ObjectivesGenome‐wide association studies (GWAS) have become increasingly popular to identify associations between single nucleotide polymorphisms (SNPs) and phenotypic traits. The GWAS method is commonly applied within the social sciences. However, statistical analyses will need to be carefully conducted and the use of dedicated genetics software will be required. This tutorial aims to provide a guideline for conducting genetic analyses.MethodsWe discuss and explain key concepts and illustrate how to conduct GWAS using example scripts provided through GitHub (https://github.com/MareesAT/GWA_tutorial/ ).In addition to the illustration of standard GWAS, we will also show how to apply polygenic risk score (PRS) analysis. PRS does not aim to identify individual SNPs but aggregates information from SNPs across the genome in order to provide individual‐level scores of genetic risk.ResultsThe simulated data and scripts that will be illustrated in the current tutorial provide hands‐on practice with genetic analyses. The scripts are based on PLINK, PRSice, and R, which are commonly used, freely available software tools that are accessible for novice users.ConclusionsBy providing theoretical background and hands‐on experience, we aim to make GWAS more accessible to researchers without formal training in the field.

No abstract

1 Little is known about the cellular effects induced by 3,4-methylenedioxymethamphetamine (MDMA, ecstasy), although changes in gene expression have been observed following treatments with other psychostimulants. Thus, the aim of this study was to investigate in mice, the relationships between the ras-dependent protein kinase ERK and MDMA-induced reinforcement using the conditioned place preference (CPP) and locomotor activity measurements. This was completed using real-time quantitative PCR method by a study of immediate early-genes (IEGs) transcription known to be involved in neuronal plasticity. 2 A significant CPP was observed after repeated MDMA treatment in CD-1 mice at a dose of 9 mg kg À1 i.p. but not at 3 and 6 mg kg À1 . This rewarding effect was abolished by the selective inhibitor of ERK activation, SL327 (50 mg kg À1 ; i.p.). Similar results were obtained on MDMA-induced locomotor activity, clearly suggesting a role of ERK pathway in these behavioral responses.3 Following acute i.p. injection, MDMA induced a strong c-fos transcription in brain structures, such as caudate putamen, nucleus accumbens and hippocampus, whereas egr-1 and egr-3 transcripts were only increased in the caudate putamen. MDMA-induced IEGs transcription was selectively suppressed by SL327 in the caudate putamen, suggesting a role for other signaling pathways in regulation of IEGs transcription in the other brain structures. In agreement with these results, MDMA-induced c-fos protein expression was blocked by SL327 in the caudate putamen. 4 This study confirms and extends to mice the reported role of ERK pathway in the development of addiction-like properties of MDMA. This could facilitate studies about the molecular mechanism of this process by using mutant mice.

The molecular components ensuring the strict exopeptidase action of aminopeptidase N (APN) and related zinc aminopeptidases of the M1 family have not yet been clearly established. The specific recognition of the N-terminal amino acid of the substrates by the enzymes has been proposed to involve either the complexation of the free amino group by the catalytic zinc ion or an interaction with an anionic binding site, which could be constituted by an aspartate or glutamate residue. To investigate the existence of such an ionic binding site, site-directed mutagenesis experiments have been performed on acidic residues of pig APN. Given that aminopeptidases of the M1 family are likely to have a common mechanism of action, only strictly conserved residues were mutated. As compared to the wild-type enzyme, the mutation D220E led only to slight modifications in the kinetic parameters of the enzyme and in the Ki values of various inhibitors, indicating that this residue is not critically involved in the hydrolytic mechanism. In contrast, the mutations E350Q and E350D induced a large decrease in enzyme activity, essentially due to modifications in kcat, whereas the E350A mutation led to an almost completely inactive enzyme. Moreover, among the inhibitors tested, only those acting as transition state analogs showed significant increases in their Ki values. These data are in favor of E350 belonging to the "anionic binding site" in APN. A mechanism of action, derived from that of thermolysin, is proposed for these aminopeptidases, which explains the importance of E350 in transition state formation, rather than in the Michaelis complex.

Morphine is well tolerated but addictive, especially for heroin consumers, as heroin is rapidly metabolised to morphine in humans. The hypothesis that psychostimulant drugs, like morphine and/or its withdrawal may cause severe stress that could affect the properties of the blood-brain barrier (BBB) by modifying BBB constitutive markers has been poorly investigated. A recent study has shown that the integrity of the BBB of rats chronically given morphine is altered from 1 day after the last morphine dose, which would be related to the morphine-induced withdrawal syndrome (Sharma and Ali 2006) Abbreviations used: ABC, ATP-binding cassette; BBB, blood-brain barrier; BSA, bovine serum albumin; GFAP, glial fibrillary acidic protein; HIP, hippocampus; Mdr, multidrug resistance; Mrp, multidrug resistance-associated protein; NA, nucleus accumbens; PB, phosphate buffer; PBS, phosphate-buffered saline; P-gp, P-glycoprotein; qRT-PCR, quantitative RT-PCR; RT, room temperature; ZO, zonula occludens. AbstractMorphine may affect the properties of the blood-brain barrier (BBB) by modifying the expression of certain BBB markers. We have determined the effect of chronic morphine treatment on the expression and function of some BBB markers in the rat. The mRNAs of 19 selected genes encoding caveolins, endothelial transporters, receptors and tight junctions proteins in the total RNA of isolated cortex microvessels were assayed by quantitative RT-PCR (qRT-PCR). The expression of genes Mdr1a, Mrp1, Bcrp, Glut-1 and Occludin, was slightly increased, while that of Flk-1 was decreased in microvessels from morphine-treated rats. The expression of the Mrd1a and Mdr1b genes encoding the P-glycoprotein (P-gp) also increased in the whole hippocampus and cortex of morphinetreated rats. The Mdr1a gene induction (1.38-fold) observed by qRT-PCR was also confirmed using in situ hybridization technique (1.40-fold). Immunoblotting revealed an increase in P-gp expression in the hippocampus (1.8-fold) and cortex (1.36-fold) of morphine-treated rats, but no effect in isolated microvessels. In contrast, morphine treatment increased by 1.48-fold the expression of P-gp in a large vessel-enriched fraction. The integrity of the BBB, measured by in situ brain perfusion of [ 14 C]-sucrose, and the activity of P-gp at the BBB, measured with the P-gp substrate [ 3 H]-colchicine, were not modified by morphine. Immunohistofluorescence experiments revealed that P-gp expression is restricted to large vessels and microvessels in control rats and that morphine treatment did not induce the expression of P-gp in the brain parenchyma (astrocytes or neurons). Taken together, our results showed that chronic morphine treatment does not significantly alter BBB integrity or P-gp activity. The impact of morphine-mediated P-gp induction observed in large vessels remains to be determined in terms of brain disposition of drugs that are P-gp substrates.

This is an open access article under the terms of the Creat ive Commo ns Attri butio n-NonCo mmerc ial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

No abstract

No abstract