum Spin Liquid Ca10Cr7O28.

Kagome antiferromagnetic lattices are of high interest because the geometric frustration is expected to give rise to highly degenerated ground states that may host exotic properties such as quantum spin liquid (QSL). Ca10Cr7O28 has been reported to display all the features expected for a QSL. At present, most of the literature reports on samples synthesized with starting materials ratio CaO/Cr2O3 3:1, which leads to a material with small amounts of CaCrO4 and CaO as secondary phases; this impurity excess affects not only the magnetic properties but also the structural ones. In this work, samples with starting material ratios CaO/Cr2O3 3:1, 2.9:1, 2.85:1, and 2.8:1 have been synthesized and studied by X-ray diffraction with Rietveld refinements, selected area electron diffraction measurements, high-resolution transmission electron microscopy (HRTEM), low-temperature magnetometry, and magnetic calorimetry. This result shows that a highly pure Ca10Cr7O28 phase is obtained for a CaO/Cr2O3 ratio of 2.85:1 instead of the 3:1 usually reported; the incorrect stoichiometric ratio leads to a larger distortion of the corner-sharing triangular arrangement of magnetic ions Cr+5 with S = 1/2 in the Kagome lattice. In addition, our study reveals that there exists another frustration pathway which is an asymmetric zigzag spin ladder along the directions [211], [12-1], and [1-1-1], in which the Cr-Cr distances are shorter than in the Kagome layers.

Principles underlying sensory map topography in primary visual cortex.

The primary visual cortex contains a detailed map of the visual scene, which is represented according to multiple stimulus dimensions including spatial location, ocular dominance and stimulus orientation. The maps for spatial location and ocular dominance arise from the spatial arrangement of thalamic afferent axons in the cortex. However, the origins of the other maps remain unclear. Here we show that the cortical maps for orientation, direction and retinal disparity in the cat (Felis catus) are all strongly related to the organization of the map for spatial location of light (ON) and dark (OFF) stimuli, an organization that we show is OFF-dominated, OFF-centric and runs orthogonal to ocular dominance columns. Because this ON-OFF organization originates from the clustering of ON and OFF thalamic afferents in the visual cortex, we conclude that all main features of visual cortical topography, including orientation, direction and retinal disparity, follow a common organizing principle that arranges thalamic axons with similar retinotopy and ON-OFF polarity in neighbouring cortical regions.

N-Hydroxy-N-Propargylamide Derivatives of Ferulic Acid: Inhibitors of Cholinesterases and Monoamine Oxidases.

Alzheimer's disease (AD) is a complex disorder characterized by impaired neurotransmission in cholinergic and monoaminergic neurons, which, in combination with the accumulation of misfolded proteins and increased oxidative stress, leads to the typical features of the disease at the biomolecular level. Given the limited therapeutic success of approved drugs, it is imperative to explore rationally supported therapeutic approaches to combat this disease. The search for novel scaffolds that bind to different receptors and inhibit AD disease-related enzymes could lead to new therapeutic solutions. Here, we describe N-hydroxy-N-propargylamide hybrids 1-6, which were designed by combining the structures of Contilisant-a multifunctional anti-AD ligand-and ferulic acid, a natural antioxidant with various other biological activities. Among the synthesized compounds, we identified compound 4 as a micromolar inhibitor of hAChE with a potent radical-scavenging capacity comparable to resveratrol and Trolox. In addition, compound 4 chelated copper(II) ions associated with amyloid ß pathology, mitochondrial dysfunction, and oxidative stress. The promising in vitro activity combined with favorable drug-like properties and predicted blood-brain barrier permeability make compound 4 a multifunctional ligand that merits further studies at the biochemical and cellular levels.

Regulation of ovule initiation by gibberellins and brassinosteroids in tomato and Arabidopsis: two plant species, two molecular mechanisms.

Ovule primordia formation is a complex developmental process with a strong impact on the production of seeds. In Arabidopsis this process is controlled by a gene network, including components of the signalling pathways of auxin, brassinosteroids (BRs) and cytokinins. Recently, we have shown that gibberellins (GAs) also play an important role in ovule primordia initiation, inhibiting ovule formation in both Arabidopsis and tomato. Here we reveal that BRs also participate in the control of ovule initiation in tomato, by promoting an increase on ovule primordia formation. Moreover, molecular and genetic analyses of the co-regulation by GAs and BRs of the control of ovule initiation indicate that two different mechanisms occur in tomato and Arabidopsis. In tomato, GAs act downstream of BRs. BRs regulate ovule number through the downregulation of GA biosynthesis, which provokes stabilization of DELLA proteins that will finally promote ovule primordia initiation. In contrast, in Arabidopsis both GAs and BRs regulate ovule number independently of the activity levels of the other hormone. Taken together, our data strongly suggest that different molecular mechanisms could operate in different plant species to regulate identical developmental processes even, as for ovule primordia initiation, if the same set of hormones trigger similar responses, adding a new level of complexity.

Gibberellins negatively modulate ovule number in plants.

Ovule formation is a complex developmental process in plants, with a strong impact on the production of seeds. Ovule primordia initiation is controlled by a gene network, including components of the signaling pathways of auxin, brassinosteroids and cytokinins. By contrast, gibberellins (GAs) and DELLA proteins, the negative regulators of GA signaling, have never been shown to be involved in ovule initiation. Here, we provide molecular and genetic evidence that points to DELLA proteins as novel players in the determination of ovule number in Arabidopsis and in species of agronomic interest, such as tomato and rapeseed, adding a new layer of complexity to this important developmental process. DELLA activity correlates positively with ovule number, acting as a positive factor for ovule initiation. In addition, ectopic expression of a dominant DELLA in the placenta is sufficient to increase ovule number. The role of DELLA proteins in ovule number does not appear to be related to auxin transport or signaling in the ovule primordia. Possible crosstalk between DELLA proteins and the molecular and hormonal network controlling ovule initiation is also discussed.

Structure-Function Analysis of Interallelic Complementation in ROOTY Transheterozygotes.

Auxin is a crucial plant growth regulator. Forward genetic screens for auxin-related mutants have led to the identification of key genes involved in auxin biosynthesis, transport, and signaling. Loss-of-function mutations in genes involved in glucosinolate biosynthesis, a metabolically related route that produces defense compounds, result in auxin overproduction. We identified an allelic series of fertile, hypomorphic Arabidopsis (Arabidopsis thaliana) mutants for the essential glucosinolate biosynthetic gene ROOTY (RTY) that exhibit a range of phenotypic defects characteristic of enhanced auxin production. Genetic characterization of these lines uncovered phenotypic suppression by cyp79b2 cyp79b3, wei2, and wei7 mutations and revealed the phenomenon of interallelic complementation in several RTY transheterozygotes. Structural modeling of RTY elucidated the relationships between structure and function in the RTY homo- and heterodimers, and unveiled the likely structural basis of interallelic complementation. This work underscores the importance of employing true null mutants in genetic complementation studies.

Ultrasound assessment of ventilator-induced diaphragmatic dysfunction in mechanically ventilated pediatric patients.

INTRODUCTION: Ultrasonography has recently emerged as a promising technique that can rapidly estimate diaphragm function, especially during the weaning period. The aims of this study were to describe the evolution of diaphragmatic morphology and functional measurements by ultrasound in ventilated children. MATERIAL AND METHODS: This was a prospective, observational, single-center study. All the children admitted to our Pediatric Intensive Care Unit requiring mechanical ventilation for more than 48 h were included. Diaphragmatic thickness and the thickening fraction were assessed by ultrasound. RESULTS: From June to December 2018, 47 patients (median age 3 months; interquartile range, 1-17) underwent 164 ultrasonographic evaluations. The median duration of mechanical ventilation was 168 h (interquartile range, 96-196). At the initial measurement, the thickness at end-inspiration was 2.2 mm (interquartile range, 1.8-2.5) and the thickness at end-expiration was 1.8 mm (interquartile range, 1.5-2.0) with a median decrease in thickness of -14% (interquartile range, -33% to -3%) and a -2% daily atrophy rate (interquartile range, -4.2% to 0%). Diaphragmatic atrophy was observed in 30/47 cases. Children who had been exposed to neuromuscular blockade infusion (n = 31) had a significantly lower mean thickness [-22% (interquartile range, -34% to -13%) vs. -6% (interquartile range, -12% to 0%); p = 0.009] and increased daily atrophy rate [-2.2% (interquartile range, -4.6 to 0%) vs. -1.4% (interquartile range, -2.6 to 0%); p = 0.049] compared to unexposed children. The decrease in thickness was significantly less in children ventilated for at least 12 hours with pressure support before extubation compared with those with shorter periods of spontaneous respiratory effort [-9.5% (interquartile range, -21 to 0%) vs. -26% (interquartile range, -37 to -12%); p = 0.011]. CONCLUSIONS: Point-of-care diaphragmatic ultrasound can detect diaphragmatic atrophy in mechanically ventilated children. Diaphragmatic atrophy was strongly associated with the use of mechanical ventilation and neuromuscular blockade. Diaphragmatic thickness also tended to decrease less in the pre-extubation stage with pressure support. We found no correlation between progressive diaphragm thinning, extubation failure, or an increased need for non-invasive ventilation post extubation.

Identification of relapse-associated gene mutations by next-generation sequencing in low-risk acute myeloid leukaemia patients.

Recommended genetic categorization of acute myeloid leukaemias (AML) includes a favourable-risk category, but not all these patients have good prognosis. Here, we used next-generation sequencing to evaluate the mutational profile of 166 low-risk AML patients: 30 core-binding factor (CBF)-AMLs, 33 nucleophosmin (NPM1)-AMLs, 4 biCEBPα-AMLs and 101 acute promyelocytic leukaemias (APLs). Functional categories of mutated genes differed among subgroups. NPM1-AMLs showed frequent variations in DNA-methylation genes (DNMT3A, TET2, IDH1/2) (79%), although without prognostic impact. Within this group, splicing-gene mutations were an independent factor for relapse-free (RFS) and overall survival (OS). In CBF-AML, poor independent factors for RFS and OS were mutations in RAS pathway and cohesin genes, respectively. In APL, the mutational profile differed according to the risk groups. High-risk APLs showed a high mutation rate in cell-signalling genes (P = 0·002), highlighting an increased incidence of FLT3 internal tandem duplication (ITD) (65%, P < 0·0001). Remarkably, in low-risk APLs (n = 28), NRAS mutations were strongly correlated with a shorter five-year RFS (25% vs. 100%, P < 0·0001). Overall, a high number of mutations (≥3) was the worst prognostic factor RFS (HR = 2·6, P = 0·003). These results suggest that gene mutations may identify conventional low-risk AML patients with poor prognosis and might be useful for better risk stratification and treatment decisions.

Gibberellin-mediated RGA-LIKE1 degradation regulates embryo sac development in Arabidopsis.

Ovule development is essential for plant survival, as it allows correct embryo and seed development upon fertilization. The female gametophyte is formed in the central area of the nucellus during ovule development, in a complex developmental programme that involves key regulatory genes and the plant hormones auxins and brassinosteroids. Here we provide novel evidence of the role of gibberellins (GAs) in the control of megagametogenesis and embryo sac development, via the GA-dependent degradation of RGA-LIKE1 (RGL1) in the ovule primordia. YPet-rgl1Δ17 plants, which express a dominant version of RGL1, showed reduced fertility, mainly due to altered embryo sac formation that varied from partial to total ablation. YPet-rgl1Δ17 ovules followed normal development of the megaspore mother cell, meiosis, and formation of the functional megaspore, but YPet-rgl1Δ17 plants had impaired mitotic divisions of the functional megaspore. This phenotype is RGL1-specific, as it is not observed in any other dominant mutants of the DELLA proteins. Expression analysis of YPet-rgl1Δ17 coupled to in situ localization of bioactive GAs in ovule primordia led us to propose a mechanism of GA-mediated RGL1 degradation that allows proper embryo sac development. Taken together, our data unravel a novel specific role of GAs in the control of female gametophyte development.

Development of a relative quantification method for infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging of Arabidopsis seedlings.

RATIONALE: Mass spectrometry imaging of young seedlings is an invaluable tool in understanding how mutations affect metabolite accumulation in plant development. However, due to numerous biological considerations, established methods for the relative quantification of analytes using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging are not viable options. In this study, we report a method for the quantification of auxin-related compounds using stable-isotope-labelled (SIL) indole-3-acetic acid (IAA) doped into agarose substrate. METHODS: Wild-type Arabidopsis thaliana seedlings, sur2 and wei8 tar2 loss-of-function mutants, and YUC1 gain-of-function line were grown for 3 days in the dark in standard growth medium. SIL-IAA was doped into a 1% low-melting-point agarose gel and seedlings were gently laid on top for IR-MALDESI imaging with Orbitrap mass spectrometry analysis. Relative quantification was performed post-acquisition by normalization of auxin-related compounds to SIL-IAA in the agarose. Amounts of auxin-related compounds were compared between genotypes to distinguish the effects of the mutations on the accumulation of indolic metabolites of interest. RESULTS: IAA added to agarose was found to remain stable, with repeatability and abundance features of IAA comparable with those of other compounds used in other methods for relative quantification in IR-MALDESI analyses. Indole-3-acetaldoxime was increased in sur2 mutants compared with wild-type and other mutants. Other auxin-related metabolites were either below the limits of quantification or successfully quantified but showing little difference among mutants. CONCLUSIONS: Agarose was shown to be an appropriate sampling surface for IR-MALDESI mass spectrometry imaging of Arabidopsis seedlings. SIL-IAA doping of agarose was demonstrated as a viable technique for relative quantification of metabolites in live seedlings or tissues with similar biological considerations.