Improved analytical technologies and data extraction algorithms enable detection of >10 000 reproducible signals by liquid chromatography–high-resolution mass spectrometry, creating a bottleneck in ...chemical identification. In principle, measurement of more than one million chemicals would be possible if algorithms were available to facilitate utilization of the raw mass spectrometry data, especially low-abundance metabolites. Here we describe an automated computational framework to annotate ions for possible chemical identity using a multistage clustering algorithm in which metabolic pathway associations are used along with intensity profiles, retention time characteristics, mass defect, and isotope/adduct patterns. The algorithm uses high-resolution mass spectrometry data for a series of samples with common properties and publicly available chemical, metabolic, and environmental databases to assign confidence levels to annotation results. Evaluation results show that the algorithm achieves an F1-measure of 0.8 for a data set with known targets and is more robust than previously reported results for cases when database size is much greater than the actual number of metabolites. MS/MS evaluation of a set of randomly selected 210 metabolites annotated using xMSannotator in an untargeted metabolomics human data set shows that 80% of features with high or medium confidence scores have ion dissociation patterns consistent with the xMSannotator annotation. The algorithm has been incorporated into an R package, xMSannotator, which includes utilities for querying local or online databases such as ChemSpider, KEGG, HMDB, T3DB, and LipidMaps.
Redox organization governs an underlying simplicity in living systems. Critically, redox reactions enable the essential characteristics of life: extraction of energy from the environment, use of ...energy to support metabolic and structural organization, use of dynamic redox responses to defend against environmental threats, and use of redox mechanisms to direct differentiation of cells and organ systems essential for reproduction. These processes are sustained through a redox context in which electron donor/acceptor couples are poised at substantially different steady-state redox potentials, some with relatively reducing steady states and others with relatively oxidizing steady states. Redox-sensitive thiols of the redox proteome, as well as low molecular weight redox-active molecules, are maintained individually by the kinetics of oxidation-reduction within this redox system. Recent research has revealed opposing network interactions of the metallome, redox proteome, metabolome and transcriptome, which appear to be an evolved redox response structure to maintain stability of an organism in the presence of variable oxidative environments. Considerable opportunity exists to improve human health through detailed understanding of these redox networks so that targeted interventions can be developed to support new avenues for redox medicine.
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•Opposing redox network interactions maintain stability in variable oxidative environments.•Network interactions exist for the metallome, proteome, transcriptome and metabolome.•Direct molecular antagonism can be discriminated from opposing network structures.•Diurnal redox oscillations could reflect opposing networks in redox stability.•Understanding of redox networks could support new avenues for redox medicine.
The reduction potentials (
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h) for the redox couples GSH/GSSG and cysteine/cystine (Cys/CySS) in plasma are useful indicators of systemic oxidative stress and other medically relevant physiological ...states. This article describes a sensitive method for determining plasma levels of GSH, GSSG, Cys, and CySS used to calculate the in vivo
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h values. The method uses iodoacetate to alkylate free thiols, derivatization with dansyl chloride to fluorescently tag amino groups, and HPLC and fluorescence to separate, detect, and quantify the molecules. Benefits of the method, such as sensitivity and dynamic range, are described, as are caveats, such as the importance of preventing red blood cell hemolysis and limitations in quantification of GSSG. General principles of redox chemistry and previous studies showing that the compounds are more oxidized than predicted from their standard reduction potentials are reviewed. The calculated in vivo
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h is a convenient and informative way of summarizing the redox environment of plasma and is also useful for studies of cerebrospinal fluid, lymph, bronchoalveolar lavage fluid, human biopsies, and a broad range of in vitro cell culture conditions.
Sten Orrenius, M.D., Ph.D., pioneered many areas of cellular and molecular toxicology and made seminal contributions to our knowledge of oxidative stress and glutathione (GSH) metabolism, organellar ...functions and Ca+2-dependent mechanisms of cell death, and mechanisms of apoptosis. On the occasion of his 80th birthday, we summarize current knowledge on redox biology of manganese (Mn) and its role in mechanisms of cell death. Mn is found in all organisms and has critical roles in cell survival and death mechanisms by regulating Mn-containing enzymes such as manganese superoxide dismutase (SOD2) or affecting expression and activity of caspases. Occupational exposures to Mn cause “manganism”, a Parkinson's disease-like condition of neurotoxicity, and experimental studies show that Mn exposure leads to accumulation of Mn in the brain, especially in mitochondria, and neuronal cell death occurs with features of an apoptotic mechanism. Interesting questions are why a ubiquitous metal that is essential for mitochondrial function would accumulate to excessive levels, cause increased H2O2 production and lead to cell death. Is this due to the interactions of Mn with other essential metals, such as iron, or with toxic metals, such as cadmium? Why is the Mn loading in the human brain so variable, and why is there such a narrow window between dietary adequacy and toxicity? Are non-neuronal tissues similarly vulnerable to insufficiency and excess, yet not characterized? We conclude that Mn is an important component of the redox interface between an organism and its environment and warrants detailed studies to understand the role of Mn as a mitochondrial life-death switch.
•Either insufficient or excess manganese activates mitochondria-mediated cell death.•The optimal healthy Mn exposure window is very narrow.•Mitochondrial H2O2 production depends on Mn across physiologic to toxicologic range.•Integrative omics needed to understand complex Mn interaction in cell fate.•Mn is central to redox interface between an organism and its environment.
The exposome is a complement to the genome that includes non-genetic causes of disease. Multiple definitions are available, with salient points being global inclusion of exposures and behaviors, and ...cumulative integration of associated biologic responses. As such, the concept is both refreshingly simple and dauntingly complex. This article reviews high-resolution metabolomics (HRM) as an affordable approach to routinely analyze samples for a broad spectrum of environmental chemicals and biologic responses. HRM has been successfully used in multiple exposome research paradigms and is suitable to implement in a prototype universal exposure surveillance system. Development of such a structure for systematic monitoring of environmental exposures is an important step toward sequencing the exposome because it builds upon successes of exposure science, naturally connects external exposure to body burden and partitions the exposome into workable components. Practical results would be repositories of quantitative data on chemicals according to geography and biology. This would support new opportunities for environmental health analysis and predictive modeling. Complementary approaches to hasten development of exposome theory and associated biologic response networks could include experimental studies with model systems, analysis of archival samples from longitudinal studies with outcome data and study of relatively short-lived animals, such as household pets (dogs and cats) and non-human primates (common marmoset). International investment and cooperation to sequence the human exposome will advance scientific knowledge and also provide an important foundation to control adverse environmental exposures to sustain healthy living spaces and improve prediction and management of disease.
Tissue interstitial fluid (ISF) surrounds cells and is an underutilized source of biomarkers that complements conventional sources such as blood and urine. However, ISF has received limited attention ...due largely to lack of simple collection methods. Here, we developed a minimally invasive, microneedle-based method to sample ISF from human skin that was well tolerated by participants. Using a microneedle patch to create an array of micropores in skin coupled with mild suction, we sampled ISF from 21 human participants and identified clinically relevant and sometimes distinct biomarkers in ISF when compared to companion plasma samples based on mass spectrometry analysis. Many biomarkers used in research and current clinical practice were common to ISF and plasma. Because ISF does not clot, these biomarkers could be continuously monitored in ISF similar to current continuous glucose monitors but without requiring an indwelling subcutaneous sensor. Biomarkers distinct to ISF included molecules associated with systemic and dermatological physiology, as well as exogenous compounds from environmental exposures. We also determined that pharmacokinetics of caffeine in healthy adults and pharmacodynamics of glucose in children and young adults with diabetes were similar in ISF and plasma. Overall, these studies provide a minimally invasive method to sample dermal ISF using microneedles and demonstrate human ISF as a source of biomarkers that may enable research and translation for future clinical applications.
“Sola dosis facit venenum.” These words of Paracelsus, “the dose makes the poison”, can lead to a cavalier attitude concerning potential toxicities of the vast array of low abundance environmental ...chemicals to which humans are exposed. Exposome research teaches that 80–85% of human disease is linked to environmental exposures. The human exposome is estimated to include >400,000 environmental chemicals, most of which are uncharacterized with regard to human health. In fact, mass spectrometry measures >200,000 m/z features (ions) in microliter volumes derived from human samples; most are unidentified. This crystallizes a grand challenge for chemical research in toxicology: to develop reliable and affordable analytical methods to understand health impacts of the extensive human chemical experience. To this end, there appears to be no choice but to abandon the limitations of measuring one chemical at a time. The present review looks at progress in computational metabolomics to provide probability-based annotation linking ions to known chemicals and serve as a foundation for unambiguous designation of unidentified ions for toxicologic study. We review methods to characterize ions in terms of accurate mass m/z, chromatographic retention time, correlation of adduct, isotopic and fragment forms, association with metabolic pathways and measurement of collision-induced dissociation products, collision cross section, and chirality. Such information can support a largely unambiguous system for documenting unidentified ions in environmental surveillance and human biomonitoring. Assembly of this data would provide a resource to characterize and understand health risks of the array of low-abundance chemicals to which humans are exposed.
Detection of low abundance metabolites is important for de novo mapping of metabolic pathways related to diet, microbiome or environmental exposures. Multiple algorithms are available to extract m/z ...features from liquid chromatography-mass spectral data in a conservative manner, which tends to preclude detection of low abundance chemicals and chemicals found in small subsets of samples. The present study provides software to enhance such algorithms for feature detection, quality assessment, and annotation.
xMSanalyzer is a set of utilities for automated processing of metabolomics data. The utilites can be classified into four main modules to: 1) improve feature detection for replicate analyses by systematic re-extraction with multiple parameter settings and data merger to optimize the balance between sensitivity and reliability, 2) evaluate sample quality and feature consistency, 3) detect feature overlap between datasets, and 4) characterize high-resolution m/z matches to small molecule metabolites and biological pathways using multiple chemical databases. The package was tested with plasma samples and shown to more than double the number of features extracted while improving quantitative reliability of detection. MS/MS analysis of a random subset of peaks that were exclusively detected using xMSanalyzer confirmed that the optimization scheme improves detection of real metabolites.
xMSanalyzer is a package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. The program was designed to integrate with existing packages such as apLCMS and XCMS, but the framework can also be used to enhance data extraction for other LC/MS data software.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The redox code of plants Mittler, Ron; Jones, Dean P.
Plant, cell and environment,
12/2023, Letnik:
47, Številka:
8
Journal Article
Recenzirano
Central metabolism is organised through high‐flux, Nicotinamide Adenine Dinucleotide (NAD+/NADH) and NADP+/NADPH systems operating at near equilibrium. As oxygen is indispensable for aerobic ...organisms, these systems are also linked to the levels of reactive oxygen species, such as H2O2, and through H2O2 to the regulation of macromolecular structures and activities, via kinetically controlled sulphur switches in the redox proteome. Dynamic changes in H2O2 production, scavenging and transport, associated with development, growth and responses to the environment are, therefore, linked to the redox state of the cell and regulate cellular function. These basic principles form the ‘redox code’ of cells and were first defined by D. P. Jones and H. Sies in 2015. Here, we apply these principles to plants in which recent studies have shown that they can also explain cell‐to‐cell and even plant‐to‐plant signalling processes. The redox code is, therefore, an integral part of biological systems and can be used to explain multiple processes in plants at the subcellular, cellular, tissue, whole organism and perhaps even community and ecosystem levels. As the environmental conditions on our planet are worsening due to global warming, climate change and increased pollution levels, new studies are needed applying the redox code of plants to these changes.
Summary statement
The H2O2 levels and redox state of cells are tightly linked and together regulate metabolism, development, growth and stress responses, as well as coordinate these responses between different organelles, cells, tissues, the entire organism and even different organisms living in a community.
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