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Clinical and Translational... Apr 2023There is increasing appreciation that small intestinal bacterial overgrowth (SIBO) drives many common gastrointestinal symptoms, including diarrhea, bloating, and... (Review)
Review
There is increasing appreciation that small intestinal bacterial overgrowth (SIBO) drives many common gastrointestinal symptoms, including diarrhea, bloating, and abdominal pain. Breath testing via measurement of exhaled hydrogen and methane gases following ingestion of a readily metabolized carbohydrate has become an important noninvasive testing paradigm to help diagnose SIBO. However, because of a number of physiological and technical considerations, how and when to use breath testing in the diagnosis of SIBO remains a nuanced clinical decision. This narrative review provides a comprehensive overview of breath testing paradigms including the indications for testing, how to administer the test, and how patient factors influence breath testing results. We also explore the performance characteristics of breath testing (sensitivity, specificity, positive and negative predictive values, likelihood ratios, and diagnostic odds ratio). Additionally, we describe complementary and alternative tests for diagnosing SIBO. We discuss applications of breath testing for research. Current estimates of SIBO prevalence among commonly encountered high-risk populations are reviewed to provide pretest probability estimates under a variety of clinical situations. Finally, we discuss how to integrate breath test performance characteristics into clinical care decisions using clinical predictors and the Fagan nomogram.
Topics: Humans; Intestine, Small; Methane; Diarrhea; Hydrogen; Breath Tests
PubMed: 36744854
DOI: 10.14309/ctg.0000000000000567 -
Science (New York, N.Y.) Mar 2020Many disease pathologies can be understood through the elucidation of localized biomolecular networks, or microenvironments. To this end, enzymatic proximity labeling...
Many disease pathologies can be understood through the elucidation of localized biomolecular networks, or microenvironments. To this end, enzymatic proximity labeling platforms are broadly applied for mapping the wider spatial relationships in subcellular architectures. However, technologies that can map microenvironments with higher precision have long been sought. Here, we describe a microenvironment-mapping platform that exploits photocatalytic carbene generation to selectively identify protein-protein interactions on cell membranes, an approach we term MicroMap (μMap). By using a photocatalyst-antibody conjugate to spatially localize carbene generation, we demonstrate selective labeling of antibody binding targets and their microenvironment protein neighbors. This technique identified the constituent proteins of the programmed-death ligand 1 (PD-L1) microenvironment in live lymphocytes and selectively labeled within an immunosynaptic junction.
Topics: B7-H1 Antigen; Catalysis; Cell Membrane; Cellular Microenvironment; Energy Transfer; Humans; Jurkat Cells; Lymphocytes; Methane; Photochemical Processes; Protein Interaction Mapping; Protein Interaction Maps; Ultraviolet Rays
PubMed: 32139536
DOI: 10.1126/science.aay4106 -
Chemical Society Reviews Mar 2021Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic... (Review)
Review
Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic methanotrophs use methane monooxygenases (MMOs) to activate methane, oxidizing it to methanol. There are two types of MMOs: a particulate, membrane-bound enzyme (pMMO) and a soluble, cytoplasmic enzyme (sMMO). The two MMOs are completely unrelated, with different architectures, metal cofactors, and mechanisms. The more prevalent of the two, pMMO, is copper-dependent, but the identity of its copper active site remains unclear. By contrast, sMMO uses a diiron active site, the catalytic cycle of which is well understood. Here we review the current state of knowledge for both MMOs, with an emphasis on recent developments and emerging hypotheses. In addition, we discuss obstacles to developing expression systems, which are needed to address outstanding questions and to facilitate future protein engineering efforts.
Topics: Bacteria; Bacterial Proteins; Catalytic Domain; Metals; Methane; Oxidation-Reduction; Oxygenases; Protein Engineering
PubMed: 33491685
DOI: 10.1039/d0cs01291b -
Mass Spectrometry Reviews Jul 2022This review is devoted to ion spectroscopy studies of complexes relevant for the understanding of methane activation with metal ions and clusters. Methane activation... (Review)
Review
This review is devoted to ion spectroscopy studies of complexes relevant for the understanding of methane activation with metal ions and clusters. Methane activation starts with the formation of a complex with a metal ion. The degree of the interaction between an intact methane molecule and the ion can be monitored by the perturbations of C-H stretch vibrations in the methane molecule. Binding mediated by the electrostatic interaction results in a η type coordination of methane. In contrast, binding governed by orbital interactions results in a η type coordination of methane. We further review the spectroscopic characterization of activation products of metal-methane reactions, such as the metal-carbene and carbyne products resulting from the interaction of selected 5d metals with methane. The focus of recent research in the field has shifted towards the investigation of interactions between methane and metal clusters. We show examples highlighting that metal clusters can be more reactive in methane activation reactions.
Topics: Ions; Mass Spectrometry; Metals; Methane; Spectrum Analysis
PubMed: 34008884
DOI: 10.1002/mas.21698 -
Microbiology and Molecular Biology... Mar 2023Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the... (Review)
Review
Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. We also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.
Topics: Humans; Archaea; Methane; Euryarchaeota; Metagenomics
PubMed: 36692297
DOI: 10.1128/mmbr.00024-22 -
Journal of Zhejiang University....Methane is the simplest hydrocarbon, consisting of one carbon atom and four hydrogen atoms. It is abundant in marsh gas, livestock rumination, and combustible ice.... (Review)
Review
Methane is the simplest hydrocarbon, consisting of one carbon atom and four hydrogen atoms. It is abundant in marsh gas, livestock rumination, and combustible ice. Little is known about the use of methane in human disease treatment. Current research indicates that methane is useful for treating several diseases including ischemia and reperfusion injury, and inflammatory diseases. The mechanisms underlying the protective effects of methane appear primarily to involve anti-oxidation, anti-inflammation, and anti-apoptosis. In this review, we describe the beneficial effects of methane on different diseases, summarize possible mechanisms by which methane may act in these conditions, and discuss the purpose of methane production in hypoxic conditions. Then we propose several promising directions for the future research.
Topics: Antioxidants; Apoptosis; Humans; Inflammation; Ischemia; Methane; Reperfusion Injury
PubMed: 32748575
DOI: 10.1631/jzus.B1900629 -
Science Advances Jan 2020Evidence is accumulating to challenge the paradigm that biogenic methanogenesis, considered a strictly anaerobic process, is exclusive to archaea. We demonstrate that...
Evidence is accumulating to challenge the paradigm that biogenic methanogenesis, considered a strictly anaerobic process, is exclusive to archaea. We demonstrate that cyanobacteria living in marine, freshwater, and terrestrial environments produce methane at substantial rates under light, dark, oxic, and anoxic conditions, linking methane production with light-driven primary productivity in a globally relevant and ancient group of photoautotrophs. Methane production, attributed to cyanobacteria using stable isotope labeling techniques, was enhanced during oxygenic photosynthesis. We suggest that the formation of methane by cyanobacteria contributes to methane accumulation in oxygen-saturated marine and limnic surface waters. In these environments, frequent cyanobacterial blooms are predicted to further increase because of global warming potentially having a direct positive feedback on climate change. We conclude that this newly identified source contributes to the current natural methane budget and most likely has been producing methane since cyanobacteria first evolved on Earth.
Topics: Cyanobacteria; Methane; Photoperiod; Soil Microbiology; Water Microbiology
PubMed: 31998836
DOI: 10.1126/sciadv.aax5343 -
Medical Gas Research 2023Methane has shown protective effects on a variety of diseases. Among these, neurological diseases have attracted much attention. However, there are many different... (Review)
Review
Methane has shown protective effects on a variety of diseases. Among these, neurological diseases have attracted much attention. However, there are many different indicators and application methods of methane in the treatment of neurological diseases. In this review, we summarize the indicators related to the protective effects of methane and evaluate the preparation and administration of methane. Thus, we hope to offer available indicators and effective ways to produce and administer methane in future research.
Topics: Methane; Nervous System Diseases; Humans
PubMed: 37077112
DOI: 10.4103/2045-9912.372663 -
Annual Review of Microbiology Sep 2022Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use... (Review)
Review
Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase complex (Mcr). Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.
Topics: Archaea; Methane; Oxidation-Reduction; Phylogeny
PubMed: 35759872
DOI: 10.1146/annurev-micro-041020-024935 -
Proceedings of the National Academy of... Aug 2022Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria...
Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic-anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, '' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox-rDsr pathway and the SI system. Strain HY1 employed the Calvin-Benson-Bassham cycle for CO fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic-anoxic interface environments.
Topics: Bacteria; Methane; Oxidation-Reduction; Proteomics; Sulfur; Thiosulfates
PubMed: 35914169
DOI: 10.1073/pnas.2114799119