1H NMR based sulfonation reaction kinetics of wine relevant thiols in comparison with known carbonyls

Sulfite addition is a common tool for ensuring wines' oxidative stability via the activity of its free and weakly bound molecular fraction. As a nucleophile, bisulfite forms covalent adducts with wine's most relevant electrophiles, such as carbonyls, polyphenols, and thiols. The equilibrium in these reactions is often represented as dissociation rather than formation. Recent studies from our laboratory demonstrate, first, the acetaldehyde sulfonate dissociation, and second, the chemical stability of cysteine and epicatechin sulfonates under wine aging conditions. Thus, the objective of this study was to monitor by 1H NMR the binding specificity of known carbonyl-derived SO2 binders (acetaldehyde and pyruvic acid) in the presence of S-containing compounds (cysteine and glutathione). We report that during simulated wine aging, the sulfur dioxide that is rapidly bound to carbonyl compounds will be released and will bind to cysteine and glutathione, demonstrating the long-term sulfur dioxide binding potential of S-containing compounds. These results are meant to serve as a complement to existing literature reviews focused on molecular markers related to wines' oxidative stability and emphasize once more the importance of S-containing compounds in wine aging chemical mechanisms.

Dearomatization drives complexity generation in freshwater organic matter

Dissolved organic matter (DOM) is one of the most complex, dynamic and abundant sources of organic carbon, but its chemical reactivity remains uncertain1-3. Greater insights into DOM structural features could facilitate understanding its synthesis, turnover and processing in the global carbon cycle4,5. Here we use complementary multiplicity-edited 13C nuclear magnetic resonance (NMR) spectra to quantify key substructures assembling the carbon skeletons of DOM from four main Amazon rivers and two mid-size Swedish boreal lakes. We find that one type of reaction mechanism, oxidative dearomatization (ODA), widely used in organic synthetic chemistry to create natural product scaffolds6-10, is probably a key driver for generating structural diversity during processing of DOM that are rich in suitable polyphenolic precursor molecules. Our data suggest a high abundance of tetrahedral quaternary carbons bound to one oxygen and three carbon atoms (OCqC3 units). These units are rare in common biomolecules but could be readily produced by ODA of lignin-derived and tannin-derived polyphenols. Tautomerization of (poly)phenols by ODA creates non-planar cyclohexadienones, which are subject to immediate and parallel cycloadditions. This combination leads to a proliferation of structural diversity of DOM compounds from early stages of DOM processing, with an increase in oxygenated aliphatic structures. Overall, we propose that ODA is a key reaction mechanism for complexity acceleration in the processing of DOM molecules, creation of new oxygenated aliphatic molecules and that it could be prevalent in nature.

Increased levels of a mycophenolic acid metabolite in patients with kidney failure negatively affect cardiomyocyte health

Chronic kidney disease (CKD) significantly increases cardiovascular risk and mortality, and the accumulation of uremic toxins in the circulation upon kidney failure contributes to this increased risk. We thus performed a screening for potential novel mediators of reduced cardiovascular health starting from dialysate obtained after hemodialysis of patients with CKD. The dialysate was gradually fractionated to increased purity using orthogonal chromatography steps, with each fraction screened for a potential negative impact on the metabolic activity of cardiomyocytes using a high-throughput MTT-assay, until ultimately a highly purified fraction with strong effects on cardiomyocyte health was retained. Mass spectrometry and nuclear magnetic resonance identified the metabolite mycophenolic acid-β-glucuronide (MPA-G) as a responsible substance. MPA-G is the main metabolite from the immunosuppressive agent MPA that is supplied in the form of mycophenolate mofetil (MMF) to patients in preparation for and after transplantation or for treatment of autoimmune and non-transplant kidney diseases. The adverse effect of MPA-G on cardiomyocytes was confirmed in vitro, reducing the overall metabolic activity and cellular respiration while increasing mitochondrial reactive oxygen species production in cardiomyocytes at concentrations detected in MMF-treated patients with failing kidney function. This study draws attention to the potential adverse effects of long-term high MMF dosing, specifically in patients with severely reduced kidney function already displaying a highly increased cardiovascular risk.

Discovery of Glycation Products: Unraveling the Unknown Glycation Space Using a Mass Spectral Library from In Vitro Model Systems

The nonenzymatic reaction between amino acids (AAs) and reducing sugars, also known as the Maillard reaction, is the primary source of free glycation products (GPs) in vivo and in vitro. The limited number of MS/MS records for GPs in public libraries hinders the annotation and investigation of nonenzymatic glycation. To address this issue, we present a mass spectral library containing the experimental MS/MS spectra of diverse GPs from model systems. Based on the conceptional reaction processes and structural characteristics of products, we classified GPs into common GPs (CGPs) and modified AAs (MAAs). A workflow for annotating GPs was established based on the structural and fragmentation patterns of each GP type. The final spectral library contains 157 CGPs, 499 MAAs, and 2426 GP spectra with synthetic model system information, retention time, precursor m/z, MS/MS, and annotations. As a proof-of-concept, we demonstrated the use of the library for screening GPs in unidentified spectra of human plasma and urine. The AAs with the C6H10O5 modification, fructosylation from Amadori rearrangement, were the most found GPs. With the help of the model system, we confirmed the existence of C6H10O5-modified Valine in human plasma by matching both retention time, MS1, and MS/MS without reference standards. In summary, our GP library can serve as an online resource to quickly screen possible GPs in an untargeted metabolomics workflow, furthermore with the model system as a practical synthesis method to confirm their identity.

Evaluating the photochemical reactivity of disinfection byproducts formed during seawater desalination processes

Reverse osmosis (RO) is widely used for seawater desalination but pre-chlorination of intake water produces halogenated disinfection byproducts (DBPs). The fate and environmental impacts associated with the discharge of DBP-containing RO brine wastewater are unknown. Therefore, to evaluate if photochemistry plays a role in DBP degradation in seawater, we collected samples at a desalination plant, which were desalted and concentrated using two-inline solid phase extraction (SPE) techniques combining reverse-phase polymeric (PPL) and weak anion exchange (WAX) resins. Both filtered water samples and SPE samples (extracts reconstituted in open ocean seawater) were exposed to simulated sunlight in a custom-built flow-through system. Optical property analysis during irradiation experiments did not provide distinguishing features between intake water and RO reject water (brine). Extractable organic bromine (organoBr) concentrations were low in intake water samples (7.8 μg Br L-1) and did not change significantly due to irradiation. OrganoBr concentrations in laboratory-chlorinated raw water were much higher (135 μg Br L-1) and on average decreased by 42 % after 24 h irradiation. However, while organoBr concentrations were highest in RO reject water (473 μg Br L-1), changes in organoBr concentrations in PPL SPE samples after 24 h irradiation were variable, ranging from a 1-46 % loss. Furthermore, most bromine-containing molecular ions identified by high resolution mass spectrometry that were present in RO reject water before irradiation were also found after both 24 h and 50 h exposures. Although only one RO reject water sample was tested in this study, results highlight that hundreds of yet to be identified brominated DBPs in RO reject water could be resistant to photodegradation or phototransform into existing DBPs in the environment. Future work examining the biolability of DBPs in RO reject water, as well as the interplay between photochemical and biological DBP cycling, is warranted.

Nickel-organo compounds as potential enzyme precursors under simulated early Earth conditions

The transition from inorganic catalysis through minerals to organic catalysis by enzymes is a necessary step in the emergence of life. Our work is elucidating likely reactions at the earliest moments of Life, prior to the existence of enzymatic catalysis, by exploring essential intersections between nickel bioinorganic chemistry and pterin biochemistry. We used a prebiotically-inspired acetylene-containing volcanic hydrothermal experimental environment to shed light on the efficient formation of nickel-organo complexes. The simplest bis(dithiolene)nickel complex (C2H2S2)2Ni was identified by UV/Vis spectroscopy, mass spectrometry, nuclear magnetic resonance. Its temporal progression and possible function in this simulated early Earth atmosphere were investigated by isolating the main bis(dithiolene)nickel species from the primordial experimental setup. Using this approach, we uncovered a significant diversity of nickel-organo compositions by identifying 156 elemental annotations. The formation of acetaldehyde through the subsequent degradation of these organo-metal complexes is intriguing, as it is reminiscent of the ability of Pelobacter acetylenicus to hydrate acetylene to acetaldehyde via its bis(dithiolene)-containing enzyme acetylene hydratase. As our findings mechanistically characterize the role of nickel sulfide in catalyzing the formation of acetaldehyde, this fundamental pre-metabolic reaction could play the role of a primitive enzyme precursor of the enzymatic acetylene metabolism and further strengthen the role of acetylene in the molecular origin of life.

Chemical Stability of Thiol and Flavanol Sulfonation Products during Wine Aging Conditions

Bisulfite (HSO3-) is the predominant form of sulfur dioxide, present as free and bound to wine relevant electrophiles under wine acidic pH. While sulfonation reactions of flavanols and thiols have been recently reported as key for wine preservation against oxidation, the transient mechanisms and physicochemical parameters responsible for that remain unknown. In the present study, sulfonation reaction kinetics of thiols and flavanols were monitored under simulated wine aging conditions. The reaction products were then characterized by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, and their chemical stability during time was determined by 1H NMR spectroscopy. Thiol and flavanol sulfonation reaction yields were both promoted by the presence of iron and oxygen, while their chemical stability was confirmed under the same conditions. The sulfonation derivatives of epicatechin and cysteine were synthesized and quantified in young and aged wines. Higher concentrations were reported for both metabolites in older wines, indicating their participation on the strongly bound sulfur dioxide fraction. These findings offer new prospects for more precise use of sulfur dioxide in winemaking.

Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet

BACKGROUND

The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly processes, and rhizosheath structure in pearl millet using four distinct lines with contrasting soil aggregation abilities.

RESULTS

Utilizing 16S rRNA gene and ITS metabarcoding for microbiota profiling, coupled with FTICR-MS metabonomic analysis of metabolite composition in distinct plant compartments and root exudates, we revealed substantial disparities in microbial diversity and interaction networks. The ß-NTI analysis highlighted bacterial rhizosphere turnover driven primarily by deterministic processes, showcasing prevalent homogeneous selection in root tissue (RT) and root-adhering soil (RAS). Conversely, fungal communities were more influenced by stochastic processes. In bulk soil assembly, a combination of deterministic and stochastic mechanisms shapes composition, with deterministic factors exerting a more pronounced role. Metabolic profiles across shoots, RT, and RAS in different pearl millet lines mirrored their soil aggregation levels, emphasizing the impact of inherent plant traits on microbiota composition and unique metabolic profiles in RT and exudates. Notably, exclusive presence of antimicrobial compounds, including DIMBOA and H-DIMBOA, emerged in root exudates and RT of low aggregation lines.

CONCLUSIONS

This research underscores the pivotal influence of root exudates in shaping the root-associated microbiota composition across pearl millet lines, entwined with their soil aggregation capacities. These findings underscore the interconnectedness of root exudates and microbiota, which jointly shape rhizosheath structure, deepening insights into soil-plant-microbe interactions and ecological processes shaping rhizosphere microbial communities. Deciphering plant-microbe interactions and their contribution to soil aggregation and microbiota dynamics holds promise for the advancement of sustainable agricultural strategies. Video Abstract.

Polycyclic aromatic hydrocarbons in samples of Ryugu formed in the interstellar medium

Polycyclic aromatic hydrocarbons (PAHs) contain ≲20% of the carbon in the interstellar medium. They are potentially produced in circumstellar environments (at temperatures ≳1000 kelvin), by reactions within cold (~10 kelvin) interstellar clouds, or by processing of carbon-rich dust grains. We report isotopic properties of PAHs extracted from samples of the asteroid Ryugu and the meteorite Murchison. The doubly-13C substituted compositions (Δ2×13C values) of the PAHs naphthalene, fluoranthene, and pyrene are 9 to 51‰ higher than values expected for a stochastic distribution of isotopes. The Δ2×13C values are higher than expected if the PAHs formed in a circumstellar environment, but consistent with formation in the interstellar medium. By contrast, the PAHs phenanthrene and anthracene in Ryugu samples have Δ2×13C values consistent with formation by higher-temperature reactions.

High-Resolution Mass Spectrometry-Based Metabolomics for Increased Grape Juice Metabolite Coverage

The composition of the juice from grape berries is at the basis of the definition of technological ripeness before harvest, historically evaluated from global sugar and acid contents. If many studies have contributed to the identification of other primary and secondary metabolites in whole berries, deepening knowledge about the chemical composition of the sole flesh of grape berries (i.e., without considering skins and seeds) at harvest is of primary interest when studying the enological potential of widespread grape varieties producing high-added-value wines. Here, we used non-targeted DI-FT-ICR-MS and RP-UHPLC-Q-ToF-MS analyses to explore the extent of metabolite coverage of up to 290 grape juices from four Vitis vinifera grape varieties, namely Chardonnay, Pinot noir, Meunier, and Aligoté, sampled at harvest from 91 vineyards in Europe and Argentina, over three successive vintages. SPE pretreatment of samples led to the identification of more than 4500 detected C,H,O,N,S-containing elemental compositions, likely associated with tens of thousands of distinct metabolites. We further revealed that a major part of this chemical diversity appears to be common to the different juices, as exemplified by Pinot noir and Chardonnay samples. However, it was possible to build significant models for the discrimination of Chardonnay from Pinot noir grape juices, and of Chardonnay from Aligoté grape juices, regardless of the geographical origin or the vintage. Therefore, this metabolomic approach opens access to a remarkable holistic molecular description of the instantaneous composition of such a biological matrix, which is the result of complex interplays among environmental, biochemical, and vine growing practices.

Molecular Characterization of Cooking Processes: A Metabolomics Decoding of Vaporous Emissions for Food Markers and Thermal Reaction Indicators

Thermal processing of food plays a fundamental role in everyday life. Whereas most researchers study thermal processes directly in the matrix, molecular information in the form of non- and semivolatile compounds conveyed by vaporous emissions is often neglected. We performed a metabolomics study of processing emissions from 96 different food items to define the interaction between the processed matrix and released metabolites. Untargeted profiling of vapor samples revealed matrix-dependent molecular spaces that were characterized by Fourier-transform ion cyclotron resonance-mass spectrometry and ultra-performance liquid chromatography-mass spectrometry. Thermal degradation products of peptides and amino acids can be used for the differentiation of animal-based food from plant-based food, which generally is characterized by secondary plant metabolites or carbohydrates. Further, heat-sensitive processing indicators were characterized and discussed in the background of the Maillard reaction. These reveal that processing emissions contain a dense layer of information suitable for deep insights into food composition and control of cooking processes based on processing emissions.

Farnesoid X receptor activation by bile acids suppresses lipid peroxidation and ferroptosis

Ferroptosis is a regulated cell death modality that occurs upon iron-dependent lipid peroxidation. Recent research has identified many regulators that induce or inhibit ferroptosis; yet, many regulatory processes and networks remain to be elucidated. In this study, we performed a chemical genetics screen using small molecules with known mode of action and identified two agonists of the nuclear receptor Farnesoid X Receptor (FXR) that suppress ferroptosis, but not apoptosis or necroptosis. We demonstrate that in liver cells with high FXR levels, knockout or inhibition of FXR sensitized cells to ferroptotic cell death, whereas activation of FXR by bile acids inhibited ferroptosis. Furthermore, FXR inhibited ferroptosis in ex vivo mouse hepatocytes and human hepatocytes differentiated from induced pluripotent stem cells. Activation of FXR significantly reduced lipid peroxidation by upregulating the ferroptosis gatekeepers GPX4, FSP1, PPARα, SCD1, and ACSL3. Together, we report that FXR coordinates the expression of ferroptosis-inhibitory regulators to reduce lipid peroxidation, thereby acting as a guardian of ferroptosis.

Selectivity of β-Cyclodextrin Polymer toward Aquatic Contaminants: Insights from Ultrahigh-Resolution Mass Spectrometry of Dissolved Organic Matter

Selectivity in solid-phase extraction (SPE) materials has become increasingly important for analyte enrichment in sensitive analytical workflows to alleviate detrimental matrix effects. Molecular-level investigation of matrix constituents, which are preferentially extracted or excluded, can provide the analytical chemist with valuable information to learn about their control on sorbent selectivity. In this work, we employ nontargeted Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) to elucidate the molecular chemodiversity of freshwater-derived dissolved organic matter (DOM) extracted by the selective model sorbent β-cyclodextrin polymer (β-CDP) in comparison to conventional, universal SPE sorbents (i.e., Oasis HLB, Supel-Select HLB, and LiChrolut EN). Statistical analysis of MS data corroborated the highly selective nature of β-CDP by revealing the extracted DOM spectra that are most dissimilar to original compositions. We found that its selectivity was characterized by pronounced discrimination against highly oxygenated and unsaturated DOM compounds, which were associated with the classes of lignin-like, tannin-like, and carboxylic-rich alicyclic molecules. In contrast, conventional sorbents excluded less highly oxygenated compounds and showed a more universal extraction behavior for a wide range of DOM compositional space. We lay these findings in a larger context that aids the analyst in obtaining an a priori estimate of sorbent selectivity toward any target analyte of interest serving thereby an optimization of sample preparation. This study highlights the great value of nontargeted ultrahigh-resolution MS for better understanding of targeted analytics and provides new insights into the selective sorption behavior of novel sorbents.

Soluble organic matter Molecular atlas of Ryugu reveals cold hydrothermalism on C-type asteroid parent body

The sample from the near-Earth carbonaceous asteroid (162173) Ryugu is analyzed in the context of carbonaceous meteorites soluble organic matter. The analysis of soluble molecules of samples collected by the Hayabusa2 spacecraft shines light on an extremely high molecular diversity on the C-type asteroid. Sequential solvent extracts of increasing polarity of Ryugu samples are analyzed using mass spectrometry with complementary ionization methods and structural information confirmed by nuclear magnetic resonance spectroscopy. Here we show a continuum in the molecular size and polarity, and no organomagnesium molecules are detected, reflecting a low temperature and water-rich environment on the parent body approving earlier mineralogical and chemical data. High abundance of sulfidic and nitrogen rich compounds as well as high abundance of ammonium ions confirm the water processing. Polycyclic aromatic hydrocarbons are also detected in a structural continuum of carbon saturations and oxidations, implying multiple origins of the observed organic complexity, thus involving generic processes such as earlier carbonization and serpentinization with successive low temperature aqueous alteration.

C2-addition patterns emerging from acetylene and nickel sulfide in simulated prebiotic hydrothermal conditions

Chemical complexity is vital not only for the origin of life but also for biological evolution. The chemical evolution of a complex prebiotic mixture containing acetylene, carbon monoxide (CO), and nickel sulfide (NiS) has been analyzed with mass spectrometry as an untargeted approach to reaction monitoring. Here we show through isotopic 13C-labelling, multiple reaction products, encompassing diverse CHO and CHOS compounds within the complex reaction mixture. Molecules within the same chemical spaces displayed varying degrees of 13C-labelling, enabling more robust functional group characterization based on targeted investigations and differences in saturation levels among the described classes. A characteristic C2-addition pattern was detected in all compound classes in conjunction with a high diversity of thio acids, reminiscent of extant microbial C2-metabolism. The analysis involved a time-resolved molecular network, which unveiled the behavior of sulfur in the system. At the onset of the reaction, early formed compounds contain more sulfur atoms compared to later emerging compounds. These results give an essential insight into the still elusive role of sulfur dynamics in the origin of life. Moreover, our results provide temporally resolved evidence of the progressively increasing molecular complexity arising from a limited number of compounds.

Discriminative Behavior of Cyclodextrin Polymers against Dissolved Organic Matter: Role of Cavity Size and Sorbate Properties

Cyclodextrin polymers (CDPs) are promising next-generation adsorbents in water purification technologies. The selectivity of the polymer derivate cross-linked with tetrafluoroterephthalonitrile (TFN-CDP) for nonionic and cationic micropollutants (MPs) over dissolved organic matter (DOM) renders the adsorbent also attractive for many analytical applications. The molecular drivers of the observed selectivity are, nonetheless, not yet fully understood. To provide new insights into the sorption mechanism, we (i) synthesized TFN-CDPs with different cavity sizes (α-, β-, γ-CDP); (ii) assessed their extraction efficiencies for selected nonionic MPs in competition with different DOM size fractions (<1, 1-3, 3-10, >10 kDa) to test for size-selectivity; and (iii) performed nontargeted, ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry analysis on CDP-extracted DOM compounds (<1 kDa) to probe for molecular sorbate properties governing their selective sorption. First, no evidence of size-selectivity was obtained through either the different CD cavity sizes (i) or the two independent approaches (ii) and (iii). Second, we found a dominant impact of sorbate oxygenation and polarity on the extraction of DOM and MPs, respectively, with relatively oxygen-poor/nonpolar molecules favorably retained on all α-, β-, and γ-CDP. Third, our data indicates exclusion of an anionic matrix, such as carboxylic acids, but preferential sorption of cationic nitrogen-bearing DOM, pointing at repulsive and attractive forces with the negatively charged cross-linker as a likely reason. Therefore, we ascribe TFN-CDP's selectivity to nonpolar and electrostatic interactions between MPs/DOM and the polymer building blocks. These molecular insights can further aid in the optimization of efficient and selective sorbent design for environmental and analytical applications.

FT-ICR-MS reveals the molecular imprints of the brewing process

The study of fermentation and brewing has a long history of pioneering discoveries that continue to influence modern industrial food production. Since then, numerous research endeavors have yielded conventional criteria that guide contemporary brewing practices. However, the intricate open challenges faced today necessitate a more exhaustive understanding of the process at the molecular scale. We have developed an ultra-high-resolution mass spectrometric analysis (FT-ICR-MS) of the brewing process that can rapidly and comprehensively resolve thousands of molecules. This approach allows us to track molecular fluctuation during brewing at the level of chemical compositions. Employing biological triplicates, our investigation of two brewing lines that are otherwise identical except for the malt used revealed over 8,000 molecular descriptors of the brewing process. Metabolite imprints of both the similarities and differences arising from deviating malting temperatures were visualized. Additionally, we translated traditional brewing attributes such as the EBC-value, free amino nitrogen, pH-value, and concentration curves of specific molecules, into highly correlative molecular patterns consisting of hundreds of metabolites. These in-depth molecular imprints provide a better understanding of the molecular circumstances leading to various changes throughout the brewing process. Such chemical maps go beyond the observation of traditional brewing attributes and are of great significance in the investigation strategies of current open challenges in brewing research. The molecular base of knowledge, along with advancements in technological and data integration schemes, can facilitate the efficient monitoring of brewing and other productions processes.

Chemical evolution of primordial salts and organic sulfur molecules in the asteroid 162173 Ryugu

Samples from the carbonaceous asteroid (162173) Ryugu provide information on the chemical evolution of organic molecules in the early solar system. Here we show the element partitioning of the major component ions by sequential extractions of salts, carbonates, and phyllosilicate-bearing fractions to reveal primordial brine composition of the primitive asteroid. Sodium is the dominant electrolyte of the salt fraction extract. Anions and NH4+ are more abundant in the salt fraction than in the carbonate and phyllosilicate fractions, with molar concentrations in the order SO42- > Cl- > S2O32- > NO3- > NH4+. The salt fraction extracts contain anionic soluble sulfur-bearing species such as Sn-polythionic acids (n < 6), Cn-alkylsulfonates, alkylthiosulfonates, hydroxyalkylsulfonates, and hydroxyalkylthiosulfonates (n < 7). The sulfur-bearing soluble compounds may have driven the molecular evolution of prebiotic organic material transforming simple organic molecules into hydrophilic, amphiphilic, and refractory S allotropes.

Formation of vesicular structures from fatty acids formed under simulated volcanic hydrothermal conditions

Microscopic compartmentalization is beneficial in synthetic chemistry and indispensable for the evolution of life to separate a reactive "inside" from a hydrolyzing "outside". Here, we show compartmentalization in aqueous solution containing mixtures of fatty acids up to 19 carbon atoms which were synthesized by one-pot reactions of acetylene and carbon monoxide in contact with nickel sulfide at 105 °C, reaction requirements which are compatible to Hadean Early Earth conditions. Based on confocal, dynamic light scattering (DLS) and transmission electron microscopy (TEM) measurements, vesicle-like structures with diameters of 10-150 nm are formed after solvent extraction and resolubilisation. Moreover fluorescent dye was encapsulated into the structures proving their vesicular properties. This self-assembly could also have occurred on Early Earth as a crucial step in establishing simple membranes of proto-cells as a prerequisite in the evolution of metabolism and life.

Interplay of Metallome and Metabolome in Amyotrophic Lateral Sclerosis: A Study on Cerebrospinal Fluid of Patients Carrying Disease-Related Gene Mutations

Amyotrophic lateral sclerosis (ALS) is a lethal progressive neurodegenerative disease, characterized by a loss of function of upper and lower motor neurons. This study aimed to explore probable pathological alterations occurring in individuals with ALS compared to neurologically healthy controls through the analysis of cerebrospinal fluid (CSF), a medium, which directly interacts with brain parenchyma. A total of 7 ALS patients with disease-associated mutations (ATXN2, C9ORF72, FUS, SOD1, and TARDBP) and 13 controls were included in the study. Multiple analytical approaches were employed, including metabolomic and metallomics profiling, as well as genetic screening, using CSF samples obtained from the brain compartment. Data analysis involved the application of multivariate statistical methods. Advanced hyphenated selenium and redox metal (iron, copper, and manganese) speciation techniques and nontargeted Fourier transform ion cyclotron resonance mass spectrometry-based metabolomics were used for data acquisition. Nontargeted metabolomics showed reduced steroids, including sex hormones; additionally, copper and manganese species were found to be the most relevant features for ALS patients. This indicates a potential alteration of sex hormone pathways in the ALS-affected brain, as reflected in the CSF.

Asthma-protective agents in dust from traditional farm environments

BACKGROUND

Growing up on traditional European or US Amish dairy farms in close contact with cows and hay protects children against asthma, and airway administration of extracts from dust collected from cowsheds of those farms prevents allergic asthma in mice.

OBJECTIVES

This study sought to begin identifying farm-derived asthma-protective agents.

METHODS

Our work unfolded along 2 unbiased and independent but complementary discovery paths. Dust extracts (DEs) from protective and nonprotective farms (European and Amish cowsheds vs European sheep sheds) were analyzed by comparative nuclear magnetic resonance profiling and differential proteomics. Bioactivity-guided size fractionation focused on protective Amish cowshed DEs. Multiple in vitro and in vivo functional assays were used in both paths. Some of the proteins thus identified were characterized by in-solution and in-gel sodium dodecyl sulfate-polyacrylamide gel electrophoresis enzymatic digestion/peptide mapping followed by liquid chromatography/mass spectrometry. The cargo carried by these proteins was analyzed by untargeted liquid chromatography-high-resolution mass spectrometry.

RESULTS

Twelve carrier proteins of animal and plant origin, including the bovine lipocalins Bos d 2 and odorant binding protein, were enriched in DEs from protective European cowsheds. A potent asthma-protective fraction of Amish cowshed DEs (≈0.5% of the total carbon content of unfractionated extracts) contained 7 animal and plant proteins, including Bos d 2 and odorant binding protein loaded with fatty acid metabolites from plants, bacteria, and fungi.

CONCLUSIONS

Animals and plants from traditional farms produce proteins that transport hydrophobic microbial and plant metabolites. When delivered to mucosal surfaces, these agents might regulate airway responses.

Distinct Non-conservative Behavior of Dissolved Organic Matter after Mixing Solimões/Negro and Amazon/Tapajós River Waters

Positive and negative electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and 1H NMR revealed major compositional and structural changes of dissolved organic matter (DOM) after mixing two sets of river waters in Amazon confluences: the Solimões and Negro Rivers (S + N) and the Amazon and Tapajós Rivers (A + T). We also studied the effects of water mixing ratios and incubation time on the composition and structure of DOM molecules. NMR spectra demonstrated large-scale structural transformations in the case of S + N mixing, with gain of pure and functionalized aliphatic units and loss of all other structures after 1d incubation. A + T mixing resulted in comparatively minor structural alterations, with a major gain of small aliphatic biomolecular binding motifs. Remarkably, structural alterations from mixing to 1d incubation were in essence reversed from 1d to 5d incubation for both S + N and A + T mixing experiments. Heterotrophic bacterial production (HBP) in endmembers S, N, and S + N mixtures remained near 0.03 μgC L-1 h-1, whereas HBP in A, T, and A + T were about five times higher. High rates of dark carbon fixation took place at S + N mixing in particular. In-depth biogeochemical characterization revealed major distinctions between DOM biogeochemical changes and temporal evolution at these key confluence sites within the Amazon basin.

Capillary electrophoresis-mass spectrometry as a tool for Caenorhabditis elegans metabolomics research

INTRODUCTION

Polar metabolites in Caenorhabditis elegans (C. elegans) have predominantly been analyzed using hydrophilic interaction liquid chromatography coupled to mass spectrometry (HILIC-MS). Capillary electrophoresis coupled to mass spectrometry (CE-MS) represents another complementary analytical platform suitable for polar and charged analytes.

OBJECTIVE

We compared CE-MS and HILIC-MS for the analysis of a set of 60 reference standards relevant for C. elegans and specifically investigated the strengths of CE separation. Furthermore, we employed CE-MS as a complementary analytical approach to study polar metabolites in C. elegans samples, particularly in the context of longevity, in order to address a different part of its metabolome.

METHOD

We analyzed 60 reference standards as well as metabolite extracts from C. elegans daf-2 loss-of-function mutants and wild-type (WT) samples using HILIC-MS and CE-MS employing a Q-ToF-MS instrument.

RESULTS

CE separations showed narrower peak widths and a better linearity of the estimated response function across different concentrations which is linked to less saturation of the MS signals. Additionally, CE exhibited a distinct selectivity in the separation of compounds compared to HILIC-MS, providing complementary information for the analysis of the target compounds. Analysis of C. elegans metabolites of daf-2 mutants and WT samples revealed significant alterations in shared metabolites identified through HILIC-MS, as well as the presence of distinct metabolites.

CONCLUSION

CE-MS was successfully applied in C. elegans metabolomics, being able to recover known as well as identify novel putative biomarkers of longevity.

Histone Deacetylases HD2A and HD2B Undergo Feedback Regulation by ABA and Modulate Drought Tolerance via Mediating ABA-Induced Transcriptional Repression

Histone deacetylation catalyzed by histone deacetylase plays a critical role in gene silencing and subsequently controls many important biological processes. It was reported that the expression of the plant-specific histone deacetylase subfamily HD2s is repressed by ABA in Arabidopsis. However, little is known about the molecular relationship between HD2A/HD2B and ABA during the vegetative phase. Here, we describe that the hd2ahd2b mutant shows hypersensitivity to exogenous ABA during the germination and post-germination period. Additionally, transcriptome analyses revealed that the transcription of ABA-responsive genes was reprogrammed and the global H4K5ac level is specifically up-regulated in hd2ahd2b plants. ChIP-Seq and ChIP-qPCR results further verified that both HD2A and HD2B could directly and specifically bind to certain ABA-responsive genes. As a consequence, Arabidopsis hd2ahd2b plants displayed enhanced drought resistance in comparison to WT, which is consistent with increased ROS content, reduced stomatal aperture, and up-regulated drought-resistance-related genes. Moreover, HD2A and HD2B repressed ABA biosynthesis via the deacetylation of H4K5ac at NCED9. Taken together, our results indicate that HD2A and HD2B partly function through ABA signaling and act as negative regulators during the drought resistance response via the regulation of ABA biosynthesis and response genes.

Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov

Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31^T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31^T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.

Lipidomic and Metallomic Alteration of Caenorhabditis elegans after Acute and Chronic Manganese, Iron, and Zinc Exposure with a Link to Neurodegenerative Disorders

Parkinson's disease (PD) progresses with the loss of dopaminergic neurons in the substantia nigra pars compacta region of the brain. The superior mechanisms and the cause of this specific localized neurodegeneration is currently unknown. However, experimental evidence indicates a link between PD progression and reactive oxygen species with imbalanced metal homeostasis. Wild-type Caenorhabditis elegans exposed to redox-active metals was used as the model organism to study cellular response to imbalanced metal homeostasis linked to neurodegenerative diseases. Using modern hyphenated techniques such as capillary electrophoresis coupled to inductively coupled plasma mass spectrometry and ultrahigh-performance liquid chromatography mass spectrometry, alterations in the lipidome and metallome were determined in vivo. In contrast to iron, most of the absorbed zinc and manganese were loosely bound. We observed changes in the phospholipid composition for acute iron and manganese exposures, as well as chronic zinc exposure. Furthermore, we focused on the mitochondrial membrane alteration due to its importance in neuronal function. However, significant changes in the inner mitochondrial membrane by determination of cardiolipin species could only be observed for acute iron exposure. These results indicate different intracellular sites of local ROS generation, depending on the redox active metal. Our study combines metallomic and lipidomic alterations as the cause and consequence to enlighten intracellular mechanisms in vivo, associated with PD progression. The mass spectrometry raw data have been deposited to the MassIVE database (https://massive.ucsd.edu) with the identifier MSV000090796 and 10.25345/C51J97C8F.

Soluble organic molecules in samples of the carbonaceous asteroid (162173) Ryugu

The Hayabusa2 spacecraft collected samples from the surface of the carbonaceous near-Earth asteroid (162173) Ryugu and brought them to Earth. The samples were expected to contain organic molecules, which record processes that occurred in the early Solar System. We analyzed organic molecules extracted from the Ryugu surface samples. We identified a variety of molecules containing the atoms CHNOS, formed by methylation, hydration, hydroxylation, and sulfurization reactions. Amino acids, aliphatic amines, carboxylic acids, polycyclic aromatic hydrocarbons, and nitrogen-heterocyclic compounds were detected, which had properties consistent with an abiotic origin. These compounds likely arose from an aqueous reaction on Ryugu's parent body and are similar to the organics in Ivuna-type meteorites. These molecules can survive on the surfaces of asteroids and be transported throughout the Solar System.

Formation, stabilization and fate of acetaldehyde and higher aldehydes in an autonomously changing prebiotic system emerging from acetylene

Many essential building blocks of life, including amino acids, sugars, and nucleosides, require aldehydes for prebiotic synthesis. Pathways for their formation under early earth conditions are therefore of great importance. We investigated the formation of aldehydes by an experimental simulation of primordial early earth conditions, in line with the metal-sulfur world theory in an acetylene-containing atmosphere. We describe a pH-driven, intrinsically autoregulatory environment that concentrates acetaldehyde and other higher molecular weight aldehydes. We demonstrate that acetaldehyde is rapidly formed from acetylene over a nickel sulfide catalyst in an aqueous solution, followed by sequential reactions progressively increasing the molecular diversity and complexity of the reaction mixture. Interestingly, through inherent pH changes, the evolution of this complex matrix leads to auto-stabilization of de novo synthesized aldehydes and alters the subsequent synthesis of relevant biomolecules rather than yielding uncontrolled polymerization products. Our results emphasize the impact of progressively generated compounds on the overall reaction conditions and strengthen the role of acetylene in forming essential building blocks that are fundamental for the emergence of terrestrial life.

The Combination of Both Heat and Water Stresses May Worsen Botryosphaeria Dieback Symptoms in Grapevine

(1) Background: Grapevine trunk diseases (GTDs) have become a global threat to vineyards worldwide. These diseases share three main common features. First, they are caused by multiple pathogenic micro-organisms. Second, these pathogens often maintain a long latent phase, which makes any research in pathology and symptomatology challenging. Third, a consensus is raising to pinpoint combined abiotic stresses as a key factor contributing to disease symptom expression. (2) Methods: We analyzed the impact of combined abiotic stresses in grapevine cuttings artificially infected by two fungi involved in Botryosphaeria dieback (one of the major GTDs), Neofusicoccum parvum and Diplodia seriata. Fungal-infected and control plants were subjected to single or combined abiotic stresses (heat stress, drought stress or both). Disease intensity was monitored thanks to the measurement of necrosis area size. (3) Results and conclusions: Overall, our results suggest that combined stresses might have a stronger impact on disease intensity upon infection by the less virulent pathogen Diplodia seriata. This conclusion is discussed through the impact on plant physiology using metabolomic and transcriptomic analyses of leaves sampled for the different conditions.

DBDIpy: a Python library for processing of untargeted datasets from real-time plasma ionization mass spectrometry

MOTIVATION

Plasma ionization is rapidly gaining popularity for mass spectrometry (MS)-based studies of volatiles and aerosols. However, data from plasma ionization are delicate to interpret as competing ionization pathways in the plasma create numerous ion species. There is no tool for detection of adducts and in-source fragments from plasma ionization data yet, which makes data evaluation ambiguous.

SUMMARY

We developed DBDIpy, a Python library for processing and formal analysis of untargeted, time-sensitive plasma ionization MS datasets. Its core functionality lies in the identification of in-source fragments and identification of rivaling ionization pathways of the same analytes in time-sensitive datasets. It further contains elementary functions for processing of untargeted metabolomics data and interfaces to an established ecosystem for analysis of MS data in Python.

AVAILABILITY AND IMPLEMENTATION

DBDIpy is implemented in Python (Version ≥ 3.7) and can be downloaded from PyPI the Python package repository (https://pypi.org/project/DBDIpy) or from GitHub (https://github.com/leopold-weidner/DBDIpy).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Comprehensive assessment of dissolved organic matter processing in the Amazon River and its major tributaries revealed by positive and negative electrospray mass spectrometry and NMR spectroscopy

Rivers are natural biogeochemical systems shaping the fates of dissolved organic matter (DOM) from leaving soils to reaching the oceans. This study focuses on Amazon basin DOM processing employing negative and positive electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI[±] FT-ICR MS) and nuclear magnetic resonance spectroscopy (NMR) to reveal effects of major processes on the compositional space and structural characteristics of black, white and clear water systems. These include non-conservative mixing at the confluences of (1) Solimões and the Negro River, (2) the Amazon River and the Madeira River, and (3) in-stream processing of Amazon River DOM between the Madeira River and the Tapajós River. The Negro River (black water) supplies more highly oxygenated and high molecular weight compounds, whereas the Solimões and Madeira Rivers (white water) contribute more CHNO and CHOS molecules to the Amazon River main stem. Aliphatic CHO and abundant CHNO compounds prevail in Tapajos River DOM (clear water), likely originating from primary production. Sorption onto particles and heterotrophic microbial degradation are probably the principal mechanisms for the observed changes in DOM composition in the Amazon River and its tributaries.

Real-Time Monitoring of Miniaturized Thermal Food Processing by Advanced Mass Spectrometric Techniques

Mass spectrometry is a popular and powerful analytical tool to study the effects of food processing. Industrial sampling, real-life sampling, or challenging academic research on process-related volatile and aerosol research often demand flexible, time-sensitive data acquisition by state-of-the-art mass analyzers. Here, we show a laboratory-scaled, miniaturized, and highly controllable setup for the online monitoring of aerosols and volatiles from thermal food processing based on dielectric barrier discharge ionization (DBDI) mass spectrometry (MS). We demonstrate the opportunities offered by the setup from a foodomics perspective to study emissions from the thermal processing of wheat bread rolls at 210 °C by Fourier transformation ion cyclotron resonance MS. As DBDI is an emerging technology, we compared its ionization selectivity to established atmospheric pressure ionization tools: we found DBDI preferably ionizes saturated, nitrogenous compounds. We likewise identified a sustainable overlap in the selectivity of detected analytes with APCI and electrospray ionization (ESI). Further, we dynamically recorded chemical fingerprints throughout the thermal process. Unsupervised classification of temporal response patterns was used to describe the dynamic nature of the reaction system. Compared to established tools for real-time MS, our setup permits one to monitor chemical changes during thermal food processing at ultrahigh resolution, establishing an advanced perspective for real-time mass spectrometric analysis of food processing.

Complex carbonaceous matter in Tissint martian meteorites give insights into the diversity of organic geochemistry on Mars

We report a huge organic diversity in the Tissint Mars meteorite and the sampling of several mineralogical lithologies, which revealed that the organic molecules were nonuniformly distributed in functionality and abundance. The range of organics in Tissint meteorite were abundant C_3-7 aliphatic branched carboxylic acids and aldehydes, olefins, and polyaromatics with and without heteroatoms in a homologous oxidation structural continuum. Organomagnesium compounds were extremely abundant in olivine macrocrystals and in the melt veins, reflecting specific organo-synsthesis processes in close interaction with the magnesium silicates and temperature stresses, as previously observed. The diverse chemistry and abundance in complex molecules reveal heterogeneity in organic speciation within the minerals grown in the martian mantle and crust that may have evolved over geological time.

Sodium arsenite-induced changes in the wood of esca-diseased grapevine at cytological and metabolomic levels

In the past, most grapevine trunk diseases (GTDs) have been controlled by treatments with sodium arsenite. For obvious reasons, sodium arsenite was banned in vineyards, and consequently, the management of GTDs is difficult due to the lack of methods with similar effectiveness. Sodium arsenite is known to have a fungicide effect and to affect the leaf physiology, but its effect on the woody tissues where the GTD pathogens are present is still poorly understood. This study thus focuses on the effect of sodium arsenite in woody tissues, particularly in the interaction area between asymptomatic wood and necrotic wood resulting from the GTD pathogens' activities. Metabolomics was used to obtain a metabolite fingerprint of sodium arsenite treatment and microscopy to visualize its effects at the histo-cytological level. The main results are that sodium arsenite impacts both metabolome and structural barriers in plant wood. We reported a stimulator effect on plant secondary metabolites in the wood, which add to its fungicide effect. Moreover, the pattern of some phytotoxins is affected, suggesting the possible effect of sodium arsenite in the pathogen metabolism and/or plant detoxification process. This study brings new elements to understanding the mode of action of sodium arsenite, which is useful in developing sustainable and eco-friendly strategies to better manage GTDs.

Large-Scale Interlaboratory DI-FT-ICR MS Comparability Study Employing Various Systems

Ultrahigh resolution mass spectrometry (UHR-MS) coupled with direct infusion (DI) electrospray ionization offers a fast solution for accurate untargeted profiling. Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers have been shown to produce a wealth of insights into complex chemical systems because they enable unambiguous molecular formula assignment even if the vast majority of signals is of unknown identity. Interlaboratory comparisons are required to apply this type of instrumentation in quality control (for food industry or pharmaceuticals), large-scale environmental studies, or clinical diagnostics. Extended comparisons employing different FT-ICR MS instruments with qualitative direct infusion analysis are scarce since the majority of detected compounds cannot be quantified. The extent to which observations can be reproduced by different laboratories remains unknown. We set up a preliminary study which encompassed a set of 17 laboratories around the globe, diverse in instrumental characteristics and applications, to analyze the same sets of extracts from commercially available standard human blood plasma and Standard Reference Material (SRM) for blood plasma (SRM1950), which were delivered at different dilutions or spiked with different concentrations of pesticides. The aim of this study was to assess the extent to which the outputs of differently tuned FT-ICR mass spectrometers, with different technical specifications, are comparable for setting the frames of a future DI-FT-ICR MS ring trial. We concluded that a cluster of five laboratories, with diverse instrumental characteristics, showed comparable and representative performance across all experiments, setting a reference to be used in a future ring trial on blood plasma.

HILIC-MS for Untargeted Profiling of the Free Glycation Product Diversity

Glycation products produced by the non-enzymatic reaction between reducing carbohydrates and amino compounds have received increasing attention in both food- and health-related research. Although liquid chromatography mass spectrometry (LC-MS) methods for analyzing glycation products already exist, only a few common advanced glycation end products (AGEs) are usually covered by quantitative methods. Untargeted methods for comprehensively analyzing glycation products are still lacking. The aim of this study was to establish a method for simultaneously characterizing a wide range of free glycation products using the untargeted metabolomics approach. In this study, Maillard model systems consisting of a multitude of heterogeneous free glycation products were chosen for systematic method optimization, rather than using a limited number of standard compounds. Three types of hydrophilic interaction liquid chromatography (HILIC) columns (zwitterionic, bare silica, and amide) were tested due to their good retention for polar compounds. The zwitterionic columns showed better performance than the other two types of columns in terms of the detected feature numbers and detected free glycation products. Two zwitterionic columns were selected for further mobile phase optimization. For both columns, the neutral mobile phase provided better peak separation, whereas the acidic condition provided a higher quality of chromatographic peak shapes. The ZIC-cHILIC column operating under acidic conditions offered the best potential to discover glycation products in terms of providing good peak shapes and maintaining comparable compound coverage. Finally, the optimized HILIC-MS method can detect 70% of free glycation product features despite interference from the complex endogenous metabolites from biological matrices, which showed great application potential for glycation research and can help discover new biologically important glycation products.

Cluster Analysis Statistical Spectroscopy for the Identification of Metabolites in 1H NMR Metabolomics

Metabolite identification in non-targeted NMR-based metabolomics remains a challenge. While many peaks of frequently occurring metabolites are assigned, there is a high number of unknowns in high-resolution NMR spectra, hampering biological conclusions for biomarker analysis. Here, we use a cluster analysis approach to guide peak assignment via statistical correlations, which gives important information on possible structural and/or biological correlations from the NMR spectrum. Unknown peaks that cluster in close proximity to known peaks form hypotheses for their metabolite identities, thus, facilitating metabolite annotation. Subsequently, metabolite identification based on a database search, 2D NMR analysis and standard spiking is performed, whereas without a hypothesis, a full structural elucidation approach would be required. The approach allows a higher identification yield in NMR spectra, especially once pathway-related subclusters are identified.

Metabolic folate profiling as a function of time during cultivation suggests potential C2-metabolism in Saccharomyces cerevisiae

Yeasts are reported to be rich in folates, a group of vitamers known to be involved in several biosynthetic reactions such as methylation reactions, oxidation and reduction processes, and nucleotide synthesis. Not being able to synthesize folates, humans rely on external folate supply. Here, we show the application of LC/MS-MS methods using SIDA (stable isotope dilution analysis) assays for the quantitative analysis of different folate mono- and polyglutamates during growth of Saccharomyces cerevisiae. Molecular networking (MN) was applied for detailed analysis of further folate metabolites. Highest folate contents of 13,120 μg/100 g were observed after 20 h of cultivation. The main vitamers 5-CH₃-H₄folate and H₄folate decreased during cultivation, while 5-CHO-H₄folate increased during cultivation. The hexa- and heptaglutamate of 5-CH₃-H₄folate accounted for >96% of the total 5-CH₃-H₄folate content. A shift of the major polyglutamate from hexa- to heptaglutamate was observed after 29 h. MN unraveled two groups of novel folates which could be assigned to a potentially existing C₂-metabolism in yeast. In detail, 5,10-ethenyl-tetrahydrofolate and a further CO-substituted 5-CH₃-H₄folate were identified as hexa- and heptaglutamates. The latter was neither identified as 5-acetyl-tetrahydrofolate nor as EthylFox, the oxidation product of 5-ethyl-tetrahydrofolate. The structure needs to be elucidated in future studies.

Current and future approaches for in vitro hit discovery in diabetes mellitus

Type 2 diabetes mellitus (T2DM) is a serious public health problem. In this review, we discuss current and promising future drugs, targets, in vitro assays and emerging omics technologies in T2DM. Importantly, we open the perspective to image-based high-content screening (HCS), with the focus of combining it with metabolomics or lipidomics. HCS has become a strong technology in phenotypic screens because it allows comprehensive screening for the cell-modulatory activity of small molecules. Metabolomics and lipidomics screen for perturbations at the molecular level. The combination of these data-intensive comprehensive technologies is enabled by the rapid development of artificial intelligence. It promises a deep cellular and molecular phenotyping directly linked to chemical information about the applied drug candidates or complex mixtures.

Molecular and spectroscopic changes of peat-derived organic matter following photo-exposure: Effects on heteroatom composition of DOM

The temporal evolution of molecular compositions and changes in structural features of Hillsboro Canal (Florida, USA) dissolved organic matter (DOM) was studied with an emphasis on nitrogen and sulfur containing molecules, after a 13 day time-series exposure to simulated sunlight. The Hillsboro Canal drains from the ridge and slough wetland environment underlain by peat soils from the northern extent of the Greater Everglades Ecosystem. The Hillsboro Canal-DOM was characterized by combining ultrahigh-resolution mass spectrometry (FT-ICR-MS), high-field nuclear magnetic resonance spectroscopy (¹H NMR), size exclusion chromatography (SEC) with UV detection, and ultraviolet/visible (UV/vis) absorbance and excitation emission matrix (EEM) fluorescence spectroscopy. Size exclusion chromatography (SEC) demonstrated progressive depletion of higher mass molecules and a concomitant decrease of absorbance during photo-irradiation. NMR and FT-ICR-MS revealed nonlinear temporal evolution of DOM. In fact, FT-ICR-MS showed an initial depletion of supposedly chromophoric molecules often carrying major unsaturation accompanied by an uneven evolution of numbers of CHO, CHOS and CHNO compounds. While CHNO compounds continually increased throughout the entire photo-exposure time, CHO and CHOS compounds temporarily increased but declined after further light exposure. Progressive loss of highly unsaturated compounds was accompanied by production of low mass CHO and CHNO compounds with high O/C ratios. Area-normalized ¹H NMR spectra of DOM in water and of the water insoluble fraction (~5%) in methanol revealed clear distinctions between irradiated and non-irradiated samples and congruent evolution of DOM structural features during irradiation, with more uniform trends in methanolic-DOM. Photoirradiation caused initial photoproduction of oxygenated aliphatic compounds, continued depletion of phenols and oxygenated aromatics, substantial change from initial natural product derived olefins to photoproduced olefins, and uneven evolution of carboxylated and alkylated benzene derivatives. This study demonstrates longer-term heteroatom-dependent photochemistry of DOM, which will affect the speciation of N and S heteroatoms, their connections to inorganic nutrients, and potentially their bioavailability.

MobilityTransformR: an R package for effective mobility transformation of CE-MS data

SUMMARY

We present MobilityTransformR, an R/Bioconductor package for the effective mobility scaling of capillary zone electrophoresis-mass spectrometry (CE-MS) data. It uses functionality from different R packages that are frequently used for data processing and analysis in MS-based metabolomics workflows, allowing the subsequent use of reproducible transformed CE-MS data in existing workflows.

AVAILABILITY AND IMPLEMENTATION

MobilityTransformR is implemented in R (Version >= 4.2) and can be downloaded directly from the Bioconductor database (https://bioconductor.org/packages/MobilityTransformR) or GitHub (https://github.com/LiesaSalzer/MobilityTransformR).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies

Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.

Synthesis, Physicochemical Characterization, and Antibacterial Performance of Silver—Lactoferrin Complexes

Antibiotic-resistant bacteria pose one of the major threats to human health worldwide. The issue is fundamental in the case of chronic wound treatment. One of the latest trends to overcome the problem is the search for new antibacterial agents based on silver. Thus, the aim of this research was to synthesize the silver-lactoferrin complex as a new generation of substances for the treatment of infected wounds. Moreover, one of the tasks was to investigate the formation mechanisms of the respective complexes and the influence of different synthesis conditions on the features of final product. The batch-sorption study was performed by applying the Langmuir and Freundlich isotherm models for the process description. Characterization of the complexes was carried out by spectroscopy, spectrometry, and separation techniques, as well as with electron microscopy. Additionally, the biological properties of the complex were evaluated, i.e., the antibacterial activity against selected bacteria and the impact on L929 cell-line viability. The results indicate the formation of a heterogeneous silver–lactoferrin complex that comprises silver nanoparticles. The complex has higher antibacterial strength than both native bovine lactoferrin and Ag⁺, while being comparable to silver toxicity.

Dihydrogen phosphate anion boosts the detection of sugars in electrospray ionization mass spectrometry: A combined experimental and computational investigation

RATIONALE

Sugars are key molecules of life but challenging to detect via electrospray ionization mass spectrometry (ESI-MS). Unfortunately, sugars are challenging analytes for mass spectrometric methods due to their high gas-phase deprotonation energies and low gas-phase proton affinities which make them difficult to ionize in high abundance for MS detection.

METHODS

Hydrogen-bond interactions in H₂ PO₄ ^- -saccharide anionic systems were studied both experimentally (via electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry, ESI-FT-ICR-MS) and computationally by several sophisticated density-functional theoretical methods (DFT and DFT-D3).

RESULTS

The H₂ PO₄ ^- dopant boosts the detection of sugars up to 51-times in the case of sucrose and up to 263-times for glucose (at 0.1 ppm concentration level). H₂ PO₄ ^- binds toward sugar molecules with noticeably more hydrogen bonds than the established dopant chloride Cl^- does, with increasing binding energies in the order: Monosaccharides < Trisaccharides < Disaccharides. Analysis of a complex oak plant sample revealed that NH₄ H₂ PO₄ specifically labeled a diverse set of sugar-type plant metabolites in the form of [M + H₂ PO₄ ]^- complexes.

CONCLUSIONS

We reveal the mechanism of interaction of H₂ PO₄ ^- with different sugars and glycosylated organic compounds, which significantly enhances their ionization in mass spectrometry. A computational and experimental investigation is presented. A strong correlation between the MS signal intensities of detected [M + H₂ PO₄ ]^- anions of different saccharides and their calculated dissociation enthalpies was revealed. Thus, the variation in MS signal intensities can be very well described to a large extent by the variation in calculated saccharide affinities toward the H₂ PO₄ ^- dopant anion, showing that DFT-D3 can very well describe experimental FT-ICR-MS observations.

Open Search of Peptide Glycation Products from Tandem Mass Spectra

Identification of chemically modified peptides in mass spectrometry (MS)-based glycation studies is a crucial yet challenging task. There is a need to establish a mode for matching tandem mass spectrometry (MS/MS) data, allowing for both known and unknown peptide glycation modifications. We present an open search approach that uses classic and modified peptide fragment ions. The latter are shifted by the mass delta of the modification. Both provide key structural information that can be used to assess the peptide core structure of the glycation product. We also leverage redundant neutral losses from the modification side chain, introducing a third ion class for matching referred to as characteristic fragment ions. We demonstrate that peptide glycation product MS/MS spectra contain multidimensional information and that most often, more than half of the spectral information is ignored if no attempt is made to use a multi-step matching algorithm. Compared to regular and/or modified peptide ion matching, our triple-ion strategy significantly increased the median interpretable fraction of the glycation product MS/MS spectra. For reference, we apply our approach for Amadori product characterization and identify all established diagnostic ions automatically. We further show how this method effectively applies the open search concept and allows for optimized elucidation of unknown structures by presenting two hitherto undescribed peptide glycation modifications with a delta mass of 102.0311 and 268.1768 Da. We characterize their fragmentation signature by integration with isotopically labeled glycation products, which provides high validity for non-targeted structure identification.

Feature Selection Pipelines with Classification for Non-targeted Metabolomics Combining the Neural Network and Genetic Algorithm

Non-targeted metabolomics via high-resolution mass spectrometry methods, such as direct infusion Fourier transform-ion cyclotron resonance mass spectrometry (DI-FT-ICR MS), produces data sets with thousands of features. By contrast, the number of samples is in general substantially lower. This disparity presents challenges when analyzing non-targeted metabolomics data sets and often requires custom methods to uncover information not always accessible via classical statistical techniques. In this work, we present a pipeline that combines a convolutional neural network with traditional statistical approaches and an adaptation of a genetic algorithm. The developed method was applied to a lifestyle intervention cohort data set, where subjects at risk of type 2 diabetes underwent an oral glucose tolerance test. Feature selection is the final result of the pipeline, achieved through classification of the data set via a neural network, with a precision-recall score of over 0.9 on the test set. The features most relevant for the described classification were then chosen via a genetic algorithm. The output of the developed pipeline encompasses approximately 200 features with high predictive scores, providing a fingerprint of the metabolic changes in the prediabetic class on the data set. Our framework presents a new approach which allows to apply complex modeling based on convolutional neural networks for the analysis of high-resolution mass spectrometric data.

Microbial Interactions in Kombucha through the Lens of Metabolomics

Kombucha is a fermented beverage obtained through the activity of a complex microbial community of yeasts and bacteria. Exo-metabolomes of kombucha microorganisms were analyzed using FT-ICR-MS to investigate their interactions. A simplified set of microorganisms including two yeasts (Brettanomyces bruxellensis and Hanseniaspora valbyensis) and one acetic acid bacterium (Acetobacter indonesiensis) was used to investigate yeast–yeast and yeast–acetic acid bacterium interactions. A yeast–yeast interaction was characterized by the release and consumption of fatty acids and peptides, possibly in relationship to commensalism. A yeast–acetic acid bacterium interaction was different depending on yeast species. With B. bruxellensis, fatty acids and peptides were mainly produced along with consumption of sucrose, fatty acids and polysaccharides. In opposition, the presence of H. valbyensis induced mainly the decrease of polyphenols, peptides, fatty acids, phenolic acids and putative isopropyl malate and phenylpyruvate and few formulae have been produced. With all three microorganisms, the formulae involved with the yeast–yeast interactions were consumed or not produced in the presence of A. indonesiensis. The impact of the yeasts’ presence on A. indonesiensis was consistent regardless of the yeast species with a commensal consumption of compounds associated to the acetic acid bacterium by yeasts. In detail, hydroxystearate from yeasts and dehydroquinate from A. indonesiensis were potentially consumed in all cases of yeast(s)–acetic acid bacterium pairing, highlighting mutualistic behavior.

Bezafibrate Reduces Elevated Hepatic Fumarate in Insulin-Deficient Mice

Glucotoxic metabolites and pathways play a crucial role in diabetic complications, and new treatment options which improve glucotoxicity are highly warranted. In this study, we analyzed bezafibrate (BEZ) treated, streptozotocin (STZ) injected mice, which showed an improved glucose metabolism compared to untreated STZ animals. In order to identify key molecules and pathways which participate in the beneficial effects of BEZ, we studied plasma, skeletal muscle, white adipose tissue (WAT) and liver samples using non-targeted metabolomics (NMR spectroscopy), targeted metabolomics (mass spectrometry), microarrays and mitochondrial enzyme activity measurements, with a particular focus on the liver. The analysis of muscle and WAT demonstrated that STZ treatment elevated inflammatory pathways and reduced insulin signaling and lipid pathways, whereas BEZ decreased inflammatory pathways and increased insulin signaling and lipid pathways, which can partly explain the beneficial effects of BEZ on glucose metabolism. Furthermore, lysophosphatidylcholine levels were lower in the liver and skeletal muscle of STZ mice, which were reverted in BEZ-treated animals. BEZ also improved circulating and hepatic glucose levels as well as lipid profiles. In the liver, BEZ treatment reduced elevated fumarate levels in STZ mice, which was probably due to a decreased expression of urea cycle genes. Since fumarate has been shown to participate in glucotoxic pathways, our data suggests that BEZ treatment attenuates the urea cycle in the liver, decreases fumarate levels and, in turn, ameliorates glucotoxicity and reduces insulin resistance in STZ mice.

Mycorrhiza-Tree-Herbivore Interactions: Alterations in Poplar Metabolome and Volatilome

Plants are continuously interacting with other organisms to optimize their performance in a changing environment. Mycorrhization is known to affect the plant growth and nutrient status, but it also can lead to adjusted plant defense and alter interactions with other trophic levels. Here, we studied the effect of Laccaria bicolor-mycorrhization on the poplar (Populus x canescens) metabolome and volatilome on trees with and without a poplar leaf beetle (Chrysomela populi) infestation. We analyzed the leaf and root metabolomes employing liquid chromatography–mass spectrometry, and the leaf volatilome employing headspace sorptive extraction combined with gas-chromatography–mass spectrometry. Mycorrhization caused distinct metabolic adjustments in roots, young/infested leaves and old/not directly infested leaves. Mycorrhization adjusted the lipid composition, the abundance of peptides and, especially upon herbivory, the level of various phenolic compounds. The greatest change in leaf volatile organic compound (VOC) emissions occurred four to eight days following the beetle infestation. Together, these results prove that mycorrhization affects the whole plant metabolome and may influence poplar aboveground interactions. The herbivores and the mycorrhizal fungi interact with each other indirectly through a common host plant, a result that emphasizes the importance of community approach in chemical ecology.