37 results on '"Nicolas Gilbert"'
Search Results
2. Detection, discrimination and quantification of amphetamine, cathinone and nor ‐ephedrine regioisomers using benchtop 1 H and 19 F nuclear magnetic resonance spectroscopy
- Author
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Rachel M. Brignall, David C. Williamson, Andrew Costello, Nicolas Gilbert, Armita Hayatbakhsh, Matthew C. Hulme, E. Kate Kemsley, Ryan E. Mewis, Oliver B. Sutcliffe, and Christopher J. Schofield
- Subjects
Chromatography ,Cathinone ,Chemistry ,010401 analytical chemistry ,General Chemistry ,Nuclear magnetic resonance spectroscopy ,01 natural sciences ,Methcathinone ,0104 chemical sciences ,03 medical and health sciences ,0302 clinical medicine ,Structural isomer ,Proton NMR ,medicine ,General Materials Science ,Sample preparation ,030216 legal & forensic medicine ,Ephedrine ,Amphetamine ,medicine.drug - Abstract
Amphetamine and cathinone derivatives are abused recreationally due to the sense of euphoria they provide to the user. Methodologies for the rapid detection of the drug derivative present in a seized sample, or an indication of the drug class, are beneficial to law enforcement and healthcare providers. Identifying the drug class is prudent because derivatisation of these drugs, to produce regioisomers, for example, occurs frequently to circumvent global and local drug laws. Thus, newly encountered derivatives might not be present in a spectral library. Employment of benchtop nuclear magnetic resonance (NMR) could be used to provide rapid analysis of seized samples as well as identifying the class of drug present. Discrimination of individual amphetamine-, methcathinone-, N-ethylcathinone and nor-ephedrine-derived fluorinated and methylated regioisomers is achieved herein using qualitative automated 1 H NMR analysis and compared to gas chromatography-mass spectrometry (GC-MS) data. Two seized drug samples, SS1 and SS2, were identified to contain 4-fluoroamphetamine by 1 H NMR (match score median = 0.9933) and GC-MS (RRt = 5.42-5.43 min). The amount of 4-fluoroamphetamine present was 42.8%-43.4% w/w and 48.7%-49.2% w/w for SS1 and SS2, respectively, from quantitative 19 F NMR analysis, which is in agreement with the amount determined by GC-MS (39.9%-41.4% w/w and 49.0%-49.3% w/w). The total time for the qualitative 1 H NMR and quantitative 19 F NMR analysis is ~10 min. This contrasts to ~40 min for the GC-MS method. The NMR method also benefits from minimal sample preparation. Thus, benchtop NMR affords rapid, and discriminatory, analysis of the drug present in a seized sample.
- Published
- 2021
3. Synthesis of Exo- and Endocyclic Enamides Through Copper-Catalyzed Regioselective Intramolecular N -Halovinylation
- Author
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Pierre Lambolez, Jodrey Bergeron, Benoit Daoust, Nicolas Gilbert, and Simon Ricard
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010405 organic chemistry ,Chemistry ,Intramolecular force ,Organic Chemistry ,Copper catalyzed ,Regioselectivity ,chemistry.chemical_element ,Physical and Theoretical Chemistry ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,Copper ,0104 chemical sciences - Published
- 2020
4. Hyperpolarization of Pyridyl Fentalogues by Signal Amplification By Reversible Exchange (SABRE)
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Oliver B. Sutcliffe, Lysbeth H. Antonides, Stuart K. Langley, Lindsey J. Munro, Thomas B. R. Robertson, Nicolas Gilbert, Ryan E. Mewis, and Sophie L. Benjamin
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fentalogues ,Full Paper ,010405 organic chemistry ,Chemistry ,Hydride ,General Chemistry ,Full Papers ,Hyperpolarization (biology) ,010402 general chemistry ,fentanyl ,01 natural sciences ,Medicinal chemistry ,NMR ,3. Good health ,0104 chemical sciences ,lcsh:Chemistry ,IMes ,chemistry.chemical_compound ,lcsh:QD1-999 ,hyperpolarisation ,exchange dynamics ,Signal amplification - Abstract
Fentanyl, also known as ‘jackpot’, is a synthetic opiate that is 50–100 times more potent than morphine. Clandestine laboratories produce analogues of fentanyl, known as fentalogues to circumvent legislation regarding its production. Three pyridyl fentalogues were synthesized and then hyperpolarized by signal amplification by reversible exchange (SABRE) to appraise the forensic potential of the technique. A maximum enhancement of ‐168‐fold at 1.4 T was recorded for the ortho pyridyl 1H nuclei. Studies of the activation parameters for the three fentalogues revealed that the ratio of ligand loss trans to hydride and hydride loss in the complex [Ir(IMes)(L)3(H)2]+ (IMes=1,3‐bis(2,4,6‐trimethylphenyl)imidazole‐2‐ylidene) ranged from 0.52 to 1.83. The fentalogue possessing the ratio closest to unity produced the largest enhancement subsequent to performing SABRE at earth's magnetic field. It was possible to hyperpolarize a pyridyl fentalogue selectively from a matrix that consisted largely of heroin (97 : 3 heroin:fentalogue) to validate the use of SABRE as a forensic tool., No more hiding for pyridyl fentalogues! The hyperpolarization technique SABRE (signal amplification by reversible exchange) is utilised for the successful enhancement of 1H NMR signals of pyridyl functionalised fentalogues. We further demonstrate the successful selective polarization of one the fentalogues against a strong background‐signal of heroin.
- Published
- 2019
5. Alkaline-sensitive two-pore domain potassium channels form functional heteromers in pancreatic β-cells
- Author
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Lamyaa Khoubza, Nicolas Gilbert, Eun-Jin Kim, Franck C. Chatelain, Sylvain Feliciangeli, Sophie Abelanet, Dawon Kang, Florian Lesage, and Delphine Bichet
- Subjects
Potassium Channels, Tandem Pore Domain ,Insulin-Secreting Cells ,Potassium ,Humans ,Insulin ,Alkalosis ,Cell Biology ,Hydrogen-Ion Concentration ,Molecular Biology ,Biochemistry - Abstract
Two-pore domain K
- Published
- 2022
6. Long non-coding RNA exploration for mesenchymal stem cell characterisation
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Anthony Boureux, Chloé Bessière, Marc Mathieu, Farida Djouad, Nicolas Gilbert, Sébastien Riquier, Jean-Marc Lemaitre, Thérèse Commes, Florence Ruffle, Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Malbec, Odile, and Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)
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Bioinformatics ,[SDV]Life Sciences [q-bio] ,Computational biology ,QH426-470 ,Biology ,Proteomics ,Stem cell marker ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Genetics ,Transcriptomics ,Mesenchymal stem cell ,030304 developmental biology ,0303 health sciences ,Base Sequence ,Sequence Analysis, RNA ,NGS analysis ,Computational Biology ,Mesenchymal Stem Cells ,RNAseq ,Long non-coding RNA ,Biomarker (cell) ,[SDV] Life Sciences [q-bio] ,Multipotent Stem Cell ,030220 oncology & carcinogenesis ,RNA, Long Noncoding ,DNA microarray ,TP248.13-248.65 ,Research Article ,Biotechnology - Abstract
Background The development of RNA sequencing (RNAseq) and the corresponding emergence of public datasets have created new avenues of transcriptional marker search. The long non-coding RNAs (lncRNAs) constitute an emerging class of transcripts with a potential for high tissue specificity and function. Therefore, we tested the biomarker potential of lncRNAs on Mesenchymal Stem Cells (MSCs), a complex type of adult multipotent stem cells of diverse tissue origins, that is frequently used in clinics but which is lacking extensive characterization. Results We developed a dedicated bioinformatics pipeline for the purpose of building a cell-specific catalogue of unannotated lncRNAs. The pipeline performs ab initio transcript identification, pseudoalignment and uses new methodologies such as a specific k-mer approach for naive quantification of expression in numerous RNAseq data. We next applied it on MSCs, and our pipeline was able to highlight novel lncRNAs with high cell specificity. Furthermore, with original and efficient approaches for functional prediction, we demonstrated that each candidate represents one specific state of MSCs biology. Conclusions We showed that our approach can be employed to harness lncRNAs as cell markers. More specifically, our results suggest different candidates as potential actors in MSCs biology and propose promising directions for future experimental investigations.
- Published
- 2021
7. Kmerator Suite: design of specific k-mer signatures and automatic metadata discovery in large RNA-Seq datasets
- Author
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Nicolas Gilbert, Thérèse Commes, Chloé Bessière, Anthony Boureux, Jérôme Audoux, Haoliang Xue, Benoit Guibert, Florence Ruffle, Sébastien Riquier, Anne-Laure Bougé, Daniel Gautheret, Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), SeqOne [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Saint Eloi (CHRU Montpellier), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la recherche [ANR-10-INBS-09], Canceropole Grand Ouest [2017-EM24], Region Occitanie[R19073FF], and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)
- Subjects
0303 health sciences ,Computer science ,Interface (computing) ,Suite ,Computational biology ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Metadata discovery ,Set (abstract data type) ,Metadata ,03 medical and health sciences ,Identification (information) ,0302 clinical medicine ,k-mer ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Human genome ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
The huge body of publicly available RNA-sequencing (RNA-seq) libraries is a treasure of functional information allowing to quantify the expression of known or novel transcripts in tissues. However, transcript quantification commonly relies on alignment methods requiring a lot of computational resources and processing time, which does not scale easily to large datasets. K-mer decomposition constitutes a new way to process RNA-seq data for the identification of transcriptional signatures, as k-mers can be used to quantify accurately gene expression in a less resource-consuming way. We present the Kmerator Suite, a set of three tools designed to extract specific k-mer signatures, quantify these k-mers into RNA-seq datasets and quickly visualize large dataset characteristics. The core tool, Kmerator, produces specific k-mers for 97% of human genes, enabling the measure of gene expression with high accuracy in simulated datasets. KmerExploR, a direct application of Kmerator, uses a set of predictor gene-specific k-mers to infer metadata including library protocol, sample features or contaminations from RNA-seq datasets. KmerExploR results are visualized through a user-friendly interface. Moreover, we demonstrate that the Kmerator Suite can be used for advanced queries targeting known or new biomarkers such as mutations, gene fusions or long non-coding RNAs for human health applications.
- Published
- 2021
8. Analytical determination of heroin, fentanyl and fentalogues using high-performance liquid chromatography with diode array and amperometric detection
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Christopher W. Foster, Christopher J. Schofield, Lysbeth H. Antonides, Nicolas Gilbert, Craig E. Banks, Loanda R. Cumba, Tarek S. Belal, Hadil M. Elbardisy, Hoda G. Daabees, Wael Talaat, and Oliver B. Sutcliffe
- Subjects
Drugs of abuse ,Reproducibility ,Chromatography ,Materials science ,General Chemical Engineering ,010401 analytical chemistry ,General Engineering ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,High-performance liquid chromatography ,Diode array ,Amperometry ,0104 chemical sciences ,Analytical Chemistry ,Fentanyl ,Heroin ,Benzocaine ,medicine ,0210 nano-technology ,medicine.drug - Abstract
Over recent years there has been a progressive increase in the adulteration of common illicit street drugs, such as heroin and cocaine, with fentanyl and its derivatives (fentalogues) being the cause of over doses ending with fatal repercussions. Consequently, there is a need for the development of sensitive, selective and reliable analytical protocols for their separation and quantification. Herein, we report for the first time, a combination of high-performance liquid chromatography with a dual-diode array and electrochemical (amperometric) detector achieved for the simultaneous detection and quantification of heroin (HRN), fentanyl and ten fentalogues; the amperometric detection is achieved using a commercially available impinging jet flow-cell that incorporates in-house screen-printed graphite macroelectrodes (SPEs). Both protocols are analytically compared and contrasted in terms of their experimental parameters and chromatographic conditions with the separation and quantification being optimized, with these protocols demonstrating a high sensitivity and reproducibility. The proposed methods were successfully applied for the analysis of the investigated drugs of abuse, in the presence of common adulterants (e.g. caffeine, paracetamol and benzocaine), co-formulated excipients (starch, lactose, aerosil 200, etc.) and simultaneously within seized street samples.
- Published
- 2019
9. Guilty by dissociation: Part B: evaluation of Supercritical Fluid Chromatography (SFC-UV) for the analysis of regioisomeric diphenidine-derived Novel Psychoactive Substances (NPS)
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Graeme, Cochrane, Jennifer K, Field, Matthew C, Hulme, Nicolas, Gilbert, Ryan E, Mewis, Melvin R, Euerby, and Oliver B, Sutcliffe
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Piperidines ,Clinical Biochemistry ,Drug Discovery ,Pharmaceutical Science ,Chromatography, Supercritical Fluid ,Carbon Dioxide ,Silicon Dioxide ,Spectroscopy ,RS ,Analytical Chemistry - Abstract
Supercritical Fluid Chromatography (SFC-UV) employing a carbon dioxide (CO 2) and 10 mM ammonium acetate in MeOH-water (95:5 v/v) gradient provides a rapid analysis (t G
- Published
- 2022
10. Hyperpolarisation of Mirfentanil by SABRE in the Presence of Heroin
- Author
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Nicolas Gilbert, Oliver B. Sutcliffe, Ryan E. Mewis, and Thomas B. R. Robertson
- Subjects
Magnetic Resonance Spectroscopy ,Molecular Structure ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Mirfentanil ,01 natural sciences ,Medicinal chemistry ,Atomic and Molecular Physics, and Optics ,3. Good health ,0104 chemical sciences ,Catalysis ,Signal enhancement ,IMes ,Fentanyl ,Heroin ,chemistry.chemical_compound ,chemistry ,Methanol ,Physical and Theoretical Chemistry ,0210 nano-technology ,Signal amplification ,Cyclooctadiene - Abstract
Mirfentanil, a fentanyl derivative that is a μ-opioid partial agonist, is hyperpolarised via Signal Amplification By Reversible Exchange (SABRE), a para-hydrogen-based technique. [Ir(IMes)(COD)Cl] (IMes=1,3-bis(2,4,6-trimethylphenyl)imidazole-2-ylidene, COD=cyclooctadiene) was employed as the polarisation transfer catalyst. Following polarisation transfer at 6.5 mT, the pyrazine-protons were enhanced by 78-fold (polarisation, P=0.04 %). The complex [Ir(IMes)(H) (mirfentanil) (MeOH)] is proposed to form based on the observation of two hydrides at δ −22.9 (trans to mirfentanil) and −24.7 (trans to methanol). In a mixture of mirfentanil and heroin, the former could be detected using SABRE at concentrations less than 1 % w/w. At the lowest concentration analyzed, the amount of mirfentanil present was 0.18 mg (812 μM) and produced a signal enhancement of −867-fold (P=0.42 %). following polarisation transfer at 6.5 mT. 2 2 +
- Published
- 2021
11. Author response for 'Detection, discrimination and quantification of amphetamine, cathinone and nor ‐ephedrine regioisomers using benchtop 1 H and 19 F NMR spectroscopy'
- Author
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Oliver B. Sutcliffe, Armita Hayatbakhsh, Andrew Costello, Christopher J. Schofield, Rachel M. Brignall, Nicolas Gilbert, David C. Williamson, E. Kate Kemsley, Matthew C. Hulme, and Ryan E. Mewis
- Subjects
Chromatography ,Cathinone ,Chemistry ,Structural isomer ,medicine ,Nuclear magnetic resonance spectroscopy ,Ephedrine ,Amphetamine ,medicine.drug - Published
- 2021
12. Detection, discrimination and quantification of amphetamine, cathinone and nor-ephedrine regioisomers using benchtop
- Author
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Matthew C, Hulme, Armita, Hayatbakhsh, Rachel M, Brignall, Nicolas, Gilbert, Andrew, Costello, Christopher J, Schofield, David C, Williamson, E Kate, Kemsley, Oliver B, Sutcliffe, and Ryan E, Mewis
- Abstract
Amphetamine and cathinone derivatives are abused recreationally due to the sense of euphoria they provide to the user. Methodologies for the rapid detection of the drug derivative present in a seized sample, or an indication of the drug class, are beneficial to law enforcement and healthcare providers. Identifying the drug class is prudent because derivatisation of these drugs, to produce regioisomers, for example, occurs frequently to circumvent global and local drug laws. Thus, newly encountered derivatives might not be present in a spectral library. Employment of benchtop nuclear magnetic resonance (NMR) could be used to provide rapid analysis of seized samples as well as identifying the class of drug present. Discrimination of individual amphetamine-, methcathinone-, N-ethylcathinone and nor-ephedrine-derived fluorinated and methylated regioisomers is achieved herein using qualitative automated
- Published
- 2021
13. 2C-B, or Not 2C-B, that is the Question: Development of a Multimodal Analytical Approach for the Discrimination and Quantification of 2,5-Dimethoxy-4-Bromophenethylamine and its Structural Isomer, 4,5-Dimethoxy-2-Bromophenethylamine, in Seized Samples
- Author
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Nicolas Gilbert, Elisa Santagostino, Callum A. Gater, Chris Hill, Kate E. Jones, Sacha Lord, Victoria R. Marsland, Kim A. O'Brian, Rachel A. Topping, Ryan E. Mewis, and Oliver B. Sutcliffe
- Published
- 2021
14. Kmerator Suite: design of specific
- Author
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Sébastien, Riquier, Chloé, Bessiere, Benoit, Guibert, Anne-Laure, Bouge, Anthony, Boureux, Florence, Ruffle, Jérôme, Audoux, Nicolas, Gilbert, Haoliang, Xue, Daniel, Gautheret, and Thérèse, Commes
- Subjects
AcademicSubjects/SCI01140 ,AcademicSubjects/SCI01060 ,AcademicSubjects/SCI00030 ,Methods Article ,AcademicSubjects/SCI00980 ,AcademicSubjects/SCI01180 - Abstract
The huge body of publicly available RNA-sequencing (RNA-seq) libraries is a treasure of functional information allowing to quantify the expression of known or novel transcripts in tissues. However, transcript quantification commonly relies on alignment methods requiring a lot of computational resources and processing time, which does not scale easily to large datasets. K-mer decomposition constitutes a new way to process RNA-seq data for the identification of transcriptional signatures, as k-mers can be used to quantify accurately gene expression in a less resource-consuming way. We present the Kmerator Suite, a set of three tools designed to extract specific k-mer signatures, quantify these k-mers into RNA-seq datasets and quickly visualize large dataset characteristics. The core tool, Kmerator, produces specific k-mers for 97% of human genes, enabling the measure of gene expression with high accuracy in simulated datasets. KmerExploR, a direct application of Kmerator, uses a set of predictor gene-specific k-mers to infer metadata including library protocol, sample features or contaminations from RNA-seq datasets. KmerExploR results are visualized through a user-friendly interface. Moreover, we demonstrate that the Kmerator Suite can be used for advanced queries targeting known or new biomarkers such as mutations, gene fusions or long non-coding RNAs for human health applications.
- Published
- 2020
15. 1,2-Dihaloalkenes in Metal-Catalyzed Reactions
- Author
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Nicolas Gilbert, François Ladouceur, Paméla Casault, Benoit Daoust, and Simon Ricard
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chemistry.chemical_classification ,010405 organic chemistry ,Alkene ,Organic Chemistry ,Forming processes ,010402 general chemistry ,01 natural sciences ,Combinatorial chemistry ,Catalysis ,Coupling reaction ,0104 chemical sciences ,Metal ,chemistry ,visual_art ,visual_art.visual_art_medium - Abstract
1,2-Dihaloalkenes readily undergo simultaneous or sequential difunctionalization through transition-metal-catalyzed reactions, which makes them attractive building blocks for complex unsaturated motifs. This review summarizes recent applications of such transformations in C–C and C–heteroatom bond forming processes. The facile synthesis of stereodefined alkene derivatives, as well as aromatic and heteroatomic compounds, from 1,2-dihaloalkenes is thus outlined.1 Introduction2 Synthesis of 1,2-Dihaloalkenes3 C–C Bond Forming Reactions4 C–Heteroatom Bond Forming Reactions5 Conclusion
- Published
- 2018
16. Synthesis, characterisation, detection and quantification of a novel hexyl-substituted synthetic cannabinoid receptor agonist: (S)-N-(1-amino-3,3-dimethyl-1-oxobutan-2-yl)-1-hexyl-1H-indazole-3-carboxamide (ADB-HINACA)
- Author
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Mark Knight, Andrew Costello, Michael J. Linnell, Nicolas Gilbert, Umer Khan, Ryan E. Mewis, Oliver B. Sutcliffe, Jamie R. Ellison, and Robert Ralphs
- Subjects
Indazole ,Chromatography ,medicine.drug_class ,medicine.medical_treatment ,Carboxamide ,Cannabinoid Receptor Agonists ,Mass spectrometry ,Pathology and Forensic Medicine ,Analytical Chemistry ,chemistry.chemical_compound ,chemistry ,Attenuated total reflection ,Materials Chemistry ,medicine ,Proton NMR ,Cannabinoid ,Physical and Theoretical Chemistry ,Law ,Spectroscopy ,Derivative (chemistry) - Abstract
Synthetic cannabinoid receptor agonists (SCRAs) are a continually evolving family of illicit drugs, with novel analogues frequently being detected. This paper reports the detection of a new N-hexyl-1H-indazole derivative, ADB-HINACA, within a herbal sample seized by law enforcement for the first time in the United Kingdom. The identity of the compound was confirmed via the synthesis of a pure ADB-HINACA reference standard and direct spectral comparison by 1H NMR and GC-EI-MS analysis. A full analytical profiling of ADB-HINACA by nuclear magnetic resonance (NMR), attenuated total reflection Fourier-transform infrared (FTIR) spectroscopy and gas chromatography-electron ionisation-mass spectrometry (GC-EI-MS) is reported and shows good concordance between the seized sample and the reference standard. A validated GC-EI-MS method for the routine quantification of the cannabinoid in seized samples (LOD: 1.7 μg/mL, LOQ: 5.8 μg/mL) was also developed and using this method, the seized herbal sample was determined to contain 4.9% w/w ADB-HINACA.
- Published
- 2021
17. DNA helicase RecQ1 regulates mutually exclusive expression of virulence genes in
- Author
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Zhou, Li, Shigang, Yin, Maoxin, Sun, Xiu, Cheng, Jieqiong, Wei, Nicolas, Gilbert, Jun, Miao, Liwang, Cui, Zhenghui, Huang, Xueyu, Dai, and Lubin, Jiang
- Subjects
Histones ,Gene Expression Regulation ,Heterochromatin ,Plasmodium falciparum ,DNA Helicases ,Protozoan Proteins ,Animals ,Gene Silencing ,Malaria, Falciparum ,Biological Sciences ,Chromatin Assembly and Disassembly ,Promoter Regions, Genetic ,Host-Parasite Interactions - Abstract
The Plasmodium falciparum var gene family encodes ∼60 surface antigens by which parasites escape the host immune responses via clonal expression of var genes. However, the mechanism controlling this mutual exclusivity, associated with alterations in chromatin assembly, is not understood. Here, we determined how expression of the var gene family is regulated by two RecQ DNA helicase family members, PfRecQ1 and PfWRN, in P. falciparum. Through genetic manipulation, we found that the complete var repertoire was silenced on PfRecQ1 knockout, whereas their expression did not show noticeable changes when PfWRN was knocked out. More important, mutually exclusive expression of var genes could be rescued by complementation of PfRecQ1. In addition, knocking out either of these two helicase genes changed the perinuclear cluster distribution of subtelomeres and subtelomeric var genes. Whereas deletion of PfRecQ1 increased the heterochromatin mark trimethylated (H3K9me3) at the transcription start site (TSS) of the var gene upsC1, that deletion had no effect on the global distribution of H3K9me3 over gene bodies, including those for the var genes. ChIP-seq assay showed that PfRecQ1 was enriched globally at the TSSs of all genes, whereas PfWRN-enriched regions occurred at the gene bodies of the var gene family, but not of other genes or at TSSs of all genes. On PfRecQ1 deletion, the upsC1 var gene moved from the active perinuclear transcription region to a silenced region of the upsC type. These findings imply that PfRecQ1, but not PfWRN, is essential for maintaining the clonal expression of var genes.
- Published
- 2019
18. Classification of fentanyl analogues through principal component analysis (PCA) and hierarchical clustering of GC–MS data
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Oliver B. Sutcliffe, Ryan E. Mewis, and Nicolas Gilbert
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Computer science ,business.industry ,010401 analytical chemistry ,Pattern recognition ,01 natural sciences ,0104 chemical sciences ,Pathology and Forensic Medicine ,Analytical Chemistry ,Hierarchical clustering ,03 medical and health sciences ,0302 clinical medicine ,Principal component analysis ,Materials Chemistry ,030216 legal & forensic medicine ,Artificial intelligence ,Physical and Theoretical Chemistry ,Gas chromatography–mass spectrometry ,Spectral data ,business ,Law ,Spectroscopy ,Chemical database - Abstract
The emergence of a wide variety of fentanyl analogues has become a problem for the identification of seized drug samples. While chemical databases are largely reactive to the emergence of new analogues, efforts should focus on the development of predictive models which can discern how new analogues differ from the parent drug. Principal component analysis (PCA) was performed on mass spectral data from 54 fentanyl analogues. Hierarchical clustering was used to group these analogues into meaningful classes. The model was able to classify 67 analogues not previously included in the model with high accuracy, based on the nature and position of the chemical modification.
- Published
- 2020
19. Comparison of various alkyl cyanoacrylates for fingerprint development
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Paméla Casault, Benoit Daoust, and Nicolas Gilbert
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chemistry.chemical_classification ,Methyl cyanoacrylate ,N-butyl-cyanoacrylate ,010401 analytical chemistry ,Fingerprint (computing) ,01 natural sciences ,0104 chemical sciences ,Pathology and Forensic Medicine ,Cyanoacrylates ,Ethyl cyanoacrylate ,law.invention ,2-Octyl cyanoacrylate ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,chemistry ,Cyanoacrylate ,law ,Organic chemistry ,030216 legal & forensic medicine ,Alkyl - Abstract
The ability of cyanoacrylates (CA) to develop fingerprints was first discovered in 1977. Since then, the cyanoacrylate fuming method has reached widespread use, becoming one of the primary techniqu...
- Published
- 2016
20. 9. Michel Gonneville. Pensée sérielle, écriture postmoderne (ou l’inverse)
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Nicolas Gilbert
- Published
- 2018
21. Analysis of emerging contaminants in water and solid samples using high resolution mass spectrometry with a Q Exactive orbital ion trap and estrogenic activity with YES-assay
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Nicolas Gilbert, André Lajeunesse, Mélanie Desrosiers, Salma Taktek, Éloïse Veilleux, Simon Comtois-Marotte, Sung Vo Duy, Thomas Hector Chappuis, and Sébastien Sauvé
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Environmental Engineering ,Health, Toxicology and Mutagenesis ,Saccharomyces cerevisiae ,010501 environmental sciences ,Endocrine Disruptors ,Mass spectrometry ,01 natural sciences ,Matrix (chemical analysis) ,Tandem Mass Spectrometry ,Environmental Chemistry ,Effluent ,0105 earth and related environmental sciences ,Chromatography ,Chemistry ,010401 analytical chemistry ,Extraction (chemistry) ,Solid Phase Extraction ,Public Health, Environmental and Occupational Health ,Estrogens ,General Medicine ,General Chemistry ,Pollution ,6. Clean water ,0104 chemical sciences ,Wastewater ,Environmental chemistry ,Water treatment ,Biological Assay ,Ion trap ,Surface water ,Water Pollutants, Chemical ,Chromatography, Liquid ,Environmental Monitoring - Abstract
Trace emerging contaminants (ECs) occur in both waste and surface waters that are rich in particulates that have been found to sorb several organic contaminants. An analytical method based on off-line solid-phase extraction (SPE) followed by liquid chromatography-mass spectrometry (LC-MS) analysis was developed for the detection and quantification of 31 ECs from surface water, wastewater, suspended particulate matter (SPM) as well as sediments. Lyophilized sediments and air-dried SPM were subjected to ultrasonic extraction. Water samples and extracts were then concentrated and cleaned-up by off-line SPE. Quantification was realized using a Q Exactive mass spectrometer in both full scan (FS) and MS2 modes. These two modes were optimized and compared to determine which one was the most suitable for each matrix studied. Yeast estrogen screen assay (YES-assay) adapted from the direct measurement of estrogenic activity without sample extraction was tested on filtered wastewater samples. An endocrine disrupting effect was detected in all effluent samples analyzed with estradiol equivalent concentrations ranging from 4.4 to 720 ng eq E2 L−1 for the WWTP-1 and 6.5–42 ng eq E2 L−1 for the WWTP-2. The analytical methods were also applied on six samples of surface water, the corresponding SPM, the sediments and thirty-nine effluent samples from two wastewater treatment plants (WWTPs) sampled over a period of five months (February to June 2014).
- Published
- 2016
22. Microbial diversity, tolerance, and biodegradation potential of urban wetlands with different input regimes
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Nicolas Gilbert, Roberta R. Fulthorpe, and Andrea E. Kirkwood
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Geologic Sediments ,Urban Population ,Immunology ,Wetland ,Applied Microbiology and Biotechnology ,Microbiology ,Ecosystem services ,RNA, Ribosomal, 16S ,Genetics ,Molecular Biology ,Soil Microbiology ,Urban runoff ,Ontario ,Pollutant ,geography ,geography.geographical_feature_category ,Bacteria ,Ecology ,food and beverages ,Biodiversity ,General Medicine ,Biodegradation, Environmental ,Microbial population biology ,Wetlands ,Constructed wetland ,Environmental science ,2,4-Dichlorophenoxyacetic Acid ,Chlorine Compounds ,Surface runoff ,Copper ,Water Pollutants, Chemical ,Temperature gradient gel electrophoresis - Abstract
Though microbial transformations are the primary mechanism of contaminant attenuation in wetlands, much remains to be known about microbial communities in urban wetlands. In this study, the microbial communities from urban wetlands with different runoff regimes (i.e., a contaminated remnant wetland, a constructed wetland, and a remnant wetland) were assessed for their capacity to attenuate and tolerate typical urban runoff pollutants. Results from denaturing gradient gel electrophoresis of 16S rRNA genes showed relatively high similarity in community composition among the wetlands. Community-level physiological profiles had similar results but exhibited within-site variation in both the contaminated remnant and remnant wetlands. All wetland communities were less tolerant to copper than 2,4-dichlorophenoxyacetic acid; however, the contaminated remnant wetland had the highest tolerance. All study wetlands had a limited capacity to biodegrade model chlorinated aromatic compounds (e.g., 2,4-dichlorophenoxyacetic acid and 3-chlorobenzoate). Though having different input regimes and contaminant exposure histories, the study wetlands were generally similar with respect to microbial community diversity and function. Additionally, the generally low capacity for these wetlands to biodegrade mobile chlorinated organic contaminants offers preliminary insight into the limited ecosystem services these wetlands may provide in urban environments.
- Published
- 2012
23. Une visite à l’atelier de José Evangelista
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Nicolas Gilbert
- Subjects
General Medicine - Abstract
Cet article présente une vue d’ensemble des outils et des méthodes de travail du compositeur José Evangelista. Après avoir discuté de la relation qu’entretient le compositeur avec le piano et l’ordinateur en tant qu’outils compositionnels, on examine le rôle des notes textuelles et des esquisses dans ses habitudes de travail. À l’aide d’exemples tirés des esquisses d’Alap et Gat (1998) et de Viola Song (2002), on découvre une méthode de travail où notes textuelles et esquisses musicales s’enchevêtrent et se fertilisent mutuellement. On constate également que le travail assidu du compositeur sur les procédés hétérophoniques a permis à sa méthode de travail de se développer de façon continue, sans grandes ruptures, au cours des 25 dernières années. On conclut de cet examen que, chez Evangelista, méthode de travail et esthétique constituent un tout organique à l’intérieur duquel la subjectivité du compositeur s’exprime sans entraves., This article presents an overview of the tools and working methods of composer José Evangelista. After discussing his relationship with the piano and the computer as compositional tools, we examine the role of textual notes and drafts in his working habits. On the basis of examples drawn from the drafts of Alap et Gat (1998) and Viola Song (2002), we discover a working method in which written text and musical drafts cohabitate and fertilize each other. We also note that the composer’s assiduous work on heterophonic processes allowed for a continuous evolution of his working method over the last 25 years. We conclude this examination by stating that in Evangelista’s work, working method and aesthetics constitute an organic whole within which the composer’s subjectivity expresses itself freely.
- Published
- 2008
24. Mammalian LINE‐1 Retrotransposons and Related Elements
- Author
-
Nicolas Gilbert and John V. Moran
- Subjects
Genome instability ,Genetics ,biology ,Pseudogene ,Intron ,biology.protein ,RNA ,Human genome ,Retrotransposon ,RNA polymerase II ,Gene - Abstract
This chapter emphasises on the studies that have focused on understanding the mechanism of L1 retrotransposition, which were conducted since the publication of Mobile DNA in 1989. In addition, when appropriate the similarities and differences between the retrotransposition mechanisms of long interspersed nuclear elements (LINE-1s or L1s), closely related L1-like elements, and more distantly related non-LTR retrotransposons, are discussed. The majority of Cin4 elements are variably 5’ truncated, rearranged, or mutated. The basic structural features of these nonautonomous retrotransposons are introduced in the chapter. The cultured cell assay also has yielded unexpected information about L1 retrotransposition. First, in cultured cells, 5 to 10% of new L1 retrotransposition events occurs into the introns of actively transcribed genes. Second, because L1s can be considered processed pseudogenes, the L1 pA signal lacks conserved elements that normally reside downstream of the poly(A) addition site in canonical RNA polymerase II pA signals. Finally, because most L1s are 5’ truncated, it is possible that many transduction events are not detected because they completely lack L1 sequences. However, biochemical data argue that ORF1 binds particular A-rich sequences in L1 RNA with relatively high affinity and that ORF1p is more abundant than ORF2p. We just are beginning to realize the consequences of L1 retrotransposition on the human genome. Clearly, L1 is a mutagen. Moreover, because of the abundance of L1s, it is likely that L1s provide scaffolds for illegitimate recombination, which may contribute to the genome instability seen in many tumors.
- Published
- 2007
25. Characterization of a mutagenic B1 retrotransposon insertion in the jittery mouse
- Author
-
John V. Moran, Nicolas Gilbert, Jamee M. Bomar, and Margit Burmeister
- Subjects
Subfamily ,Cerebellar Ataxia ,Retroelements ,Molecular Sequence Data ,Retrotransposon ,Biology ,Genome ,Mice ,Exon ,Endonuclease ,Sequence Homology, Nucleic Acid ,Chromosome 19 ,Gene duplication ,Genetics ,Animals ,Humans ,Gene ,Genetics (clinical) ,Short Interspersed Nucleotide Elements ,Mice, Inbred BALB C ,Base Sequence ,Molecular biology ,Mutagenesis, Insertional ,Genes ,biology.protein ,Nucleic Acid Conformation ,RNA - Abstract
B1 elements are an abundant class of short interspersed elements (SINEs) in the mouse genome and mobilize by a process known as retrotransposition. Here, we report the characterization of a mutagenic B1 insertion into exon 4 of the Atcay gene, which was previously shown to be responsible for the jittery mouse. Mutations in the human ortholog of this gene, ATCAY, are responsible for Cayman ataxia. The B1 insertion is B150-bp long, ends in a 45–50-bp polyadenylic acid (poly A) tail, is flanked by a perfect 13-bp target-site duplication, and is inserted into a sequence that resembles a LINE-1 endonuclease consensus cleavage site. Computational analysis indicates that the mutagenic insertion is most closely related to elements of the B1-C subfamily, and we have identified two possible progenitor B1 sequences on mouse chromosome 19. Together, these data demonstrate that B1 retrotransposition is ongoing in the mouse genome and is consistent with the hypothesis that the reverse transcriptase and endonuclease encoded by LINE-1 elements mediate B1 mobility. Hum Mutat 24:9–13, 2004. r 2004 Wiley-Liss, Inc.
- Published
- 2004
26. Instabilité génomique associée à la rétrotransposition du LINE-1 humain
- Author
-
Aurélien J. Doucet, Alain Bucheton, and Nicolas Gilbert
- Subjects
Aging ,Cell Biology - Abstract
Le retrotransposon LINE-1 (Ll) represente environ 17 % du genome humain. Du fait de son grand nombre de copies, il est implique dans des remaniements genomiques associes a des evenements de recombinaison homologue entre sites heterologues. De plus, meme si la vaste majorite des elements Ll sont inactifs, certains sont encore capables de se mobiliser par retrotransposition. Ll est donc un agent mutagene par insertion. De plus, des travaux ont aussi montre que les retrotransposons actifs etaient impliques dans la mobilisation d'autres sequences pour produire des retro-pseudogenes ou amplifier d’autres sequences repetees. Finalement, des etudes recentes ont montre que l’element Ll pourrait etre associe a de nouveaux rearrangements genomiques produits lors de l'insertion, tels que des deletions genomiques de grande taille. En conclusion, Ll peut etre considere comme un facteur important qui a affecte et modele le genome humain par l'intermediaire de plusieurs mecanismes.
- Published
- 2004
27. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition
- Author
-
Mark A. Batzer, Jeremy S. Myers, Nicolas Gilbert, Tammy A. Morrish, Thomas D. Stamato, John V. Moran, Guillermo E. Taccioli, and Bethaney J. Vincent
- Subjects
DNA Repair ,Retroelements ,DNA repair ,Molecular Sequence Data ,Retrotransposon ,CHO Cells ,Biology ,Polymerase Chain Reaction ,Molecular biology ,Reverse transcriptase ,Long interspersed nuclear element ,genomic DNA ,chemistry.chemical_compound ,Long Interspersed Nucleotide Elements ,chemistry ,Cricetinae ,Complementary DNA ,Genetics ,Animals ,Humans ,Primer (molecular biology) ,DNA - Abstract
Long interspersed elements (LINE-1s) are abundant retrotransposons in mammalian genomes that probably retrotranspose by target site-primed reverse transcription (TPRT). During TPRT, the LINE-1 endonuclease cleaves genomic DNA, freeing a 3' hydroxyl that serves as a primer for reverse transcription of LINE-1 RNA by LINE-1 reverse transcriptase. The nascent LINE-1 cDNA joins to genomic DNA, generating LINE-1 structural hallmarks such as frequent 5' truncations, a 3' poly(A)+ tail and variable-length target site duplications (TSDs). Here we describe a pathway for LINE-1 retrotransposition in Chinese hamster ovary (CHO) cells that acts independently of endonuclease but is dependent upon reverse transcriptase. We show that endonuclease-independent LINE-1 retrotransposition occurs at near-wildtype levels in two mutant cell lines that are deficient in nonhomologous end-joining (NHEJ). Analysis of the pre- and post-integration sites revealed that endonuclease-independent retrotransposition results in unusual structures because the LINE-1s integrate at atypical target sequences, are truncated predominantly at their 3' ends and lack TSDs. Moreover, two of nine endonuclease-independent retrotranspositions contained cDNA fragments at their 3' ends that are probably derived from the reverse transcription of endogenous mRNA. Thus, our results suggest that LINE-1s can integrate into DNA lesions, resulting in retrotransposon-mediated DNA repair in mammalian cells.
- Published
- 2002
28. Human L1 Retrotransposition: cisPreference versus trans Complementation
- Author
-
Wei Wei, Eric M. Ostertag, Siew Loon Ooi, Nicolas Gilbert, Haig H. Kazazian, Jef D. Boeke, Joseph F. Lawler, and John V. Moran
- Subjects
Pseudogene ,Mutant ,Retrotransposon ,Biology ,medicine.disease_cause ,Evolution, Molecular ,Open Reading Frames ,medicine ,Humans ,RNA, Messenger ,RNA Processing, Post-Transcriptional ,Molecular Biology ,DNA Primers ,Recombination, Genetic ,Mutation ,Base Sequence ,Models, Genetic ,Genetic Complementation Test ,RNA ,Cell Biology ,DNA Dynamics and Chromosome Structure ,Molecular biology ,Complementation ,Long interspersed nuclear element ,Long Interspersed Nucleotide Elements ,Trans-acting ,Pseudogenes ,HeLa Cells - Abstract
Long interspersed nuclear elements (LINEs or L1s) comprise approximately 17% of human DNA; however, only about 60 of the approximately 400,000 L1s are mobile. Using a retrotransposition assay in cultured human cells, we demonstrate that L1-encoded proteins predominantly mobilize the RNA that encodes them. At much lower levels, L1-encoded proteins can act in trans to promote retrotransposition of mutant L1s and other cellular mRNAs, creating processed pseudogenes. Mutant L1 RNAs are mobilized at 0.2 to 0.9% of the retrotransposition frequency of wild-type L1s, whereas cellular RNAs are mobilized at much lower frequencies (ca. 0.01 to 0.05% of wild-type levels). Thus, we conclude that L1-encoded proteins demonstrate a profound cis preference for their encoding RNA. This mechanism could enable L1 to remain retrotransposition competent in the presence of the overwhelming number of nonfunctional L1s present in human DNA.
- Published
- 2001
29. A transcriptional analysis of the S1Bn (Brassica napus) family of SINE retroposons
- Author
-
Laurent Rouquet, Alain Lenoir, Philippe Arnaud, Georges Picard, Nicolas Gilbert, and Jean-Marc Deragon
- Subjects
DNA, Plant ,Retroelements ,Transcription, Genetic ,Molecular Sequence Data ,Population ,Alu element ,Brassica ,Plant Science ,Biology ,Polymerase Chain Reaction ,RNA polymerase III ,Short Interspersed Element ,Rapid amplification of cDNA ends ,Complementary DNA ,Genetics ,education ,DNA Polymerase III ,education.field_of_study ,Base Sequence ,Retroposon ,RNA ,General Medicine ,Blotting, Northern ,Molecular biology ,Agronomy and Crop Science - Abstract
S1Bn is a plant short interspersed element (SINE) whose amplification probably involves the reverse transcription of an RNA intermediate. In this report, we identified and characterized S1Bn transcripts from different Brassica napus tissues. Despite the presence of a consensus internal POL III promoter in a large number of genomic S1Bn elements, we observed that S1Bn transcripts are rare in B. napus cells. The use of two very sensitive methods (RT-PCR and RACE PCR) allowed the characterization of 102 independent S1Bn cDNA clones from three different tissues (shoot, root and callus). From this analysis, we conclude that the majority of S1Bn transcripts probably result from a small number of cotranscriptional events where an S1Bn element is transcribed due to its presence in a POL II transcriptional unit. Specific POL III RNA transcripts, initiating at the first 5' nucleotide of the DNA element, are also present in the tested tissues and possibly result from the transcriptional activity of as few as three genomic elements. Two of these transcripts could represent master transcripts responsible for the amplification of S1Bn subfamilies. We also observed that the population of specific POL III transcripts varies among the three tested tissues and that some transcripts appear completely tissue-specific.
- Published
- 1996
30. Ancient repeat sequence derived from U6 snRNA in primate genomes
- Author
-
Oussama Meziane, Aurélien J. Doucet, Nicolas Gilbert, Manel Hasnaoui, Institut de génétique humaine (IGH), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Primates ,Pseudogene ,Molecular Sequence Data ,Retrotransposon ,Biology ,Genome ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,RNA, Small Nuclear ,Sequence Homology, Nucleic Acid ,Genetics ,Animals ,Humans ,Small nucleolar RNA ,ComputingMilieux_MISCELLANEOUS ,Phylogeny ,030304 developmental biology ,Sequence (medicine) ,Repetitive Sequences, Nucleic Acid ,0303 health sciences ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,Base Sequence ,General Medicine ,Scandentia ,Transfer RNA ,Human genome ,030217 neurology & neurosurgery - Abstract
LINE-1 (L1) is the most represented sequence of the human genome (17% of the total genomic mass). Moreover, it has been proposed for many years and demonstrated more recently that L1 has contributed to the mobilization of pseudogenes, small non-coding RNAs, such as tRNAs or snRNAs, and SINEs. In fact, it is estimated that L1 is responsible for at least 30% of our genome. The mobilization of non-L1 RNAs can occur in different ways and at different steps of the retrotransposition cycle. Here, by looking at U6 snRNA sequences mobilized by L1, we have observed an ancient repeat sequence derived from U6, present in all primate genomes. We were able to trace its origin in Euarchota genomes, most likely during the divergence of the four orders; Scandentia, Dermoptera, Plesiadapiform (extinct) and Primates.
- Published
- 2009
31. Les Bretons et la Séparation
- Author
-
Balcou, Jean, Beloeil, Dominique, Bensoussan, David, Botouropoulou, Iphigénie, Boudon, Jacques-Olivier, Broudic, Fañch, Carluer, Jean-Yves, Clément, Jean-Paul, Cloître, Marie-Thérèse, Dufief, Pierre-Jean, Elégoët, Louis, Fabre, Rémi, Forestier, Yann, Frélaut, Bertrand, Gall, Jean André Le, Gicquel, Samuel, Glon, Thierry, Goff, Joëlle Edon-Le, Guillou, Louis Le, Guyvarc’h, Didier, Kermoal, Christian, Lagadec, Yann, Laot, Laurent, Laperrière, Guy, Marjou, Jean-Yves, Ménégaki, Maria, Mérian, Jean-Yves, Michel, Youenn, Moigne, Frédéric Le, Morisset, Lucie K., Nicolas, Gilbert, Noppen, Luc, Nossowska, Małgorzata, Poulat, Émile, Prével-Montagne, Corinne, Redissi, Hamadi, Tanguy, Nicolas, Tranvouez, Yvon, and Tripier, Yves
- Subjects
Religion ,vie sociale ,History ,Église catholique ,laïcité ,Political science ,Séparation des Églises et de l'État (France ,1905-1906) ,HIS013000 ,histoire de France ,HBJD - Abstract
Comment la Bretagne devait-elle commémorer le centenaire de la loi de la Séparation des Églises et de l'État ? En réunissant pour un colloque commun, sous l'égide du Comité Renan de Tréguier et en collaboration avec l'Institut culturel de Bretagne, les principaux chercheurs des universités de Rennes, Brest et Nantes. En imposant d'elle-même une spécificité où la langue bretonne, la question scolaire, la force de la religion et des traditions jouent un rôle essentiel. En creusant cette spécificité par l'inscription de l'événement dans la longue durée d'un avant et d'un après. En éclairant les travaux des historiens à la lumière de la littérature et des arts. En choisissant pour centre de la manifestation Tréguier, le berceau de Renan : Tréguier où l'inauguration tumultueuse de son monument sous la présidence d'Émile Combes fait date. Et la puissante pensée même de Renan amenait naturellement à l'internationalisation du débat. C'est pourquoi ce colloque fut à son tour un événement. C'est pourquoi aussi ces actes sont à considérer comme lieu de mémoire dont l'actualité fait toujours un lieu de leçon.
- Published
- 2006
32. Multiple fates of L1 retrotransposition intermediates in cultured human cells
- Author
-
Sheila M Lutz, Tammy A. Morrish, Nicolas Gilbert, John V. Moran, Institut de génétique humaine (IGH), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Untranslated region ,Genome instability ,Genome evolution ,DNA, Complementary ,Retrotransposon ,Chromosome Structure and Dynamics ,Biology ,medicine.disease_cause ,Translocation, Genetic ,Substrate Specificity ,03 medical and health sciences ,0302 clinical medicine ,Consensus Sequence ,medicine ,Humans ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,Molecular Biology ,Cells, Cultured ,030304 developmental biology ,Genetics ,0303 health sciences ,Mutation ,Models, Genetic ,Genome, Human ,Nucleotides ,food and beverages ,Cell Biology ,Long interspersed nuclear element ,genomic DNA ,Mutagenesis, Insertional ,Long Interspersed Nucleotide Elements ,030220 oncology & carcinogenesis ,Human genome ,Genetic Engineering - Abstract
Long interspersed element 1 (LINE-1 or L1) is an abundant retrotransposon that comprises ∼17% of human DNA (43, 69). Most L1s are retrotransposition defective because they are 5′ truncated, contain internal rearrangements, or harbor mutations within their open reading frames (25, 43). However, the average human genome is estimated to contain ∼80 to 100 retrotransposition-competent L1s (RC-L1s), and approximately 10% of these elements are classified as highly active or “hot” (6, 63). Human RC-L1s are ∼6.0 kb and contain a 5′ untranslated region (UTR), two nonoverlapping open reading frames (ORF1 and ORF2), and a 3′ UTR that ends in a poly(A) tail (Fig. (Fig.1A)1A) (13, 53, 66). ORF1 encodes a 40-kDa nucleic acid binding protein (30, 31, 33), whereas ORF2 has the potential to encode a 150-kDa protein with demonstrated endonuclease (L1 EN) and reverse transcriptase (L1 RT) activities (15, 19, 22, 51). ORF2p also contains a cysteine-rich domain (CX3CX7HX4C) of unknown function (17, 54). Both proteins are required for retrotransposition in cis (54), which most probably occurs by a mechanism termed “target site primed reverse transcription” (TPRT) (19, 47, 54, 72). However, how L1 integration is completed remains a mystery. FIG. 1. Simple sequence alterations at the 5′ genomic DNA/L1 junction. A. Rationale of the assay. The 3′ UTR of a human RC-L1 was tagged with a reporter cassette designed to detect retrotransposition events. Open rectangles indicate L1 ORF1 and ... We recently developed a plasmid-based rescue system that allows the recovery of L1 insertions in cultured human HeLa cells with minimal influence from selective pressures that occur during genome evolution. We found that L1 retrotransposition is associated with various forms of genetic instability and that the nascent L1 cDNA can undergo recombination with endogenous L1 elements, resulting in the formation of chimeric L1s. Consistent findings by Symer et al., using a colon cell line (HCT116) with an essentially normal karyotype, have led to the hypothesis that L1 retrotransposition can lead to various types of genomic instability (21, 72). Here, we describe the analysis of 100 L1 retrotransposition events in HeLa cells derived from four previously characterized RC-L1s (L1.2A, LRE-2, L1.3, and L1RP). Consistent with previous studies, we have found that retrotransposition is associated with the generation of intrachromosomal deletions, the creation of chimeric L1 elements, and the addition of non-L1 nucleotides at the 5′ insertion junction (21, 56, 72). In addition, we have observed novel rearrangements, including the mobilization of U6 small uracil-rich nuclear RNA (U6 snRNA) to a new genomic location, the formation of intrachromosomal duplications, intra-L1 rearrangements, and the generation of a possible interchromosomal translocation. Finally, we have determined that the L1 RT can faithfully replicate its own transcript and has a base misincorporation error rate of ∼1/7,000 bases. Together, these data indicate that the resolution of L1 retrotransposition intermediates in transformed human cell lines can lead to a variety of genomic rearrangements and lead us to propose that host processes act to restrict L1 retrotransposition during integration, limiting the number of full-length L1s in the genome.
- Published
- 2005
33. Genomic deletions created upon LINE-1 retrotransposition
- Author
-
Sheila Lutz-Prigge, John V. Moran, and Nicolas Gilbert
- Subjects
DNA, Complementary ,Retroelements ,Recombinant Fusion Proteins ,Molecular Sequence Data ,Mutagenesis (molecular biology technique) ,Retrotransposon ,Biology ,medicine.disease_cause ,Genome ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Plasmid ,medicine ,Humans ,Cloning, Molecular ,030304 developmental biology ,Genetics ,0303 health sciences ,Mutation ,Polymorphism, Genetic ,Base Sequence ,Biochemistry, Genetics and Molecular Biology(all) ,Genome, Human ,Long interspersed nuclear element ,Eukaryotic Cells ,Long Interspersed Nucleotide Elements ,chemistry ,030220 oncology & carcinogenesis ,Mutagenesis, Site-Directed ,Human genome ,Genetic Engineering ,DNA ,Gene Deletion ,HeLa Cells - Abstract
LINE-1 (L1) retrotransposition continues to impact the human genome, yet little is known about how L1 integrates into DNA. Here, we developed a plasmid-based rescue system and have used it to recover 37 new L1 retrotransposition events from cultured human cells. Sequencing of the insertions revealed the usual L1 structural hallmarks; however, in four instances, retrotransposition generated large target site deletions. Remarkably, three of those resulted in the formation of chimeric L1s, containing the 5′ end of an endogenous L1 fused precisely to our engineered L1. Thus, our data demonstrate multiple pathways for L1 integration in cultured cells, and show that L1 is not simply an insertional mutagen, but that its retrotransposition can result in significant deletions of genomic sequence.
- Published
- 2002
34. Evolutionary inventions and continuity of CORE-SINEs in mammals
- Author
-
Damian Labuda and Nicolas Gilbert
- Subjects
Databases, Factual ,Transcription, Genetic ,Molecular Sequence Data ,Gene Dosage ,Retrotransposon ,Biology ,DNA, Satellite ,Genome ,Evolution, Molecular ,Structural Biology ,Consensus Sequence ,Direct repeat ,Animals ,Humans ,Sine ,Clade ,Molecular Biology ,Phylogeny ,Sequence (medicine) ,Short Interspersed Nucleotide Elements ,Genetics ,Mammals ,Recombination, Genetic ,Base Sequence ,Models, Genetic ,Monotremata ,Gene Amplification ,RNA ,Blotting, Southern ,Long Interspersed Nucleotide Elements ,Marsupialia ,Mutation ,Adaptation ,Sequence Alignment - Abstract
We characterized short interspersed elements (SINEs), of the CORE-suprafamily in egg-laying (monotremes), pouched (marsupials) and placental mammals. Five families of these repeats distinguished by the presence of distinct LINE-related 3′-segments shared tRNA-like promoter and the central core region. The putative active elements were reconstructed from the alignment of genomic repeats representing molecular fossils of sequences that amplified in the past and since then underwent multiple mutations. Their mode of proliferation by retroposition was indicated by the presence of: (1) internal RNA PolIII promoter; (2) simple sequence repeated tail; (3) direct repeats; and (4) subfamilies recording the evolution of elements. The copy number of CORE-SINEs in placental genomes was estimated at about 300,000; they were highly divergent and apparently ceased to amplify before radiation of these lineages. On the other hand, among almost half a million fossil elements present in marsupials and monotremes, the youngest subfamilies could still be retropositionally active. CORE-SINEs terminate in sequence repeats of a few nucleotides similar to their 3′-segment LINE-homologues, CR1, L2 and Bov-B. These three LINE elements fall into clades distinct from that of L1 elements which, similar to their co-amplifying SINEs, end in a poly(A) tail. We propose a model in which new CORE-families, with distinct 3′-segments, are created at the RNA level due to template switching between LINE and CORE-RNA during reverse transcription. The proposed mechanism suggests that such an adaptation to the changing amplification machinery facilitated the survival and prosperity of CORE-elements over long evolutionary periods in different lineages.
- Published
- 2000
35. CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs
- Author
-
Damian Labuda and Nicolas Gilbert
- Subjects
Genetics ,Multidisciplinary ,Base Sequence ,Sequence analysis ,Genome, Human ,Interspersed repeat ,Molecular Sequence Data ,Sequence Analysis, DNA ,Biology ,Biological Sciences ,Genome ,behavioral disciplines and activities ,Long interspersed nuclear element ,DNA-Binding Proteins ,Evolution, Molecular ,Consensus sequence ,DNA Transposable Elements ,Short Interspersed Nucleotide Elements ,Animals ,Humans ,Human genome ,Sequence (medicine) ,Repetitive Sequences, Nucleic Acid - Abstract
A 65-bp “core” sequence is dispersed in hundreds of thousands copies in the human genome. This sequence was found to constitute the central segment of a group of short interspersed elements (SINEs), referred to as mammalian-wide interspersed repeats, that proliferated before the radiation of placental mammals. Here, we propose that the core identifies an ancient tRNA-like SINE element, which survived in different lineages such as mammals, reptiles, birds, and fish, as well as mollusks, presumably for >550 million years. This element gave rise to a number of sequence families (CORE-SINEs), including mammalian-wide interspersed repeats, whose distinct 3′ ends are shared with different families of long interspersed elements (LINEs). The evolutionary success of the generic CORE-SINE element can be related to the recruitment of the internal promoter from highly transcribed host RNA as well as to its capacity to adapt to changing retropositional opportunities by sequence exchange with actively amplifying LINEs. It reinforces the notion that the very existence of SINEs depends on the cohabitation with both LINEs and the host genome.
- Published
- 1999
36. Plant S1 SINEs as a model to study retroposition
- Author
-
Philippe Arnaud, Jean-Marc Deragon, Georges Picard, Nicolas Gilbert, A. Lenoir, and S. I. Warwick
- Subjects
Transposable element ,Genetics ,Short Interspersed Element ,Evolutionary biology ,Transcription (biology) ,fungi ,Retroposon ,food and beverages ,RNA ,Alu element ,Sine ,Biology ,Low copy number - Abstract
The S1 element is a plant SINE (Short INterspersed Element) that was first described and studied in Brassica napus and is widely distributed among Cruciferae, especially in species of the Brassiceae tribe. We propose that S1 amplification in Cruciferae could represent a good eukaryotic model to study retroposition. This is based on the fact that S1 elements share clear structural and evolutionary characteristics with mammalian SINEs but are present in a much lower copy number (500 loci by haploid genome for the S1 element in B. napus compared to 700,000 loci by haploid genome for the Alu element in human). This low copy number allows the characterization of a large portion of SINEs from a given plant species. This can lead to a more precise understanding of the evolutionary history of SINE amplification and can more easily allow an evaluation of the impact of retroposition on the evolution of that species. It can also lead more rapidly to the characterization of genomic elements active in transcription and retroposition so that the cellular control of these elements can be addressed. Finally, we show that the study of S1 insertion sites can reveal information on the RNA reverse transcription and integration step of the retroposition process.
- Published
- 1997
37. Le Forum 2002 du NEM
- Author
-
Nicolas Gilbert
- Subjects
General Medicine - Published
- 2003
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