Biology subjects

Garcia-Altares, M.

Publications and source records attributed to Garcia-Altares, M..

6 recordsLinked to original sources

bioRxiv2025

Solid Ionic Matrices applied via Low-Temperature Evaporation enable High-Resolution and Sensitive MALDI Imaging of Metabolites

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) has become a key technology for spatially resolved molecular analysis. However, imaging of low molecular weight compounds remains challenging due to spectral interferences in the low m/z range caused by conventional organic matrices. Ionic matrices (IMs), in contrast, reduce matrix-related background signals, improve spectral reproducibility, and enhance sensitivity for detecting metabolites and lipids, but their use in MALDI-MSI has so far been limited, primarily focusing on lipid imaging above m/z 500. Here, we present a novel approach combining solid ionic matrices (ISMs) with low-temperature thermal evaporation (LTE) to enhance MALDI-MSI performance for small metabolites. ISMs based on -cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB) provided superior sensitivity, with CHCA + N,N-diethylaniline enabling the detection and annotation of 73 small metabolites (m/z <500) in mouse brain at 20 {micro}m spatial resolution. When applied to the pancreas, this matrix enabled the first specific localization of melatonin and 3-iodotyrosine within the islets of Langerhans, opening new avenues for spatial metabolomics in endocrine research.

bioengineering↗

bioRxiv2025

Improving MALDI Mass Spectrometry Imaging Performance: Low-Temperature Thermal Evaporation for Controlled Matrix Deposition and Improved Image Quality

The deposition of matrix compounds significantly influences the effectiveness of matrix-assisted laser desorption/ionization (MALDI) Mass Spectrometry Imaging (MSI) experiments, impacting sensitivity, spatial resolution, and reproducibility. Dry deposition methods offer advantages by producing homogeneous matrix layers and minimizing analyte delocalization without the use of solvents. However, refining these techniques to precisely control matrix thickness, minimize heating temperatures, and ensure high-purity matrix layers is crucial for optimizing MALDI-MSI performance. Here, we present a novel approach utilizing low-temperature thermal evaporation (LTE) for organic matrix deposition under reduced vacuum pressure. Our method allows for reproducible control of matrix layer thickness, as demonstrated by linear calibration for two organic matrices, 2,5-dihydroxybenzoic acid (DHB), and 1,5-Diaminonaphthalene (DAN). The environmental scanning electron microscopy images reveal a uniform distribution of small-sized matrix crystals, consistently on the submicrometer scale, across tissue slides following LTE deposition. Remarkably, LTE serves as an additional purification step for organic matrices, producing very pure layers irrespective of initial matrix purity. Furthermore, stability assessment of MALDI-MSI data from mouse brain sections coated with LTE-deposited DHB or DAN matrix indicates minimal impact on ionization efficiency, signal intensity, and image quality even after storage at - 80{degrees}C for two weeks, underscoring the robustness of LTE-deposited matrices for MSI applications. Comparative analysis with the spray-coating method highlights several advantages of LTE deposition, including enhanced ionization, reduced analyte diffusion, and improved MSI image quality.

bioengineering↗

bioRxiv2023

Discovering Matrix Adducts for Enhanced Metabolite Profiling with Stable Isotope-Labeled MALDI-MSI

Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) is a widely used technique for spatial metabolomics analysis, but the matrix introduces spectral interferences that impede data processing. In this study, we present an experimental and computational workflow utilizing isotopic labeling to discover and annotate matrix adducts in MALDI-MSI. Our approach enables the removal of matrix-related signals, improving metabolite annotation accuracy, extending metabolome coverage, and facilitating the interpretation of tissue morphology.

bioinformatics↗

bioRxiv2020

Grazing results in mobilization of spherulous cells and re-allocation of secondary metabolites to the surface in the sponge Aplysina aerophoba

On the sea floor, prey and predator commonly engage in a chemical warfare. Here, sponges thrive due to their specific and diverse chemical arsenal. Yet, some animals use these chemically-defended organisms as food and home. Most research on sponge chemical ecology has characterized crude extracts and investigated defences against generalist predators like fish. Consequently, we know little about intraindividual chemical dynamics and responses to specialist grazers. Here, we studied the response of the sponge Aplysina aerophoba to grazing by the opistobranch Tylodina perversa, in comparison to mechanical damage, at the cellular (via microscopy) and chemical level (via matrix-assisted laser desorption/ionization imaging mass spectrometry). We characterized the distribution of two major brominated compounds in A. aerophoba, aerophobin-2 and aeroplysinin-1, and identified a generalized wounding response that was similar in both wounding treatments: (i) brominated compound-carrying cells (spherulous cells) accumulated at the wound and (ii) secondary metabolites reallocated to the sponge surface. Upon mechanical damage, the wound turned dark due to oxidized compounds, causing T. perversa deterrence. During grazing, T. perversas way of feeding prevented oxidation. Thus, the sponge has not evolved a specific response to this specialist predator, but rather relies on rapid regeneration and flexible allocation of constitutive defences.

ecology↗

bioRxiv2019

rMSIcleanup: An open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization

Mass spectrometry imaging (MSI) has become a mature, widespread analytical technique to perform non-targeted spatial metabolomics. However, the compounds used to promote desorption and ionization of the analyte during acquisition cause spectral interferences in the low mass range that hinder downstream data processing in metabolomics applications. Thus, it is advisable to annotate and remove matrix-related peaks to reduce the number of redundant and non-biologically-relevant variables in the dataset. We have developed rMSIcleanup, an open-source R package to annotate and remove matrix-related signals based on its chemical formula and the spatial distribution of its ions. To validate the annotation method, rMSIcleanup was challenged with several images acquired using silver-assisted laser desorption ionization MSI (AgLDI MSI). The algorithm was able to correctly classify m/z signals related to silver clusters. Visual exploration of the data using Principal Component Analysis (PCA) demonstrated that annotation and removal of matrix-related signals improved spectral data post-processing. The results highlight the need for including matrix-related peak annotation tools such as rMSIcleanup in MSI workflows. Resources availabilityThe R package presented in this publication is freely available under the terms of the GNU General Public License v3.0 at https://github.com/gbaquer/rMSIcleanup. The datasets used in the experiments can be accessed upon request to the corresponding author.

bioinformatics↗

bioRxiv2017

Bacterium-triggered remodeling of chromatin identifies BasR, a novel regulator of fungal natural product biosynthesis

The eukaryotic epigenetic machinery is targeted by bacteria to reprogram the response of eukaryotes during their interaction with microorganisms. In line, we discovered that the bacterium Streptomyces rapamycinicus triggered increased chromatin acetylation and thus activation of the silent secondary metabolism ors gene cluster leading to the production of orsellinic acid in the fungus Aspergillus nidulans. Using this model we aim at understanding molecular mechanisms of communication between bacteria and eukaryotic microorganisms based on bacteria-triggered chromatin modification. By genome-wide ChIP-seq analysis of acetylated histone H3 (H3K9ac, H3K14ac) we uncovered the unique chromatin landscape in A. nidulans upon co-cultivation with S. rapamycinicus. Genome-wide acetylation of H3K9 correlated with increased gene expression, whereas H3K14 appears to function in transcriptional initiation by providing a docking side for regulatory proteins. In total, histones belonging to six secondary metabolism gene clusters showed higher acetylation during co-cultivation including the ors, aspercryptin, cichorine, sterigmatocystin, anthrone and 2,4-dihydroxy-3-methyl-6-(2-oxopropyl)benzaldehyde gene cluster with the emericellamide cluster being the only one with reduced acetylation and expression. Differentially acetylated histones were also detected in genes involved in amino acid and nitrogen metabolism, signaling, and genes encoding transcription factors. In conjunction with LC-MS/MS and MALDI-MS imaging, molecular analyses revealed the cross-pathway control and Myb-like transcription factor BasR as regulatory nodes for transduction of the bacterial signal in the fungus. The presence of basR in other fungal species allowed forecasting the inducibility of ors-like gene clusters by S. rapamycinicus in these fungi, and thus their effective interaction with activation of otherwise silent gene clusters.

microbiology↗