More Like this

1. Measurement report: Molecular composition and volatility of gaseous organic compounds in a boreal forest – from volatile organic compounds to highly oxygenated organic molecules

   https://doi.org/10.5194/acp-21-8961-2021  

   Huang, Wei ; Li, Haiyan ; Sarnela, Nina ; Heikkinen, Liine ; Tham, Yee Jun ; Mikkilä, Jyri ; Thomas, Steven J. ; Donahue, Neil M. ; Kulmala, Markku ; Bianchi, Federico ( January 2021 , Atmospheric Chemistry and Physics)

   Abstract. The molecular composition and volatility of gaseous organiccompounds were investigated during April–July 2019 at the Station forMeasuring Ecosystem – Atmosphere Relations (SMEAR) II situated in a borealforest in Hyytiälä, southern Finland. In order to obtain a morecomplete picture and full understanding of the molecular composition andvolatility of ambient gaseous organic compounds (from volatile organiccompounds, VOCs, to highly oxygenated organic molecules, HOMs), twodifferent instruments were used. A Vocus proton-transfer-reactiontime-of-flight mass spectrometer (Vocus PTR-ToF; hereafter Vocus) wasdeployed to measure VOCs and less oxygenated VOCs (i.e., OVOCs). Inaddition, a multi-scheme chemical ionization inlet coupled to an atmosphericpressure interface time-of-flight mass spectrometer (MION API-ToF) was usedto detect less oxygenated VOCs (using Br− as the reagent ion; hereafterMION-Br) and more oxygenated VOCs (including HOMs; using NO3- asthe reagent ion; hereafter MION-NO3). The comparison among differentmeasurement techniques revealed that the highest elemental oxygen-to-carbonratios (O : C) of organic compounds were observed by the MION-NO3 (0.9 ± 0.1, average ± 1 standard deviation), followed by the MION-Br(0.8 ± 0.1); lowest O : C ratios were observed by Vocus (0.2 ± 0.1). Diurnal patternsof the measured organic compounds were found to vary among differentmeasurement techniques, even for compounds with the same molecular formula,suggesting contributions of different isomers detected by the differenttechniques and/or fragmentation from different parent compounds inside theinstruments.more »Based on the complementary molecular information obtained fromVocus, MION-Br, and MION-NO3, a more complete picture of the bulkvolatility of all measured organic compounds in this boreal forest wasobtained. As expected, the VOC class was the most abundant (about 53.2 %), followed by intermediate-volatility organic compounds (IVOCs, about45.9 %). Although condensable organic compounds (low-volatility organiccompounds, LVOCs; extremely low volatility organic compounds, ELVOCs; andultralow-volatility organic compounds, ULVOCs) only comprised about 0.2 %of the total gaseous organic compounds, they play an important role in newparticle formation as shown in previous studies in this boreal forest. Ourstudy shows the full characterization of the gaseous organic compounds inthe boreal forest and the advantages of combining Vocus and MION API-ToF formeasuring ambient organic compounds with different oxidation extents (fromVOCs to HOMs). The results therefore provide a more comprehensiveunderstanding of the molecular composition and volatility of atmosphericorganic compounds as well as new insights into interpreting ambientmeasurements or testing/improving parameterizations in transport and climatemodels.« less
2. Jasmonate‐mediated stomatal closure under elevated CO ₂ revealed by time‐resolved metabolomics

   https://doi.org/10.1111/tpj.13296  

   Geng, Sisi ; Misra, Biswapriya B. ; de Armas, Evaldo ; Huhman, David V. ; Alborn, Hans T. ; Sumner, Lloyd W. ; Chen, Sixue ( October 2016 , The Plant Journal)

   Foliar stomatal movements are critical for regulating plant water loss and gas exchange. Elevated carbon dioxide (CO₂) levels are known to induce stomatal closure. However, the current knowledge onCO₂signal transduction in stomatal guard cells is limited. Here we report metabolomic responses ofBrassica napusguard cells to elevatedCO₂using three hyphenated metabolomics platforms: gas chromatography‐mass spectrometry (MS); liquid chromatography (LC)‐multiple reaction monitoring‐MS; and ultra‐high‐performanceLC‐quadrupole time‐of‐flight‐MS. A total of 358 metabolites from guard cells were quantified in a time‐course response to elevatedCO₂level. Most metabolites increased under elevatedCO₂, showing the most significant differences at 10 min. In addition, reactive oxygen species production increased and stomatal aperture decreased with time. Major alterations in flavonoid, organic acid, sugar, fatty acid, phenylpropanoid and amino acid metabolic pathways indicated changes in both primary and specialized metabolic pathways in guard cells. Most interestingly, the jasmonic acid (JA) biosynthesis pathway was significantly altered in the course of elevatedCO₂treatment. Together with results obtained fromJAbiosynthesis and signaling mutants as well asCO₂signaling mutants, we discovered thatCO₂‐induced stomatal closure is mediated byJAsignaling.
3. Viscosity and liquid–liquid phase separation in healthy and stressed plant SOA

   https://doi.org/10.1039/d0ea00020e  

   Smith, Natalie R. ; Crescenzo, Giuseppe V. ; Huang, Yuanzhou ; Hettiyadura, Anusha P. ; Siemens, Kyla ; Li, Ying ; Faiola, Celia L. ; Laskin, Alexander ; Shiraiwa, Manabu ; Bertram, Allan K. ; et al ( January 2021 , Environmental Science: Atmospheres)

   Molecular composition, viscosity, and liquid–liquid phase separation (LLPS) were investigated for secondary organic aerosol (SOA) derived from synthetic mixtures of volatile organic compounds (VOCs) representing emission profiles for Scots pine trees under healthy and aphid-herbivory stress conditions. Model “healthy plant SOA” and “stressed plant SOA” were generated in a 5 m 3 environmental smog chamber by photooxidation of the mixtures at 50% relative humidity (RH). SOA from photooxidation of α-pinene was also prepared for comparison. Molecular composition was determined with high resolution mass spectrometry, viscosity was determined with the poke-flow technique, and liquid–liquid phase separation was investigated with optical microscopy. The stressed plant SOA had increased abundance of higher molecular weight species, reflecting a greater fraction of sesquiterpenes in the stressed VOC mixture compared to the healthy plant VOC mixture. LLPS occurred in both the healthy and stressed plant SOA; however, stressed plant SOA exhibited phase separation over a broader humidity range than healthy plant SOA, with LLPS persisting down to 23 ± 11% RH. At RH ≤25%, both stressed and healthy plant SOA viscosity exceeded 10 8 Pa s, a value similar to that of tar pitch. At 40% and 50% RH, stressed plant SOA had the highest viscosity,more »followed by healthy plant SOA and then α-pinene SOA in descending order. The observed peak abundances in the mass spectra were also used to estimate the SOA viscosity as a function of RH and volatility. The predicted viscosity of the healthy plant SOA was lower than that of the stressed plant SOA driven by both the higher glass transition temperatures and lower hygroscopicity of the organic molecules making up stressed plant SOA. These findings suggest that plant stress influences the physicochemical properties of biogenic SOA. Furthermore, a complex mixture of VOCs resulted in a higher SOA viscosity compared to SOA generated from α-pinene alone at ≥25% RH, highlighting the importance of studying properties of SOA generated from more realistic multi-component VOC mixtures.« less
4. Dual cationic–anionic profiling of metabolites in a single identified cell in a live Xenopus laevis embryo by microprobe CE-ESI-MS

   https://doi.org/10.1039/C8AN01999A  

   Portero, Erika P. ; Nemes, Peter ( January 2019 , The Analyst)

   In situ capillary microsampling with capillary electrophoresis (CE) electrospray ionization (ESI) mass spectrometry (MS) enabled the characterization of cationic metabolites in single cells in complex tissues and organisms. For deeper coverage of the metabolome and metabolic networks, analytical approaches are needed that provide complementary detection for anionic metabolites, ideally using the same instrumentation. Described here is one such approach that enables sequential cationic and anionic (dual) analysis of metabolites in the same identified cell in a live vertebrate embryo. A calibrated volume was microaspirated from the animal-ventral cell in a live 8-cell embryo of Xenopus laevis , and cationic and anionic metabolites were one-pot microextracted from the aspirate, followed by CE-ESI-MS analysis of the same extract. A laboratory-built CE-ESI interface was reconfigured to enable dual cationic–anionic analysis with ∼5–10 nM (50–100 amol) lower limit of detection and a capability for quantification. To provide robust separation and efficient ion generation, the CE-ESI interface was enclosed in a nitrogen gas filled chamber, and the operational parameters were optimized for the cone-jet spraying regime in both the positive and negative ion mode. A total of ∼250 cationic and ∼200 anionic molecular features were detected from the cell between m / z 50–550, includingmore »60 and 24 identified metabolites, respectively. With only 11 metabolites identified mutually, the duplexed approach yielded complementary information on metabolites produced in the cell, which in turn deepened network coverage for several metabolic pathways. With scalability to smaller cells and adaptability to other types of tissues and organisms, dual cationic–anionic detection with in situ microprobe CE-ESI-MS opens a door to better understand cell metabolism.« less
5. MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data

   https://doi.org/10.1186/s40168-023-01476-3  

   Ayala-Ortiz, Christian ; Graf-Grachet, Nathalia ; Freire-Zapata, Viviana ; Fudyma, Jane ; Hildebrand, Gina ; AminiTabrizi, Roya ; Howard-Varona, Cristina ; Corilo, Yuri E. ; Hess, Nancy ; Duhaime, Melissa B. ; et al ( February 2023 , Microbiome)

   Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking.

   Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is alsomore »uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses.

   Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and aSphagnumleachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively.

   « less