Introducing "Identification Probability" for Automated and Transferable Assessment of Metabolite Identification Confidence in Metabolomics and Related Studies.

Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence─the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies.

Mammalian hydroxylation of microbiome-derived obesogen, delta-valerobetaine, to homocarnitine, a 5-carbon carnitine analogue.

The recently discovered microbiome-generated obesogen, δ-valerobetaine (5-(trimethylammonio)pentanoate), is a 5-carbon structural analogue of the carnitine precursor, γ-butyrobetaine. Here, we report that δ-valerobetaine is enzymatically hydroxylated by mammalian γ-butyrobetaine dioxygenase (BBOX) to form 3-hydroxy-5-(trimethylammonio)pentanoate, a 5-carbon analogue of carnitine, which we term homocarnitine. Homocarnitine production by human liver extracts depends upon the required BBOX cofactors, 2-oxoglutarate, Fe, and ascorbate.

Introducing 'identification probability' for automated and transferable assessment of metabolite identification confidence in metabolomics and related studies.

Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence - the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies.

Shining a Light on Inflammation as a Critical Modulator of Drug Metabolism.

Since his graduate studies on alcohol induction of a novel cytochrome P450 (P450) enzyme, through his postdoctoral work on hormonal regulation of sexually differentiated cytochrome P450s (P450s), the author has maintained an interest in the regulation of drug metabolizing enzymes. This article is a recounting of his scientific career and focuses on his laboratory's work on inflammatory regulation of P450 enzymes that formed the basis for the Bernard B. Brodie Award.

Acetabular Wall Weakening in Total Hip Arthroplasty: A Pilot Study.

Total hip arthroplasty is a widely performed operation allowing disabled patients to improve their quality of life to a degree greater than any other elective procedure. Planning for a THA requires adequate patient assessment and preoperative characterizations of acetabular bone loss via radiographs and specific classification schemes. Some surgeons may be inclined to ream at a larger diameter thinking it would lead to a more stable press-fit, but this could be detrimental to the acetabular wall, leading to intraoperative fracture.

Community evaluation of forest and REDD+ governance quality in the Democratic Republic of the Congo.

The Democratic Republic of Congo (DRC) has over 100 million Ha of forest and has significant potential to benefit from these forests, including through REDD+ if they are managed effectively. Effective governance of forest landscapes is essential for environmental management and equitable harnessing of ecosystem service benefits for communities. Poor governance, political instability, and capacity limitations in the DRC are widely highlighted.

The Evolution of : A Perspective From the Editors.

This article was solicited to commemorate the 50th anniversary of and features perspectives from five former editors spanning the years 1994 to 2020. During that time frame the journal underwent significant changes in manuscript submission and processing as well as multiple generational changes in the composition of the editorial board and associate editors. A constant, however, has been the commitment to be the premier journal for publications of articles in the areas of drug metabolism, absorption, distribution, excretion, and pharmacokinetics.

High-Throughput Production of Diverse Xenobiotic Metabolites with Cytochrome P450-Transduced Huh7 Hepatoma Cell Lines.

Precision medicine and exposomics require methods to assess xenobiotic metabolism in human metabolomic analyses, including the identification of known and undocumented drug and chemical exposures as well as their metabolites. Recent work demonstrated the use of high-throughput generation of xenobiotic metabolites with human liver S-9 fractions for their detection in human plasma and urine. Here, we tested whether a panel of lentivirally transduced human hepatoma cell lines (Huh7) that express individual cytochrome P450 (P450) enzymes could be used to generate P450-specific metabolites in a high-throughput manner, while simultaneously identifying the enzymes responsible.

GJ 367b: A dense, ultrashort-period sub-Earth planet transiting a nearby red dwarf star.

Ultrashort-period (USP) exoplanets have orbital periods shorter than 1 day. Precise masses and radii of USP exoplanets could provide constraints on their unknown formation and evolution processes. We report the detection and characterization of the USP planet GJ 367b using high-precision photometry and radial velocity observations.

Large scale enzyme based xenobiotic identification for exposomics.

Advances in genomics have revealed many of the genetic underpinnings of human disease, but exposomics methods are currently inadequate to obtain a similar level of understanding of environmental contributions to human disease. Exposomics methods are limited by low abundance of xenobiotic metabolites and lack of authentic standards, which precludes identification using solely mass spectrometry-based criteria. Here, we develop and validate a method for enzymatic generation of xenobiotic metabolites for use with high-resolution mass spectrometry (HRMS) for chemical identification.

Regulation of cytochrome P450 enzyme activity and expression by nitric oxide in the context of inflammatory disease.

Many hepatic cytochrome P450 enzymes and their associated drug metabolizing activities are down-regulated in disease states, and much of this has been associated with inflammatory cytokines and their signaling pathways. One such pathway is the induction of inducible nitric oxide synthase (NOS2) and generation of nitric oxide (NO) in many tissues and cells including the liver and hepatocytes. Experiments in the 1990s demonstrated that NO could bind to and inhibit P450 enzymes, and suggested that inhibition of NOS could attenuate, and NO generation could mimic, the down-regulation by inflammatory stimuli of not only P450 catalytic activities but also of mRNA expression and protein levels of certain P450 enzymes.

Tyrosine Nitration Contributes to Nitric Oxide-Stimulated Degradation of CYP2B6.

Human cytochrome P450 (P450) CYP2B6 undergoes nitric oxide (NO)-dependent proteasomal degradation in response to the NO donor dipropylenetriamine NONOate (DPTA) and biologic NO in HeLa and HuH7 cell lines. CYP2B6 is also downregulated by NO in primary human hepatocytes. We hypothesized that NO or derivative reactive nitrogen species may generate adducts of tyrosine and/or cysteine residues, causing CYP2B6 downregulation, and selected Tyr and Cys residues for mutation based on predicted solvent accessibility.

Nitric Oxide Mediated Degradation of CYP2A6 via the Ubiquitin-Proteasome Pathway in Human Hepatoma Cells.

Several cytochrome P450 enzymes are known to be down-regulated by nitric oxide (NO). CYP2A6 is responsible for the metabolism of nicotine and several other xenobiotics, but its susceptibility to down-regulation by NO has not been reported. To address this question, we used Huh7 human hepatoma cell lines to express CYP2A6 with a C-terminal V5 tag (CYP2A6V5).

A non-lethal malarial infection results in reduced drug metabolizing enzyme expression and drug clearance in mice.

Background: Given the central importance of anti-malarial drugs in the treatment of malaria, there is a need to understand the effect of Plasmodium infection on the broad spectrum of drug metabolizing enzymes. Previous studies have shown reduced clearance of quinine, a treatment for Plasmodium infection, in individuals with malaria.

Methods: The hepatic expression of a large panel of drug metabolizing enzymes was studied in the livers of mice infected with the AS strain of Plasmodium chabaudi chabaudi, a nonlethal parasite in most strains of mice with several features that model human Plasmodium infections.

Posttranslational regulation of CYP2J2 by nitric oxide.

Nitric oxide (NO) is an essential signaling molecule in the body, regulating numerous biological processes. Beside its physiological roles, NO affects drug metabolism by modulating the activity and/or expression of cytochrome P450 enzymes. Previously, our lab showed that NO generation caused by inflammatory stimuli results in CYP2B6 degradation via the ubiquitin-proteasome pathway.

Understanding urban water performance at the city-region scale using an urban water metabolism evaluation framework.

Water sensitive interventions are being promoted to reduce the adverse impacts of urban development on natural water cycles. However it is currently difficult to know the best strategy for their implementation because current and desired urban water performance is not well quantified. This is particularly at the city-region scale, which is important for strategic urban planning.

Physiological Regulation of Drug Metabolism and Transport: Pregnancy, Microbiome, Inflammation, Infection, and Fasting.

This article is a report on a symposium entitled "Physiological Regulation of Drug Metabolism and Transport" sponsored by the American Society for Pharmacology and Experimental Therapeutics and held at the Experimental Biology 2017 meeting in Chicago, IL. The contributions of physiologic and pathophysiological regulation of drug-metabolizing enzymes and transporters to interindividual variability in drug metabolism are increasingly recognized but in many cases are not well understood. The presentations herein discuss the phenomenology, consequences, and mechanism of such regulation.

A Comparative Analysis of Climate-Risk and Extreme Event-Related Impacts on Well-Being and Health: Policy Implications.

There are various climate risks that are caused or influenced by climate change. They are known to have a wide range of physical, economic, environmental and social impacts. Apart from damages to the physical environment, many climate risks (climate variability, extreme events and climate-related hazards) are associated with a variety of impacts on human well-being, health, and life-supporting systems.

Nitric oxide stimulates cellular degradation of human CYP51A1, the highly conserved lanosterol 14α-demethylase.

Nitric oxide (NO) is known to down-regulate drug-metabolizing cytochrome P450 enzymes in an enzyme-selective manner. Ubiquitin-proteasome-dependent and -independent pathways have been reported. Here, we studied the regulation of expression of human CYP51A1, the lanosterol 14α-demethylase required for synthesis of cholesterol and other sterols in mammals, which is found in every kingdom of life.

Nitric oxide-regulated proteolysis of human CYP2B6 via the ubiquitin-proteasome system.

We showed previously that rat cytochrome P450 CYP2B1 undergoes NO-dependent proteasomal degradation in response to inflammatory stimuli, and that the related human enzyme CYP2B6 is also down-regulated by NO in primary human hepatocytes. To investigate the mechanism of CYP2B6 down-regulation, we made several cell lines (HeLa and HuH7 cells) in which native CYP2B6 or CYP2B6 with a C-terminal V5 tag (CYP2B6V5) are expressed from a lentiviral vector with a cytomegalovirus promoter. Native CYP2B6 protein was rapidly down-regulated in HeLa cells within 3h of treatment with the NO donor (Z)-1-[2-(2-Aminoethyl)-N-(2-ammonioethyl)amino]diazen-1-ium-1,2-diolate, while its mRNA level was not down-regulated.

Regulation of drug metabolism and toxicity by multiple factors of genetics, epigenetics, lncRNAs, gut microbiota, and diseases: a meeting report of the 21 International Symposium on Microsomes and Drug Oxidations (MDO).

Variations in drug metabolism may alter drug efficacy and cause toxicity; better understanding of the mechanisms and risks shall help to practice precision medicine. At the 21 International Symposium on Microsomes and Drug Oxidations held in Davis, California, USA, in October 2-6, 2016, a number of speakers reported some new findings and ongoing studies on the regulation mechanisms behind variable drug metabolism and toxicity, and discussed potential implications to personalized medications. A considerably insightful overview was provided on genetic and epigenetic regulation of gene expression involved in drug absorption, distribution, metabolism, and excretion (ADME) and drug response.

The receptor tyrosine kinase EphB2 promotes hepatic fibrosis in mice.

Unlabelled: Beyond the well-defined role of the Eph (erythropoietin-producing hepatocellular) receptor tyrosine kinases in developmental processes, cell motility, cell trafficking/adhesion, and cancer, nothing is known about their involvement in liver pathologies. During blood-stage rodent malaria infection we have found that EphB2 transcripts and proteins were up-regulated in the liver, a result likely driven by elevated surface expression on immune cells including macrophages. This was significant for malaria pathogenesis because EphB2(-/-) mice were protected from malaria-induced liver fibrosis despite having a similar liver parasite burden compared with littermate control mice.