Chronic cypermethrin induced toxicity and molecular fate assessment within common carp (Cyprinus carpio) using multiple biomarkers approach and its novel therapeutic detoxification.

Cypermethrin (CYP) is a chemical of emerging concern which has persistent and bioaccumulating impacts as it can be found extensively in freshwater ecosystem and agricultural products. It has exposure risk and toxic effects over human edible fish, as common carp. Four groups were designed for toxicity assessment and detoxification approach: control group (CL), CYP exposure group (CYP), CYP + 10% M. oleifera leaves and 10% M. oleifera seeds (CMO group), 10% M. oleifera leaves and 10% M. oleifera seeds (MO group). Trial period was forty days during which cohort of 240 fish in CYP and CMO group was exposed to 1/5 of 96h LC50 of CYP (0.1612 µg/L). CYP-exposed carp exhibited lower growth parameters, but carp fed with 10% M. oleifera seeds and leaves showed significant improvement in growth rate (SGR, RGR) and weight gain (WG) as compared to the control group. CYP exposure negatively affected haemato-biochemical parameters. Moreover, CYP exposure also led to oxidative stress, damaged immunological parameters, genotoxicity and histopathological damage in liver and intestinal cells. Whereas, M. oleifera supplementation has ameliorated these conditions. Thereby, supplementation with M. oleifera is potential and novel therapeutic detoxication approach for common carp and human health against persistent and bioaccumulating emerging chemicals.

Costs of molecular adaptation to the chemical exposome: a focus on xenobiotic metabolism pathways.

Organisms adapt to their environment through different pathways. In vertebrates, xenobiotics are detected, metabolized and eliminated through the inducible xenobiotic-metabolizing pathways (XMP) which can also generate reactive toxic intermediates. In this review, we will discuss the impacts of the chemical exposome complexity on the balance between detoxication and side effects. There is a large discrepancy between the limited number of proteins involved in these pathways (few dozens) and the diversity and complexity of the chemical exposome (tens of thousands of chemicals). Several XMP proteins have a low specificity which allows them to bind and/or metabolize a large number of chemicals. This leads to undesired consequences, such as cross-inhibition, inefficient metabolism, release of toxic intermediates, etc. Furthermore, several XMP proteins have endogenous functions that may be disrupted upon exposure to exogenous chemicals. The gut microbiome produces a very large number of metabolites that enter the body and are part of the chemical exposome. It can metabolize xenobiotics and either eliminate them or lead to toxic derivatives. The complex interactions between chemicals of different origins will be illustrated by the diverse roles of the aryl hydrocarbon receptor which binds and transduces the signals of a large number of xenobiotics, microbiome metabolites, dietary chemicals and endogenous compounds. This article is part of the theme issue 'Endocrine responses to environmental variation: conceptual approaches and recent developments'.

Computational Prediction of Metabolic α-Carbon Hydroxylation Potential of N-Nitrosamines: Overcoming Data Limitations for Carcinogenicity Assessment.

Recent withdrawal of several drugs from the market due to elevated levels of N-nitrosamine impurities underscores the need for computational approaches to assess the carcinogenicity risk of nitrosamines. However, current approaches are limited because robust animal carcinogenicity data are only available for a few simple nitrosamines, which do not represent the structural diversity of the many possible nitrosamine drug substance related impurities (NDSRIs). In this paper, we present a novel method that uses data on CYP-mediated metabolic hydroxylation of CH2 groups in non-nitrosamine xenobiotics to identify structural features that may also help in predicting the likelihood of metabolic α-carbon hydroxylation in N-nitrosamines. Our approach offers a new avenue for tapping into potentially large experimental data sets on xenobiotic metabolism to improve risk assessment of nitrosamines. As α-carbon hydroxylation is the crucial rate-limiting step in nitrosamine metabolic activation, identifying and quantifying the influence of various structural features on this step can provide valuable insights into their carcinogenic potential. This is especially important considering the scarce information available on factors that affect NDSRI metabolic activation. We have identified hundreds of structural features and calculated their impact on hydroxylation, a significant advancement compared to the limited findings from the small nitrosamine carcinogenicity data set. While relying solely on α-carbon hydroxylation prediction is insufficient for forecasting carcinogenic potency, the identified features can help in the selection of relevant structural analogues in read across studies and assist experts who, after considering other factors such as the reactivity of the resulting electrophilic diazonium species, can establish the acceptable intake (AI) limits for nitrosamine impurities.

Unusual Biotransformation Reactions of Drugs and Drug Candidates.

Detailed assessment of the fate of drugs in nonclinical test species and humans is essential to ensure the safety and efficacy of medicines in patients. In this context, biotransformation of drugs and drug candidates has been an area of keen interest over many decades in the pharmaceutical industry as well as academia. Although many of the enzymes and biotransformation pathways involved in the metabolism of xenobiotics and more specifically drugs have been well characterized, each drug molecule is unique and constitutes specific challenges for the biotransformation scientist. In this mini-review written for the special issue on the occasion of the 50th Anniversary celebration of Drug Metabolism and Disposition and to celebrate contributions of F. Peter Guengerich, one of the pioneers of the drug metabolism field, recently reported "unusual" biotransformation reactions are presented. Scientific and technological advances in the "toolbox" of the biotransformation scientists are summarized. As the pharmaceutical industry continues to explore therapeutic modalities different from the traditional small molecule drugs, the new challenges confronting the biotransformation scientist as well as future opportunities are discussed. SIGNIFICANCE STATEMENT: For the biotransformation scientists, it is essential to share and be aware of unexpected biotransformation reactions so that they can increase their confidence in predicting metabolites of drugs in humans to ensure the safety and efficacy of these metabolites before the medicines reach large numbers of patients. The purpose of this review is to highlight recent observations of "unusual" metabolites so that the scientists working in the area of drug metabolism can strengthen their readiness in expecting the unexpected.

Sobre dias em que me senti sem ar: desassossegos do pesquisar / On days when i felt breathless: unrest of search / Sobre días que me sentí sin aliento: disurbios de investigación

Resumo Conceitos como o de alteridade, encontro de saberes, polifasia cognitiva, o princípio de familiaridade e de representações sociais operaram na complexa tarefa de compreender como os encontros entre profissionais e usuários sustentavam e/ou transformavam as práticas de acolhimento. Entretanto, a experiência da minha pesquisa de doutorado me levou a questionar os próprios conceitos utilizados da Teoria das Representações Sociais. Ao final do ensaio, após discutir aspectos teórico-metodológicos, o princípio de familiaridade e a questão da tensão e dos afetos nas representações sociais, espero evidenciar como o movimento provocado pelo encontro com usuários e profissionais de uma Rede de Atenção Psicossocial levou-me a questionar pontos essenciais da teoria: o papel domesticador das representações, a forma ainda estática de evidenciar os fenômenos, a separação entre um sujeito que representa e o objeto representado e a dificuldade em usar suas ferramentas conceituais para acompanhar processos me fazem repensar meu lugar e minha função de pesquisador.

Abstract Concepts such as alterity, encounter of knowledge, cognitive polyphasia, the principle of familiarity and the very concept of social representations operated in the complex task of understanding how the encounters between professionals and users supported and / or transformed user embracement practices. However, the experience of my doctoral research led me to question the very concepts used in the Theory of Social Representations. At the end of the essay, after discussing theoretical and methodological aspects, the principle of familiarity and the issue of tension and affects in social representations, I hope to show how the movement caused by the encounter with users and professionals of a Psychosocial Care Network, led me to question essential points of the theory: the domesticating role of representations, the still static way of showing phenomena, the separation between a subject that represents and the object represented and the difficulty in using their conceptual tools to accompany processes makes me rethink my place and role as a researcher.

Resumen Conceptos como la alteridad, el encuentro de saberes, la polifasia cognitiva, el principio de familiaridad y el concepto mismo de representaciones sociales operaron en la compleja tarea de comprender cómo los encuentros entre profesionales y usuarios apoyaron y / o transformaron las prácticas de acogimiento. Sin embargo, la experiencia de mi investigación doctoral me llevó a cuestionar los propios conceptos utilizados en la Teoría de las Representaciones Sociales. Al final del ensayo, después de discutir aspectos teóricos y metodológicos, el principio de familiaridad y el tema de tensión y afectos en las representaciones sociales, Espero mostrar cómo el movimiento provocado por el encuentro con usuarios y profesionales de una Red de Atención Psicosocial, me llevó a cuestionar puntos esenciales de la teoría: el rol domesticador de las representaciones, la forma todavía estática de mostrar los fenómenos, la separación entre un sujeto que representa y el objeto representado y la dificultad para utilizar sus herramientas conceptuales para acompañar procesos, me hace repensar mi lugar y rol como investigador.

A novel machine learning-based approach for the computational functional assessment of pharmacogenomic variants.

BACKGROUND: The field of pharmacogenomics focuses on the way a person's genome affects his or her response to a certain dose of a specified medication. The main aim is to utilize this information to guide and personalize the treatment in a way that maximizes the clinical benefits and minimizes the risks for the patients, thus fulfilling the promises of personalized medicine. Technological advances in genome sequencing, combined with the development of improved computational methods for the efficient analysis of the huge amount of generated data, have allowed the fast and inexpensive sequencing of a patient's genome, hence rendering its incorporation into clinical routine practice a realistic possibility. METHODS: This study exploited thoroughly characterized in functional level SNVs within genes involved in drug metabolism and transport, to train a classifier that would categorize novel variants according to their expected effect on protein functionality. This categorization is based on the available in silico prediction and/or conservation scores, which are selected with the use of recursive feature elimination process. Toward this end, information regarding 190 pharmacovariants was leveraged, alongside with 4 machine learning algorithms, namely AdaBoost, XGBoost, multinomial logistic regression, and random forest, of which the performance was assessed through 5-fold cross validation. RESULTS: All models achieved similar performance toward making informed conclusions, with RF model achieving the highest accuracy (85%, 95% CI: 0.79, 0.90), as well as improved overall performance (precision 85%, sensitivity 84%, specificity 94%) and being used for subsequent analyses. When applied on real world WGS data, the selected RF model identified 2 missense variants, expected to lead to decreased function proteins and 1 to increased. As expected, a greater number of variants were highlighted when the approach was used on NGS data derived from targeted resequencing of coding regions. Specifically, 71 variants (out of 156 with sufficient annotation information) were classified as to "Decreased function," 41 variants as "No" function proteins, and 1 variant in "Increased function." CONCLUSION: Overall, the proposed RF-based classification model holds promise to lead to an extremely useful variant prioritization and act as a scoring tool with interesting clinical applications in the fields of pharmacogenomics and personalized medicine.

Midgut transcriptome assessment of the cockroach-hunting wasp Ampulex compressa (Apoidea: Ampulicidae).

The emerald jewel wasp Ampulex compressa (Hymenoptera: Ampulicidae) is a solitary wasp that is widely known for its specialized hunting of cockroaches as larvae provision. Adult wasps mainly feed on pollen and nectar, while their larvae feed on the cockroachs' body, first as ecto- and later as endoparsitoids. Little is known about the expression of digestive, detoxification and stress-response-related genes in the midgut of A. compressa, or about its transcriptional versatility between life stages. To identify gut-biased genes related to digestion, detoxification, and stress response, we explored the midgut transcriptome of lab-reared A. compressa, for both adults and larvae, by focusing on the top 100 significantly up- and down-regulated genes. From the top 100 significantly differentially expressed genes (DEGs), we identified 39 and 36 DEGs putatively related to digestion and detoxification in the adult wasps and larvae, respectively. The two carbohydrases alpha-glucosidase (containing an alpha-amylase domain) and glycosyl hydrolase family 31, as well as the two proteinases chymotrypsin and trypsin, revealed the highest gene diversity. We identified six significant DEGs related to detoxification, which comprise glutathione S-transferase, cytochrome P450s and UDP-glucuronosyltransferase. The gene expression levels that were significantly expressed in both life stages vary strongly between life stages, as found in genes encoding for chymotrypsin and trypsin or glycosyl hydrolases family 31. The number of genes related to alpha-glucosidase, glycosyl hydrolase family 31, and cytochrome P450s was found to be similar across nine reference hymenopteran species, except for the identified glycosyl hydrolase family 31 gene, which was absent in all reference bee species. Phylogenetic analyses of the latter candidate genes revealed that they cluster together with their homologous genes found in the reference hymenopteran species. These identified candidate genes provide a basis for future comparative genomic and proteomic studies on (ontogenetic) dietary transitions in Hymenoptera.

Recent advances in computational metabolite structure predictions and altered metabolic pathways assessment to inform drug development processes.

Many drug candidates fail during preclinical and clinical trials due to variable or unexpected metabolism which may lead to variability in drug efficacy or adverse drug reactions. The drug metabolism field aims to address this important issue from many angles which range from the study of drug-drug interactions, pharmacogenomics, computational metabolic modeling, and others. This manuscript aims to provide brief but comprehensive manuscript summaries highlighting the conclusions and scientific importance of seven exceptional manuscripts published in recent years within the field of drug metabolism. Two main topics within the field are reviewed: novel computational metabolic modeling approaches which provide complex outputs beyond site of metabolism predictions, and experimental approaches designed to discern the impacts of interindividual variability and species differences on drug metabolism. The computational approaches discussed provide novel outputs in metabolite structure and formation likelihood and/or extend beyond the saturated field of drug phase I metabolism, while the experimental metabolic pathways assessments aim to highlight the impacts of genetic polymorphisms and clinical animal model metabolic differences on human metabolism and subsequent health outcomes.

Mycotoxins: Biotransformation and Bioavailability Assessment Using Caco-2 Cell Monolayer.

The determination of mycotoxins content in food is not sufficient for the prediction of their potential in vivo cytotoxicity because it does not reflect their bioavailability and mutual interactions within complex matrices, which may significantly alter the toxic effects. Moreover, many mycotoxins undergo biotransformation and metabolization during the intestinal absorption process. Biotransformation is predominantly the conversion of mycotoxins meditated by cytochrome P450 and other enzymes. This should transform the toxins to nontoxic metabolites but it may possibly result in unexpectedly high toxicity. Therefore, the verification of biotransformation and bioavailability provides valuable information to correctly interpret occurrence data and biomonitoring results. Among all of the methods available, the in vitro models using monolayer formed by epithelial cells from the human colon (Caco-2 cell) have been extensively used for evaluating the permeability, bioavailability, intestinal transport, and metabolism of toxic and biologically active compounds. Here, the strengths and limitations of both in vivo and in vitro techniques used to determine bioavailability are reviewed, along with current detailed data about biotransformation of mycotoxins. Furthermore, the molecular mechanism of mycotoxin effects is also discussed regarding the disorder of intestinal barrier integrity induced by mycotoxins.

In vivo assessment of the protection conferred by ß-glucans from Pleurotus ostreatus against the harmful effects of acrylamide intake (Part I).

INTRODUCTION: Introduction: acrylamide is formed in food through Maillard's reaction during thermal processing, and has been shown to be neurotoxic in humans, and a possible carcinogen. Studies have shown that ß-glucans from Pleurotus ostreatus have diverse biological properties such as antioxidant and anticancer activities. Objective: the aim of this work was to evaluate the protective effect of ß-glucans from Pleurotus ostreatus against the harmful effects of acrylamide consumption in mice. Methods: ß-glucans were obtained by alkaline-acid hydrolysis of Pleurotus ostreatus, and the content was characterized by liquid chromatography. To evaluate the effect of ß-glucans on the expression of glutathione, Balb/c mice were used, and 4 test groups were established. All groups were fed normally, and the groups treated with acrylamide were administered the compound intragastrically at a concentration of 50 g/mL; ß-glucans were administered at a concentration of 50 g/mL. Results: mice exposed to acrylamide showed a marked variation in the activity of glutathione enzymes in the liver. Significant differences (p < 0.05) were only found in the expression of glutathione transferase, which was increased almost 3 times in the group treated with ß-glucans as compared with the control group, and 1.5 times as compared with the group treated with acrylamide. Conclusions: the results show that ß-glucans could act by increasing the activity of enzymes involved in xenobiotic detoxification, thus protecting the biological system against the harmful effects caused by acrylamide intake.

INTRODUCCIÓN: Introducción: la acrilamida se forma en los alimentos a través de la reacción de Maillard durante el proceso térmico, y ha demostrado ser neurotóxica en humanos y un posible carcinógeno. Algunos estudios han demostrado que los ß-glucanos de Pleurotus ostreatus tienen diversas propiedades biológicas, como actividades antioxidantes y anticancerígenas. Objetivo: el objetivo de este trabajo fue evaluar el efecto protector de los ß-glucanos de Pleurotus ostreatus contra los efectos nocivos por consumo de acrilamida en ratones (prueba in vivo). Métodos: los ß-glucanos se obtuvieron por hidrólisis ácido-alcalina de Pleurotus ostreatus y su contenido se caracterizó por cromatografía líquida. La oxidación de los lípidos se evaluó mediante el método de TBARS, y para evaluar el efecto de los ß-glucanos en la expresión de glutatión se usaron ratones Balb/c, y se establecieron 4 grupos de prueba. Todos los grupos fueron alimentados normalmente; a lo grupos tratados con acrilamida, esta se les administró intragástricamente en una concentración de 50 µg/ml, y los ß-glucanos en una concentración de 50 µg/ml. Resultados: en el presente trabajo, los ratones expuestos a acrilamida mostraron una marcada variación en la actividad de las enzimas de glutatión determinadas en el hígado. Solo se encontraron diferencias significativas (p < 0,05) en la expresión de glutatión-transferasa, que aumentó casi 3 veces en el grupo tratado con ß-glucano en comparación con el grupo de control, y 1,5 veces con respecto al grupo tratado con acrilamida. Conclusiones: los resultados muestran que los ß-glucanos podrían actuar como agentes antioxidantes que protegen el hígado contra el estrés oxidativo causado por la ingesta de acrilamida.

High-Throughput Assessment of Metabolism-Induced Toxicity of Compounds on a 384-Pillar Plate.

A variety of oxidative and conjugative enzymes are involved in the metabolism of compounds including drugs, which can be converted into toxic metabolites by Phase I drug-metabolizing enzymes (DMEs), such as the cytochromes P450 (CYP450s), and/or detoxified by Phase II DMEs, such as UDP-glucuronosyltransferases (UGTs), sulfotransferases (SULTs), and glutathione S-transferases (GSTs). Traditionally, primary hepatocytes containing a complete set of DMEs have been widely used as a gold standard to assess metabolism-induced compound toxicity. However, primary hepatocytes are expensive, have high donor variability in expression levels of DMEs, and rapidly lose liver-specific functions when the cells are maintained under standard in vitro cell culture conditions over time. To address this issue and rapidly profile metabolism-induced drug toxicity, we have developed a 384-pillar plate, which is complementary to conventional 384-well plates. In this chapter, we provide step-by-step procedures for three-dimensional (3D) cell printing on the 384-pillar plate coupled with DMEs and compounds in the 384-well plate for high-throughput assessment of metabolism-induced toxicity.

A Decade in the MIST: Learnings from Investigations of Drug Metabolites in Drug Development under the "Metabolites in Safety Testing" Regulatory Guidance.

Since the introduction of metabolites in safety testing (MIST) guidance by the Food and Drug Administration in 2008, major changes have occurred in the experimental methods for the identification and quantification of metabolites, ways to evaluate coverage of metabolites, and the timing of critical clinical and nonclinical studies to generate this information. In this cross-industry review, we discuss how the increased focus on human drug metabolites and their potential contribution to safety and drug-drug interactions has influenced the approaches taken by industry for the identification and quantitation of human drug metabolites. Before the MIST guidance was issued, the method of choice for generating comprehensive metabolite profile was radio chromatography. The MIST guidance increased the focus on human drug metabolites and their potential contribution to safety and drug-drug interactions and led to changes in the practices of drug metabolism scientists. In addition, the guidance suggested that human metabolism studies should also be accelerated, which has led to more frequent determination of human metabolite profiles from multiple ascending-dose clinical studies. Generating a comprehensive and quantitative profile of human metabolites has become a more urgent task. Together with technological advances, these events have led to a general shift of focus toward earlier human metabolism studies using high-resolution mass spectrometry and to a reduction in animal radiolabel absorption/distribution/metabolism/excretion studies. The changes induced by the MIST guidance are highlighted by six case studies included herein, reflecting different stages of implementation of the MIST guidance within the pharmaceutical industry.

The Influence of Obesity on the Pharmacokinetics of Dioxin in Mice: An Assessment Using Classical and PBPK Modeling.

The effects of body fat mass on the elimination of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) was examined in mice. When male C57BL/6J mice are fed a high-fat, simple carbohydrate diet (HFD) for 13 weeks, they develop an obese phenotype. In contrast, A/J mice fed an HFD do not become obese. After 13 weeks on a normal diet (ND) or HFD, male C57BL/6J and A/J mice received a single dose by gavage of 0.1 or 5.0 µg of 2,3,7,8-tetrachloro[1,6-3H] dibenzo-p-dioxin per kg body weight. Using classical pharmacokinetics, the blood elimination half-life of TCDD was approximately 10 and 2 times longer in the C57BL/6J on the HFD compared with the mice on the ND at 0.1 and 5.0 µg/kg doses, respectively. The diet did not increase the blood half-life of TCDD in the A/J mice, which did not get obese. Using a physiologically based pharmacokinetic model for TCDD that incorporated experimentally derived percent body fat mass and tissue partition coefficients, as well as data on hepatic sequestration, did not provide accurate predictions to the data and could not explain the increase in half-life of TCDD in the HFD groups. This work demonstrates that obesity influences the half-life of TCDD, but other undetermined factors are involved in its elimination because the increase in body fat mass, decreases in cytochrome P4501A2, and altered partition coefficients could not completely explain the prolonged half-life.

Fitness costs of infection with Serratia symbiotica are associated with greater susceptibility to insecticides in the pea aphid Acyrthosiphon pisum.

BACKGROUND: Aphids are agricultural pests that damage crops by direct feeding and by vectoring important plant viruses. Bacterial symbionts can influence aphid biology, e.g. by providing essential nutrients or facilitating adaptations to biotic and abiotic stress. RESULTS: We investigated the pea aphid (Acyrthosiphon pisum Harris) and its commonly associated secondary bacterial symbiont Serratia symbiotica to study the effect of this symbiont on host fitness and susceptibility to the insecticides imidacloprid, chlorpyrifos methyl, methomyl, cyantraniliprole and spirotetramat. There is emerging evidence that members of the genus Serratia can degrade and/or detoxify diverse insecticides. Therefore, we hypothesized that S. symbiotica may promote resistance to these artificial stress agents in aphids. Our results showed that Serratia-infected aphids were more susceptible to most of the tested insecticides than non-infected aphids. This probably reflects the severe fitness costs associated with S. symbiotica, which negatively affects development, reproduction and body weight. CONCLUSION: Our study demonstrates that S. symbiotica plays an important role in the ability of aphid hosts to tolerate insecticides. These results provide insight into the potential changes in tolerance to insecticides in the field because there is a continuous and dynamic process of symbiont acquisition and loss that may directly affect host biology. © 2018 Society of Chemical Industry.

Simultaneous Assessment In Vitro of Transporter and Metabolic Processes in Hepatic Drug Clearance: Use of a Media Loss Approach.

Hepatocyte drug depletion-time assays are well established for determination of metabolic clearance in vitro. The present study focuses on the refinement and evaluation of a "media loss" assay, an adaptation of the conventional depletion assay involving centrifugation of hepatocytes prior to sampling, allowing estimation of uptake in addition to metabolism. Using experimental procedures consistent with a high throughput, a selection of 12 compounds with a range of uptake and metabolism characteristics (atorvastatin, cerivastatin, clarithromycin, erythromycin, indinavir, pitavastatin, repaglinide, rosuvastatin, saquinavir, and valsartan, with two control compounds-midazolam and tolbutamide) were investigated in the presence and absence of the cytochrome P450 inhibitor 1-aminobenzotriazole and organic anion transporter protein inhibitor rifamycin SV in rat hepatocytes. Data were generated simultaneously for a given drug, and provided, through the use of a mechanistic cell model, clearance terms characterizing metabolism, active and passive uptake, together with intracellular binding and partitioning parameters. Results were largely consistent with the particular drug characteristics, with active uptake, passive diffusion, and metabolic clearances ranging between 0.4 and 777, 3 and 383, and 2 and 236 µl/min per milligram protein, respectively. The same experiments provided total and unbound drug cellular partition coefficients ranging between 3.8 and 254 and 2.3 and 8.3, respectively, and intracellular unbound fractions between 0.014 and 0.263. Following in vitro-in vivo extrapolation, the lowest prediction bias was noted using uptake clearance, compared with metabolic clearance or apparent clearance from the media loss assay alone. This approach allows rapid and comprehensive characterization of hepatocyte drug disposition valuable for prediction of hepatic processes in vivo.

Functional assessment of genetic variants located in the promoter of SHP1 (NR0B2).

Small heterodimer partner 1 (SHP1, NR0B2) is a member of the superfamily of nuclear receptors (NRs). Even if this orphan receptor, unlike other NRs, lacks the DNA-binding domain, it is capable of regulating transcription by repressing the activity of other NRs by direct protein-protein interaction. Accordingly, SHP1 is part of negative feedback loops of the transcriptional regulation of genes involved in drug metabolism and various metabolic pathways including bile acid and glucose homeostasis. Although it is known that several interacting partners of SHP1 also modulate its expression, there is little information about genetic variability of this regulatory mechanism. Our study aimed to identify genetic variants in the NR0B2 promoter region and to determine their impact on NR0B2 transcription. For this, DNA samples originating from 119 participants of the population-based cohort Study of Health in Pomerania were analyzed by Sanger sequencing revealing four genetic variants: NR0B2:c.-594T>C (rs71636795), NR0B2:c.-414G>C (newly identified), NR0B2:c.-423C>T (rs78182695), and NR0B2:c.-224delCTGA (rs145613139) localized in the 5' untranslated region of NR0B2. The impact of these variants on transactivation of the NR0B2 promoter by NRs known to be regulators of SHP1 expression (hepatocyte nuclear factor 4α, liver receptor homolog-1, and farnesoid X receptor) was assessed in a cell-based reporter gene assay, showing that transactivation by hepatocyte nuclear factor 4α and liver receptor homolog-1 was significantly decreased in the presence of the genetic variant NR0B2:c.-594T>C, even though this effect was cell specific. However, SHP1 mRNA expression in a small collection of human kidney samples was not affected by these genetic variants.

Generation of carbamoyl phosphate synthetase 1 reporter cell lines for the assessment of ammonia metabolism.

Both primary hepatocytes and stem cells-derived hepatocyte-like cells (HLCs) are major sources for bioartificial liver (BAL). Maintenance of hepatocellular functions and induction of functional maturity of HLCs are critical for BAL's support effect. It remains difficult to assess and improve detoxification functions inherent to hepatocytes, including ammonia clearance. Here, we aim to assess ammonia metabolism and identify ammonia detoxification enhancer by developing an imaging strategy. In hepatoma cell line HepG2, and immortalized hepatic cell line LO2, carbamoyl phosphate synthetase 1 (CPS1) gene, the first enzyme of ammonia-eliminating urea cycle, was labelled with fluorescence protein via CRISPR/Cas9 system. With the reporter-based screening approach, cellular detoxification enhancers were selected among a collection of 182 small molecules. In both CPS1 reporter cell lines, the fluorescence intensity is positively correlated with cellular CPS1 mRNA expression, ammonia elimination and secreted urea, and reflected ammonia detoxification in a dose-dependent manner. Surprisingly, high-level CPS1 reporter clones also reserved many other critical hepatocellular functions, for example albumin secretion and cytochrome 450 metabolic functions. Sodium phenylbutyrate and resveratrol were identified to enhance metabolism-related gene expression and liver-enriched transcription factors C/EBPα, HNF4α. In conclusion, the CPS1-reporter system provides an economic and effective platform for assessment of cellular metabolic function and high-throughput identification of chemical compounds that improve detoxification activities in hepatic lineage cells.

The Impact of Detoxification Costs and Predation Risk on Foraging: Implications for Mimicry Dynamics.

Prey often evolve defences to deter predators, such as noxious chemicals including toxins. Toxic species often advertise their defence to potential predators by distinctive sensory signals. Predators learn to associate toxicity with the signals of these so-called aposematic prey, and may avoid them in future. In turn, this selects for mildly toxic prey to mimic the appearance of more toxic prey. Empirical evidence shows that mimicry could be either beneficial ('Mullerian') or detrimental ('quasi-Batesian') to the highly toxic prey, but the factors determining which are unknown. Here, we use state-dependent models to explore how tri-trophic interactions could influence the evolution of prey defences. We consider how predation risk affects predators' optimal foraging strategies on aposematic prey, and explore the resultant impact this has on mimicry dynamics between unequally defended species. In addition, we also investigate how the potential energetic cost of metabolising a toxin can alter the benefits to eating toxic prey and thus impact on predators' foraging decisions. Our model predicts that both how predators perceive their own predation risk, and the cost of detoxification, can have significant, sometimes counterintuitive, effects on the foraging decisions of predators. For example, in some conditions predators should: (i) avoid prey they know to be undefended, (ii) eat more mildly toxic prey as detoxification costs increase, (iii) increase their intake of highly toxic prey as the abundance of undefended prey increases. These effects mean that the relationship between a mimic and its model can qualitatively depend on the density of alternative prey and the cost of metabolising toxins. In addition, these effects are mediated by the predators' own predation risk, which demonstrates that, higher trophic levels than previously considered can have fundamental impacts on interactions among aposematic prey species.

Carbapenem inactivation: a very affordable and highly specific method for phenotypic detection of carbapenemase-producing Pseudomonas aeruginosa isolates compared with other methods.

This investigation was undertaken to compare phenotypic and molecular methods for detection of carbapenemase-producing Pseudomonas aeruginosa. A total of 245 non-duplicated isolates of P. aeruginosa were collected from hospitalized patients. Disc diffusion method was used to identify carbapenem-resistant bacteria. Three phenotypic methods, including Modified Hodge Test (MHT), Modified Carba NP (MCNP) test and Carbapenem Inactivation Method (CIM) were used for investigation of carbapenemase production. In addition, polymerase chain reaction (PCR) was used to detect carbapenemase encoding genes. Of 245 P. aeruginosa isolates investigated, 121 isolates were carbapenem-resistant. Among carbapenem-resistant isolates, 40, 39 and 35 isolates exhibited positive results using MHT, MCNP test and CIM, respectively. PCR indicated the presence of carbapenemase genes in 35 of carbapenem-resistant isolates. MHT showed low sensitivity and specificity for carbapenemase detection among P. aeruginosa isolates in comparison to PCR. CIM was most affordable and highly specific than MCNP test compared with the molecular method.

New Arsenate Reductase Gene (arrA) PCR Primers for Diversity Assessment and Quantification in Environmental Samples.

The extent of arsenic contamination in drinking water and its potential threat to human health have resulted in considerable research interest in the microbial species responsible for arsenic reduction. The arsenate reductase gene (arrA), an important component of the microbial arsenate reduction system, has been widely used as a biomarker to study arsenate-reducing microorganisms. A new primer pair was designed and evaluated for quantitative PCR (qPCR) and high-throughput sequencing of the arrA gene, because currently available PCR primers are not suitable for these applications. The primers were evaluated in silico and empirically tested for amplification of arrA genes in clones and for amplification and high-throughput sequencing of arrA genes from soil and groundwater samples. In silico, this primer pair matched (≥90% DNA identity) 86% of arrA gene sequences from GenBank. Empirical evaluation showed successful amplification of arrA gene clones of diverse phylogenetic groups, as well as amplification and high-throughput sequencing of independent soil and groundwater samples without preenrichment, suggesting that these primers are highly specific and can amplify a broad diversity of arrA genes. The arrA gene diversity from soil and groundwater samples from the Cache Valley Basin (CVB) in Utah was greater than anticipated. We observed a significant correlation between arrA gene abundance, quantified through qPCR, and reduced arsenic (AsIII) concentrations in the groundwater samples. Furthermore, we demonstrated that these primers can be useful for studying the diversity of arsenate-reducing microbial communities and the ways in which their relative abundance in groundwater may be associated with different groundwater quality parameters. IMPORTANCE: Arsenic is a major drinking water contaminant that threatens the health of millions of people worldwide. The extent of arsenic contamination and its potential threat to human health have resulted in considerable interest in the study of microbial species responsible for the reduction of arsenic, i.e., the conversion of AsV to AsIII In this study, we developed a new primer pair to evaluate the diversity and abundance of arsenate-reducing microorganisms in soil and groundwater samples from the CVB in Utah. We observed significant arrA gene diversity in the CVB soil and groundwater samples, and arrA gene abundance was significantly correlated with the reduced arsenic (AsIII) concentrations in the groundwater samples. We think that these primers are useful for studying the ecology of arsenate-reducing microorganisms in different environments.