136 results on '"Leleu, M."'
Search Results
2. Programme d’évaluation de l’administration des chimiothérapies en hôpital de jour en Champagne-Ardenne (PEACH) : satisfaction et délais d’attente des patients
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Debreuve-Theresette, A., Jovenin, N., Stona, A.C., Kraïem-Leleu, M., Burde, F., Parent, D., Hettler, D., and Rey, J.B.
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- 2015
- Full Text
- View/download PDF
3. Photocatalytic degradation of estradiol under simulated solar light and assessment of estrogenic activity
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Mboula, V. Maroga, Héquet, V., Andrès, Y., Gru, Y., Colin, R., Doña-Rodríguez, J.M., Pastrana-Martínez, L.M., Silva, A.M.T., Leleu, M., Tindall, A.J., Mateos, S., and Falaras, P.
- Published
- 2015
- Full Text
- View/download PDF
4. Stress et charge mentale en hôpital de jour de cancérologie et en unité de reconstitution des cytotoxiques
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Debreuve-Theresette, A., Kraïem-Leleu, M., Stona, A.-C., Burde, F., Parent, D., Hettler, D., Rey, J.-B., and Jovenin, N.
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- 2014
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- View/download PDF
5. Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development
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Fabre, P. J., Leleu, M., Mascrez, B., Lo Giudice, Q., Cobb, J., and Duboule, D.
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- 2018
- Full Text
- View/download PDF
6. Essais de visualisation in situ de certains types d'écoulements dphasiques en milieux poreux In-Situ Visualization Test of Some Types of Two-Phase Flows in Porous Media
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Martin J. -M., Crouzil G., Leleu M., and Combarnous M.
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Chemical technology ,TP1-1185 ,Energy industries. Energy policy. Fuel trade ,HD9502-9502.5 - Published
- 2006
- Full Text
- View/download PDF
7. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes
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Loviglio MN, Leleu M, Männik K, Passeggeri M, Giannuzzi G, van der Werf I, Waszak SM, Zazhytska M, Roberts-Caldeira I, Gheldof N, Migliavacca E, Alfaiz AA, Hippolyte L, Maillard AM, 2p15 Consortium, 16p112 Consortium, Merla G, Van Dijck A, Kooy RF, Sanlaville D, Rosenfeld JA, Shaffer LG, Andrieux J, Marshall C, Scherer SW, Shen Y, Gusella JF, Thorsteinsdottir U, Thorleifsson G, Dermitzakis ET, Deplancke B, Beckmann JS, Rougemont J, Jacquemont S, Reymond A, Loviglio, Mn, Leleu, M, Männik, K, Passeggeri, M, Giannuzzi, G, van der Werf, I, Waszak, Sm, Zazhytska, M, Roberts-Caldeira, I, Gheldof, N, Migliavacca, E, Alfaiz, Aa, Hippolyte, L, Maillard, Am, 2p15, Consortium, 16p112, Consortium, Merla, G, Van Dijck, A, Kooy, Rf, Sanlaville, D, Rosenfeld, Ja, Shaffer, Lg, Andrieux, J, Marshall, C, Scherer, Sw, Shen, Y, Gusella, Jf, Thorsteinsdottir, U, Thorleifsson, G, Dermitzakis, Et, Deplancke, B, Beckmann, J, Rougemont, J, Jacquemont, S, and Reymond, A
- Abstract
Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.
- Published
- 2017
8. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes
- Author
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Loviglio, M.N., Leleu, M., Mannik, K., Passeggeri, M., Giannuzzi, G., Werf, I. van der, Waszak, S.M., Zazhytska, M., Roberts-Caldeira, I., Gheldof, N., Migliavacca, E., Alfaiz, A.A., Hippolyte, L., Maillard, A.M., Dijck, A. Van, Kooy, R.F., Sanlaville, D., Rosenfeld, J.A., Shaffer, L.G., Andrieux, J., Marshall, C., Scherer, S.W., Shen, Y., Gusella, J.F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E.T., Deplancke, B., Beckmann, J.S., Rougemont, J., Jacquemont, S., Reymond, A., Vulto-van Silfhout, A.T., Schouten, M.I., Pfundt, R.P., Leeuw, N. de, et al., Loviglio, M.N., Leleu, M., Mannik, K., Passeggeri, M., Giannuzzi, G., Werf, I. van der, Waszak, S.M., Zazhytska, M., Roberts-Caldeira, I., Gheldof, N., Migliavacca, E., Alfaiz, A.A., Hippolyte, L., Maillard, A.M., Dijck, A. Van, Kooy, R.F., Sanlaville, D., Rosenfeld, J.A., Shaffer, L.G., Andrieux, J., Marshall, C., Scherer, S.W., Shen, Y., Gusella, J.F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E.T., Deplancke, B., Beckmann, J.S., Rougemont, J., Jacquemont, S., Reymond, A., Vulto-van Silfhout, A.T., Schouten, M.I., Pfundt, R.P., Leeuw, N. de, and et al.
- Abstract
Contains fulltext : 174530.pdf (publisher's version ) (Open Access), Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.
- Published
- 2017
9. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes
- Author
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Loviglio, M. N., Leleu, M., Männik, K., Passeggeri, M., Giannuzzi, G., Van Der Werf, I., Waszak, S. M., Zazhytska, M., Roberts-Caldeira, I., Gheldof, N., Migliavacca, E., Alfaiz, A. A., Hippolyte, L., Maillard, A. M., Zollino, Marcella, Van Dijck, A., Kooy, R. F., Sanlaville, D., Rosenfeld, J. A., Shaffer, L. G., Andrieux, J., Marshall, C., Scherer, S. W., Shen, Y., Gusella, J. F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E. T., Deplancke, B., Beckmann, J. S., Rougemont, J., Jacquemont, S., Reymond, A., Zollino, M. (ORCID:0000-0003-4871-9519), Loviglio, M. N., Leleu, M., Männik, K., Passeggeri, M., Giannuzzi, G., Van Der Werf, I., Waszak, S. M., Zazhytska, M., Roberts-Caldeira, I., Gheldof, N., Migliavacca, E., Alfaiz, A. A., Hippolyte, L., Maillard, A. M., Zollino, Marcella, Van Dijck, A., Kooy, R. F., Sanlaville, D., Rosenfeld, J. A., Shaffer, L. G., Andrieux, J., Marshall, C., Scherer, S. W., Shen, Y., Gusella, J. F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E. T., Deplancke, B., Beckmann, J. S., Rougemont, J., Jacquemont, S., Reymond, A., and Zollino, M. (ORCID:0000-0003-4871-9519)
- Abstract
Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.
- Published
- 2017
10. Experimental Studies of Rock-Water Interactions Occuring During the Circulation of a Geothermal Doublet in a Carbonate Environment
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Desplan, A., Leleu, M., Massard, P., Rochon, J., Strub, A. S., editor, and Ungemach, P., editor
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- 1980
- Full Text
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11. Geochemistry of Thermal Water in the Mont-Dore Area
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Bosch, B., Degranges, P., Fouillac, C., Leleu, M., Sarcia, C., Strub, A. S., editor, and Ungemach, P., editor
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- 1980
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- View/download PDF
12. Geothermal Survey of the South-East Margin of the French Massif-Central
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Bosch, B., Degranges, P., Demange, J., Leleu, M., Marce, A., Sarcia, C., Strub, A. S., editor, and Ungemach, P., editor
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- 1980
- Full Text
- View/download PDF
13. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes
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Loviglio, M. N, Leleu, M., Männik, K., Passeggeri, M., Giannuzzi, G., van der Werf, I., Waszak, S. M., Zazhytska, M., Roberts Caldeira, I., Gheldof, N., Migliavacca, E., Alfaiz, A. A., Hippolyte, L., Maillard, A. M., van Dijck, A., Kooy, R. F., Sanlaville, D., Rosenfeld, J. A., Shaffer, L. G., Andrieux, J., Marshall, C., Scherer, S. W., Shen, Y., Gusella, J. F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E. T., Deplancke, B., Beckmann, J. S., Rougemont, J., Jacquemont, S., Reymond, A., Collaborators: Loviglio MN, Männik, K, van der Werf, I, Giannuzzi, G, Zazhytska, M, Gheldof, N, Migliavacca, E, Alfaiz, Aa, Roberts Caldeira, I, Hippolyte, L, Maillard, Am, Ferrarini, A, Butschi, Fn, Conrad, B, Addor, Mc, Belfiore, M, Roetzer, K, Dijck, Av, Blaumeiser, B, Kooy, F, Roelens, F, Dheedene, A, Chiaie, Bd, Menten, B, Oostra, A, Caberg, Jh, Carter, M, Kellam, B, Stavropoulos, Dj, Marshall, C, Scherer, Sw, Weksberg, R, Cytrynbaum, C, Bassett, A, Lowther, C, Gillis, J, Mackay, S, Bache, I, Ousager, Lb, Smerdel, Mp, Graakjaer, J, Kjaergaard, S, Metspalu, A, Mathieu, M, Bonneau, D, Guichet, A, Parent, P, Férec, C, Gerard, M, Plessis, G, Lespinasse, J, Masurel, A, Marle, N, Faivre, L, Callier, P, Layet, V, Meur, Nl, Le Goff, C, Duban Bedu, B, Sukno, S, Boute, O, Andrieux, J, Blanchet, P, Geneviève, D, Puechberty, J, Schneider, A, Leheup, B, Jonveaux, P, Mercier, S, David, A, Le Caignec, C, de Pontual, L, Pipiras, E, Jacquette, A, Keren, B, Gilbert Dussardier, B, Bilan, F, Goldenberg, A, Chambon, P, Toutain, A, Till, M, Sanlaville, D, Leube, B, Royer Pokora, B, Grabe, Hj, Schmidt, Co, Schurmann, C, Homuth, G, Thorleifsson, G, Thorsteinsdottir, U, Bernardini, L, Novelli, A, Micale, L, Merla, G, Zollino, M, Mari, Francesca, Rizzo, Cl, Renieri, Alessandra, Silengo, M, Vulto van Silfhout AT, Schouten, M, Pfundt, R, de Leeuw, N, Vansenne, F, Maas, Sm, Barge Schaapveld DQ, Knegt, Ac, Stadheim, B, Rodningen, O, Houge, G, Price, S, Hawkes, L, Campbell, C, Kini, U, Vogt, J, Walters, R, Blakemore, A, Gusella, Jf, Shen, Y, Scott, D, Bacino, Ca, Tsuchiya, K, Ladda, R, Sell, S, Asamoah, A, Hamati, Ai, Rosenfeld, Ja, Shaffer, Lg, Mitchell, E, Hodge, Jc, Beckmann, Js, Jacquemont, S, Reymond, A, Ewans, Lj, Mowat, D, Walker, J, Amor, Dj, Esch, Hv, Leroy, P, Bamforth, Js, Babu, D, Isidor, B, Didonato, N, Hackmann, K, Passeggeri, M, Haeringen, Av, Smith, R, Ellingwood, S, Farber, Dm, Puri, V, Zadeh, N, Weaver, Dd, Miller, M, Wilks, T, Jorgez, Cj, Lafayette, D, Blaumeiser, Bettina, 2p15 Consortium, 16p11.2 Consortium, Loviglio, M.N., Männik, K., van der Werf, I., Giannuzzi, G., Zazhytska, M., Gheldof, N., Migliavacca, E., Alfaiz, A.A., Roberts-Caldeira, I., Hippolyte, L., Maillard, A.M., Ferrarini, A., Butschi, F.N., Conrad, B., Addor, M.C., Belfiore, M., Roetzer, K., Dijck, A.V., Blaumeiser, B., Kooy, F., Roelens, F., Dheedene, A., Chiaie, B.D., Menten, B., Oostra, A., Caberg, J.H., Carter, M., Kellam, B., Stavropoulos, D.J., Marshall, C., Scherer, S.W., Weksberg, R., Cytrynbaum, C., Bassett, A., Lowther, C., Gillis, J., MacKay, S., Bache, I., Ousager, L.B., Smerdel, M.P., Graakjaer, J., Kjaergaard, S., Metspalu, A., Mathieu, M., Bonneau, D., Guichet, A., Parent, P., Férec, C., Gerard, M., Plessis, G., Lespinasse, J., Masurel, A., Marle, N., Faivre, L., Callier, P., Layet, V., Meur, N.L., Le Goff, C., Duban-Bedu, B., Sukno, S., Boute, O., Andrieux, J., Blanchet, P., Geneviève, D., Puechberty, J., Schneider, A., Leheup, B., Jonveaux, P., Mercier, S., David, A., Le Caignec, C., de Pontual, L., Pipiras, E., Jacquette, A., Keren, B., Gilbert-Dussardier, B., Bilan, F., Goldenberg, A., Chambon, P., Toutain, A., Till, M., Sanlaville, D., Leube, B., Royer-Pokora, B., Grabe, H.J., Schmidt, C.O., Schurmann, C., Homuth, G., Thorleifsson, G., Thorsteinsdottir, U., Bernardini, L., Novelli, A., Micale, L., Merla, G., Zollino, M., Mari, F., Rizzo, C.L., Renieri, A., Silengo, M., Vulto-van Silfhout, A.T., Schouten, M., Pfundt, R., de Leeuw, N., Vansenne, F., Maas, S.M., Barge-Schaapveld, D.Q., Knegt, A.C., Stadheim, B., Rodningen, O., Houge, G., Price, S., Hawkes, L., Campbell, C., Kini, U., Vogt, J., Walters, R., Blakemore, A., Gusella, J.F., Shen, Y., Scott, D., Bacino, C.A., Tsuchiya, K., Ladda, R., Sell, S., Asamoah, A., Hamati, A.I., Rosenfeld, J.A., Shaffer, L.G., Mitchell, E., Hodge, J.C., Beckmann, J.S., Jacquemont, S., Reymond, A., Ewans, L.J., Mowat, D., Walker, J., Amor, D.J., Esch, H.V., Leroy, P., Bamforth, J.S., Babu, D., Isidor, B., DiDonato, N., Hackmann, K., Passeggeri, M., Haeringen, A.V., Smith, R., Ellingwood, S., Farber, D.M., Puri, V., Zadeh, N., Weaver, D.D., Miller, M., Wilks, T., Jorgez, C.J., Lafayette, D., Other departments, and Human Genetics
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0301 basic medicine ,Male ,Microcephaly ,Autism Spectrum Disorder ,Obesity/genetics ,Settore MED/03 - GENETICA MEDICA ,Body Mass Index ,Microcephaly/genetics ,Gene duplication ,Chromosome Duplication ,ddc:576.5 ,Copy-number variation ,Child ,In Situ Hybridization ,In Situ Hybridization, Fluorescence ,Genetics ,medicine.diagnostic_test ,Chromosome Mapping ,Middle Aged ,Phenotype ,Chromatin ,Chemistry ,Psychiatry and Mental Health ,Child, Preschool ,Female ,Original Article ,Chromosomes, Human, Pair 16/genetics ,Megalencephaly/genetics ,Chromosome Deletion ,Autistic Disorder/genetics ,Molecular Biology ,Cellular and Molecular Neuroscience ,Human ,Rare cancers Radboud Institute for Health Sciences [Radboudumc 9] ,Adult ,Adolescent ,DNA Copy Number Variations ,Locus (genetics) ,DNA Copy Number Variations/genetics ,Biology ,Aged ,Autistic Disorder ,Chromosomes, Human, Pair 16 ,Humans ,Infant ,Intellectual Disability ,Megalencephaly ,Obesity ,Chromosomes ,Fluorescence ,Chromatin/metabolism ,03 medical and health sciences ,medicine ,Preschool ,Gene ,Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7] ,Pair 16 ,medicine.disease ,Intellectual Disability/genetics ,Autism Spectrum Disorder/genetics ,030104 developmental biology ,Human medicine ,Chromosome Mapping/methods ,Fluorescence in situ hybridization - Abstract
Contains fulltext : 174530.pdf (Publisher’s version ) (Open Access) Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.
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- 2015
14. A switch between topological domains underlies collinearity in mouse limbs. Science
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Andrey, G, Montavon, T, Mascrez, B, Gonzalez, F, Noordermeer, D, Leleu, M, Trono, D, Spitz, F. and Duboule, D., Andrey, G., Montavon, T., Mascrez, B., Gonzalez, F., Noordermeer, D., Leleu, M., Trono, D., Spitz, F., and Duboule, D.
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- 2013
15. The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases
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Bultet, LA, Aguilar-Rodriguez, J, Ahrens, CH, Ahrne, EL, Ai, N, Aimo, L, Akalin, A, Aleksiev, T, Alocci, D, Altenhoff, A, Alves, I, Ambrosini, G, Pedone, PA, Angelina, P, Anisimova, M, Appel, R, Argoud-Puy, G, Arnold, K, Arpat, B, Artimo, P, Ascencao, K, Auchincloss, A, Axelsen, K, Gerritsen, VB, Bairoch, A, Barisal, P, Baratin, D, Barbato, A, Barbie, V, Barras, D, Barreiro, M, Barret, S, Bastian, F, Batista Neto, TM, Baudis, M, Beaudoing, E, Beckmann, JS, Bekkar, AK, Cammoun, LBH, Benmohammed, S, Bernard, M, Bertelli, C, Bertoni, M, Bienert, S, Bignucolo, O, Bilbao, A, Bilican, A, Blank, D, Blatter, M-C, Blum, L, Bocquet, J, Boeckmann, B, Bolleman, JT, Bordoli, L, Bosshard, L, Boucher, G, Bougueleret, L, Boutet, E, Bovigny, C, Bratulic, S, Breuza, L, Bridge, AJ, Britan, A, Brito, F, Frazao, JB, Bruggmann, R, Bucher, P, Burdet, F, Burger, L, Cabello, EM, Gomez, RMC, Calderon, S, Cannarozzi, G, Carl, S, Casas, CC, Catherinet, S, Perier, RC, Charpilloz, C, Chaskar, PD, Chen, W, Pepe, AC, Chopard, B, Chu, HY, Civic, N, Claassen, M, Clottu, S, Colombo, M, Cosandier, I, Coudert, E, Crespo, I, Creus, M, Cuche, B, Cuendet, MA, Cusin, I, Daga, N, Daina, A, Dauvillier, J, David, F, Davydov, I, Ferreira, MDSRM, de Beer, T, de Castro, E, de Santana, C, Delafontaine, J, Delorenzi, M, Delucinge-Vivier, C, Demirel, O, Derham, R, Dermitzakis, EM, Dib, L, Diene, S, Dilek, N, Dilmi, J, Domagalski, MJ, Dorier, J, Dornevil, D, Dousse, A, Dreos, R, Duchen, P, Roggli, PD, Duperret, ID, Durinx, C, Duvaud, S, Engler, R, Frkek, S, Lopez, PE, Fstreicher, A, Excoffier, L, Fabbretti, R, Falcone, J-L, Falquet, L, Famiglietti, ML, Ferreira, A-M, Feuermann, M, Filliettaz, M, Hegel, V, Foucal, A, Franceschini, A, Fucile, G, Gaidatzis, D, Garcia, V, Gasteiger, E, Gateau, A, Gatti, L, Gaudet, P, Gaudinat, A, Gehant, S, Gfeller, D, Gharib, WH, Ghraichy, M, Gidoin, C, Gil, M, Gleizes, A, Gobeill, J, Gonnet, G, Gos, A, Gotz, L, Gouy, A, Grbic, D, Groux, R, Gruaz-Gumowski, N, Grun, D, Gschwind, A, Guex, N, Gupta, S, Getaz, M, Haake, D, Haas, J, Hatzimanikatis, V, Heckel, G, Gardiol, DFH, Hinard, V, Hinz, U, Homicsko, K, Horlacher, O, Hosseini, S-R, Hotz, H-R, Hulo, C, Hundsrucker, C, Ibberson, M, Ilmjarv, S, Ioannidis, V, Ioannidis, P, Iseli, C, Ivanek, R, Iwaszkiewicz, J, Jacquet, P, Jacquot, M, Jagannathan, V, Jan, M, Jensen, J, Johansson, MU, Johner, N, Jungo, F, Junier, T, Kahraman, A, Katsantoni, M, Keller, G, Kerhornou, A, Khalid, F, Klingbiel, D, Kimljenovic, A, Kriventseva, E, Kryuchkova, N, Kumar, S, Kutalik, Z, Kuznetsov, D, Kuzyakiv, R, Lane, L, Lara, V, Ledesma, L, Leleu, M, Lemercier, P, Lew, D, Lieberherr, D, Liechti, R, Lisacek, F, Fischer, H, Litsios, G, Liu, J, Lombardot, T, Mace, A, Maffioletti, S, Mahi, M-A, Maiolo, M, Majjigapu, SR, Malmstrom, L, Mangold, V, Marek, D, Mariethoz, J, Marin, R, Martin, O, Martin, X, Martin-Campos, T, Mary, C, Masclaux, F, Masson, P, Meier, C, Messina, A, Lenoir, MM, Meyer, X, Michel, P-A, Michielin, O, Milanese, A, Missiaglia, E, Perez, JM, Caria, VM, Moret, P, Moretti, S, Morgat, A, Mottaz, A, Mottin, L, Mouscaz, Y, Mueller, M, Murri, R, Mylonas, R, Neuenschwander, S, Nikitin, F, Niknejad, A, Nouspikel, N, Nso, LN, Okoniewski, M, Omasits, U, Paccaud, B, Pachkov, M, Paesano, SG, Pagni, M, Palagi, PM, Pasche, E, Payne, JL, Pedruzzi, I, Peischl, S, Peitsch, M, Perlini, S, Pilbout, S, Podvinec, M, Pohlmann, R, Polizzi, D, Potter, D, Poux, S, Pozzato, M, Pradervand, S, Praz, V, Pruess, M, Pujadas, E, Racle, J, Raschi, M, Ratib, O, Rausell, A, de Laval, VR, Redaschi, N, Rempfer, C, Ren, G, Vandati, RAR, Rib, L, Grognuz, OR, Altimiras, ER, Rivoire, C, Robin, T, Robinson-Rechavi, M, Rodrigues, J, Roechert, B, Roelli, P, Romano, V, Rossier, G, Roth, A, Rougemont, J, Roux, J, Royo, H, Ruch, P, Ruinelli, M, Rustom, M, Sates, A, Roehrig, UF, Rueeger, S, Salamin, N, Sankar, M, Sarkar, N, Saxenhofer, M, Schaeffer, M, Schaerli, Y, Schaper, E, Schmid, A, Schmid, E, Schmid, C, Schmid, M, Schmidt, S, Schmocker, D, Schneider, M, Schuepbach, T, Schwede, T, Schuetz, F, Sengstag, T, Serrano, M, Sethi, A, Shahmirzadi, O, Sigrist, C, Silvestro, D, Simao Neto, FA, Simillion, C, Simonovic, M, Skunca, N, Sluzek, K, Soneson, C, Sprouffske, K, Stadler, M, Staehli, S, Stevenson, B, Stockinger, H, Straszewski, J, Stricker, T, Studer, G, Stutz, A, Suffiotti, M, Sundaram, S, Szklarczyk, D, Szovenyi, P, Tegenfeldt, F, Teixeira, D, Tellenbach, S, Smith, AAT, Tognolli, M, Topolsky, I, Thuong, VDT, Tsantoulis, P, Tzika, AC, Agote, AU, van Nimwegen, E, von Mering, C, Varadarajan, A, Veranneman, M, Verbregue, L, Veuthey, A-L, Vishnyakova, D, Vyas, R, Wagner, A, Walther, D, Wan, HW, Wang, M, Waterhouse, R, Waterhouse, A, Wicki, A, Wigger, L, Wirapati, P, Witschi, U, Wyder, S, Wyler, K, Wuethrich, D, Xenarios, I, Yamada, K, Yan, Z, Yasrebi, H, Zahn, M, Zangger, N, Zdobnov, E, Zerzion, D, Zoete, V, Zoller, S, Bultet, LA, Aguilar-Rodriguez, J, Ahrens, CH, Ahrne, EL, Ai, N, Aimo, L, Akalin, A, Aleksiev, T, Alocci, D, Altenhoff, A, Alves, I, Ambrosini, G, Pedone, PA, Angelina, P, Anisimova, M, Appel, R, Argoud-Puy, G, Arnold, K, Arpat, B, Artimo, P, Ascencao, K, Auchincloss, A, Axelsen, K, Gerritsen, VB, Bairoch, A, Barisal, P, Baratin, D, Barbato, A, Barbie, V, Barras, D, Barreiro, M, Barret, S, Bastian, F, Batista Neto, TM, Baudis, M, Beaudoing, E, Beckmann, JS, Bekkar, AK, Cammoun, LBH, Benmohammed, S, Bernard, M, Bertelli, C, Bertoni, M, Bienert, S, Bignucolo, O, Bilbao, A, Bilican, A, Blank, D, Blatter, M-C, Blum, L, Bocquet, J, Boeckmann, B, Bolleman, JT, Bordoli, L, Bosshard, L, Boucher, G, Bougueleret, L, Boutet, E, Bovigny, C, Bratulic, S, Breuza, L, Bridge, AJ, Britan, A, Brito, F, Frazao, JB, Bruggmann, R, Bucher, P, Burdet, F, Burger, L, Cabello, EM, Gomez, RMC, Calderon, S, Cannarozzi, G, Carl, S, Casas, CC, Catherinet, S, Perier, RC, Charpilloz, C, Chaskar, PD, Chen, W, Pepe, AC, Chopard, B, Chu, HY, Civic, N, Claassen, M, Clottu, S, Colombo, M, Cosandier, I, Coudert, E, Crespo, I, Creus, M, Cuche, B, Cuendet, MA, Cusin, I, Daga, N, Daina, A, Dauvillier, J, David, F, Davydov, I, Ferreira, MDSRM, de Beer, T, de Castro, E, de Santana, C, Delafontaine, J, Delorenzi, M, Delucinge-Vivier, C, Demirel, O, Derham, R, Dermitzakis, EM, Dib, L, Diene, S, Dilek, N, Dilmi, J, Domagalski, MJ, Dorier, J, Dornevil, D, Dousse, A, Dreos, R, Duchen, P, Roggli, PD, Duperret, ID, Durinx, C, Duvaud, S, Engler, R, Frkek, S, Lopez, PE, Fstreicher, A, Excoffier, L, Fabbretti, R, Falcone, J-L, Falquet, L, Famiglietti, ML, Ferreira, A-M, Feuermann, M, Filliettaz, M, Hegel, V, Foucal, A, Franceschini, A, Fucile, G, Gaidatzis, D, Garcia, V, Gasteiger, E, Gateau, A, Gatti, L, Gaudet, P, Gaudinat, A, Gehant, S, Gfeller, D, Gharib, WH, Ghraichy, M, Gidoin, C, Gil, M, Gleizes, A, Gobeill, J, Gonnet, G, Gos, A, Gotz, L, Gouy, A, Grbic, D, Groux, R, Gruaz-Gumowski, N, Grun, D, Gschwind, A, Guex, N, Gupta, S, Getaz, M, Haake, D, Haas, J, Hatzimanikatis, V, Heckel, G, Gardiol, DFH, Hinard, V, Hinz, U, Homicsko, K, Horlacher, O, Hosseini, S-R, Hotz, H-R, Hulo, C, Hundsrucker, C, Ibberson, M, Ilmjarv, S, Ioannidis, V, Ioannidis, P, Iseli, C, Ivanek, R, Iwaszkiewicz, J, Jacquet, P, Jacquot, M, Jagannathan, V, Jan, M, Jensen, J, Johansson, MU, Johner, N, Jungo, F, Junier, T, Kahraman, A, Katsantoni, M, Keller, G, Kerhornou, A, Khalid, F, Klingbiel, D, Kimljenovic, A, Kriventseva, E, Kryuchkova, N, Kumar, S, Kutalik, Z, Kuznetsov, D, Kuzyakiv, R, Lane, L, Lara, V, Ledesma, L, Leleu, M, Lemercier, P, Lew, D, Lieberherr, D, Liechti, R, Lisacek, F, Fischer, H, Litsios, G, Liu, J, Lombardot, T, Mace, A, Maffioletti, S, Mahi, M-A, Maiolo, M, Majjigapu, SR, Malmstrom, L, Mangold, V, Marek, D, Mariethoz, J, Marin, R, Martin, O, Martin, X, Martin-Campos, T, Mary, C, Masclaux, F, Masson, P, Meier, C, Messina, A, Lenoir, MM, Meyer, X, Michel, P-A, Michielin, O, Milanese, A, Missiaglia, E, Perez, JM, Caria, VM, Moret, P, Moretti, S, Morgat, A, Mottaz, A, Mottin, L, Mouscaz, Y, Mueller, M, Murri, R, Mylonas, R, Neuenschwander, S, Nikitin, F, Niknejad, A, Nouspikel, N, Nso, LN, Okoniewski, M, Omasits, U, Paccaud, B, Pachkov, M, Paesano, SG, Pagni, M, Palagi, PM, Pasche, E, Payne, JL, Pedruzzi, I, Peischl, S, Peitsch, M, Perlini, S, Pilbout, S, Podvinec, M, Pohlmann, R, Polizzi, D, Potter, D, Poux, S, Pozzato, M, Pradervand, S, Praz, V, Pruess, M, Pujadas, E, Racle, J, Raschi, M, Ratib, O, Rausell, A, de Laval, VR, Redaschi, N, Rempfer, C, Ren, G, Vandati, RAR, Rib, L, Grognuz, OR, Altimiras, ER, Rivoire, C, Robin, T, Robinson-Rechavi, M, Rodrigues, J, Roechert, B, Roelli, P, Romano, V, Rossier, G, Roth, A, Rougemont, J, Roux, J, Royo, H, Ruch, P, Ruinelli, M, Rustom, M, Sates, A, Roehrig, UF, Rueeger, S, Salamin, N, Sankar, M, Sarkar, N, Saxenhofer, M, Schaeffer, M, Schaerli, Y, Schaper, E, Schmid, A, Schmid, E, Schmid, C, Schmid, M, Schmidt, S, Schmocker, D, Schneider, M, Schuepbach, T, Schwede, T, Schuetz, F, Sengstag, T, Serrano, M, Sethi, A, Shahmirzadi, O, Sigrist, C, Silvestro, D, Simao Neto, FA, Simillion, C, Simonovic, M, Skunca, N, Sluzek, K, Soneson, C, Sprouffske, K, Stadler, M, Staehli, S, Stevenson, B, Stockinger, H, Straszewski, J, Stricker, T, Studer, G, Stutz, A, Suffiotti, M, Sundaram, S, Szklarczyk, D, Szovenyi, P, Tegenfeldt, F, Teixeira, D, Tellenbach, S, Smith, AAT, Tognolli, M, Topolsky, I, Thuong, VDT, Tsantoulis, P, Tzika, AC, Agote, AU, van Nimwegen, E, von Mering, C, Varadarajan, A, Veranneman, M, Verbregue, L, Veuthey, A-L, Vishnyakova, D, Vyas, R, Wagner, A, Walther, D, Wan, HW, Wang, M, Waterhouse, R, Waterhouse, A, Wicki, A, Wigger, L, Wirapati, P, Witschi, U, Wyder, S, Wyler, K, Wuethrich, D, Xenarios, I, Yamada, K, Yan, Z, Yasrebi, H, Zahn, M, Zangger, N, Zdobnov, E, Zerzion, D, Zoete, V, and Zoller, S
- Abstract
The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.
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- 2016
16. Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy
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Cerase A, Smeets D, Amy Tang, Gdula M, Kraus F, Spivakov M, Moindrot B, Leleu M, Tattermusch A, Demmerle J, Tb, Nesterova, Green C, Ap, Otte, Schermelleh L, and Brockdorff N
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Xist, Polycomb, PRC1, PRC2, 3D-SIM, Super-resolution Microscopy ,Xist ,Polycomb ,Super-resolution Microscopy ,3D-SIM ,macromolecular substances ,PRC2 ,PRC1 - Abstract
In female mammals, one of the two X chromosomes is transcriptionally silenced to equalize X-linked gene dosage relative to XY males, a process termed X chromosome inactivation. Mechanistically, this is thought to occur via directed recruitment of chromatin modifying factors by the master regulator, X-inactive specific transcript (Xist) RNA, which localizes in cis along the entire length of the chromosome. A well-studied example is the recruitment of polycomb repressive complex 2 (PRC2), for which there is evidence of a direct interaction involving the PRC2 proteins Enhancer of zeste 2 (Ezh2) and Supressor of zeste 12 (Suz12) and the A-repeat region located at the 5' end of Xist RNA. In this study, we have analyzed Xist-mediated recruitment of PRC2 using two approaches, microarray-based epigenomic mapping and superresolution 3D structured illumination microscopy. Making use of an ES cell line carrying an inducible Xist transgene located on mouse chromosome 17, we show that 24 h after synchronous induction of Xist expression, acquired PRC2 binding sites map predominantly to gene-rich regions, notably within gene bodies. Paradoxically, these new sites of PRC2 deposition do not correlate with Xist-mediated gene silencing. The 3D structured illumination microscopy was performed to assess the relative localization of PRC2 proteins and Xist RNA. Unexpectedly, we observed significant spatial separation and absence of colocalization both in the inducible Xist transgene ES cell line and in normal XX somatic cells. Our observations argue against direct interaction between Xist RNA and PRC2 proteins and, as such, prompt a reappraisal of the mechanism for PRC2 recruitment in X chromosome inactivation.
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- 2014
17. Synthèse de wurtzite par voie bactérienne
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Leleu, M., Gugalski, T., and Goni, J.
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- 1975
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18. Sur la formation biogéochimique de stalactites de galène
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Leleu, M. and Goni, J.
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- 1974
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19. Sur des minéralisations de type skarn au Laurium (Grèce)
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Leleu, M., Morikis, A., and Picot, P.
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- 1973
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20. Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
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Bonhoure, N, Bounova, G, Bernasconi, D, Praz, V, Lammers, F, Canella, D, Willis, I M, Herr, W, Hernandez, N, Delorenzi, M, Deplancke, B, Desvergne, B, Guex, N, Naef, F, Rougemont, J, Schibler, U, Andersin, T, Cousin, P, Gilardi, F, Gos, P, Raghav, S, Villeneuve, D, Fabbretti, R, Vlegel, V, Xenarios, I, Migliavacca, E, David, F, Jarosz, Y, Kuznetsov, D, Liechti, R, Martin, O, Delafontaine, J, Cajan, J, Gustafson, K, Krier, I, Leleu, M, Molina, N, Naldi, A, Rib, L, Symul, L, Bonhoure, N, Bounova, G, Bernasconi, D, Praz, V, Lammers, F, Canella, D, Willis, I M, Herr, W, Hernandez, N, Delorenzi, M, Deplancke, B, Desvergne, B, Guex, N, Naef, F, Rougemont, J, Schibler, U, Andersin, T, Cousin, P, Gilardi, F, Gos, P, Raghav, S, Villeneuve, D, Fabbretti, R, Vlegel, V, Xenarios, I, Migliavacca, E, David, F, Jarosz, Y, Kuznetsov, D, Liechti, R, Martin, O, Delafontaine, J, Cajan, J, Gustafson, K, Krier, I, Leleu, M, Molina, N, Naldi, A, Rib, L, and Symul, L
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- 2014
21. The Dynamic Architecture of Hox Gene Clusters
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Noordermeer, D., Leleu, M., Splinter, E., Rougemont, J., de Laat, W., Duboule, D., Noordermeer, D., Leleu, M., Splinter, E., Rougemont, J., de Laat, W., and Duboule, D.
- Abstract
The spatial and temporal control of Hox gene transcription is essential for patterning the vertebrate body axis. Although this process involves changes in histone posttranslational modifications, the existence of particular three-dimensional (3D) architectures remained to be assessed in vivo. Using high-resolution chromatin conformation capture methodology, we examined the spatial configuration of Hox clusters in embryonic mouse tissues where different Hox genes are active. When the cluster is transcriptionally inactive, Hox genes associate into a single 3D structure delimited from flanking regions. Once transcription starts, Hox clusters switch to a bimodal 3D organization where newly activated genes progressively cluster into a transcriptionally active compartment. This transition in spatial configurations coincides with the dynamics of chromatin marks, which label the progression of the gene clusters from a negative to a positive transcription status. This spatial compartmentalization may be key to process the colinear activation of these compact gene clusters., The spatial and temporal control of Hox gene transcription is essential for patterning the vertebrate body axis. Although this process involves changes in histone posttranslational modifications, the existence of particular three-dimensional (3D) architectures remained to be assessed in vivo. Using high-resolution chromatin conformation capture methodology, we examined the spatial configuration of Hox clusters in embryonic mouse tissues where different Hox genes are active. When the cluster is transcriptionally inactive, Hox genes associate into a single 3D structure delimited from flanking regions. Once transcription starts, Hox clusters switch to a bimodal 3D organization where newly activated genes progressively cluster into a transcriptionally active compartment. This transition in spatial configurations coincides with the dynamics of chromatin marks, which label the progression of the gene clusters from a negative to a positive transcription status. This spatial compartmentalization may be key to process the colinear activation of these compact gene clusters.
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- 2012
22. Blé tendre. Des intrants en moins por des marges en plus
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Leleu, M., Lenne, N., Maurice, Aurélie, Le Gouis, Jacques, Heumez, Emmanuel, Brancourt-Hulmel, M., Pluchard, P., Domaine expérimental de Brunehaut (LILL MONS UE), Institut National de la Recherche Agronomique (INRA), Unité de recherche Génétique et amélioration des plantes (GAP), and ProdInra, Migration
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[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] ,ComputingMilieux_MISCELLANEOUS - Abstract
National audience
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- 2000
23. Growing winter wheat cultivars under different management intensities in France: A multicriteria assessment based on economic, energetic and environmental indicators
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Loyce, C., primary, Meynard, J.M., additional, Bouchard, C., additional, Rolland, B., additional, Lonnet, P., additional, Bataillon, P., additional, Bernicot, M.H., additional, Bonnefoy, M., additional, Charrier, X., additional, Debote, B., additional, Demarquet, T., additional, Duperrier, B., additional, Félix, I., additional, Heddadj, D., additional, Leblanc, O., additional, Leleu, M., additional, Mangin, P., additional, Méausoone, M., additional, and Doussinault, G., additional
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- 2012
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24. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes
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Loviglio, M N, Leleu, M, Männik, K, Passeggeri, M, Giannuzzi, G, van der Werf, I, Waszak, S M, Zazhytska, M, Roberts-Caldeira, I, Gheldof, N, Migliavacca, E, Alfaiz, A A, Hippolyte, L, Maillard, A M, Van Dijck, A, Kooy, R F, Sanlaville, D, Rosenfeld, J A, Shaffer, L G, Andrieux, J, Marshall, C, Scherer, S W, Shen, Y, Gusella, J F, Thorsteinsdottir, U, Thorleifsson, G, Dermitzakis, E T, Deplancke, B, Beckmann, J S, Rougemont, J, Jacquemont, S, and Reymond, A
- Abstract
Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts’ maps could uncover functionally and clinically related genes.
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- 2017
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25. Breeding and yield stability of winter wheat
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Brancourt-Humel, M., Lecomte, C., Leleu, M., Berard, P., Galic, B., Sausseau, C., Unité de recherche Génétique et amélioration des plantes (GAP), Institut National de la Recherche Agronomique (INRA), UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité d'Amélioration des plantes (CL CLERMONT GENETQ), and Service d'expérimentation de La Minière
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variété botanique ,maladie ,RUSTICITE ,[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,blé ,analyse statistique ,triticum ,STABILITE ,sélection ,rendement ,Sciences agricoles ,Agricultural sciences - Abstract
Douze lignées de blé tendre en cours de sélection à l’INRA et 3 témoins ont été étudiés pour la stabilité du rendement dans le réseau multilocal INRA. Ce matériel a été évalué dans des dispositifs à 2 blocs randomisés, les parcelles élémentaires totalisant au moins 5,9 m2. Au total, 24 milieux diversifiés ont été étudiés durant les campagnes 1990-1991, 1991-1992 et 1992-1993. Le facteur milieu a été défini par la combinaison des niveaux des facteurs lieu, mode cultural et année. Dans chaque milieu, une description biologique a été réalisée pendant les phases de mise en place du nombre de grains par m2 et de remplissage du grain. L’analyse de la stabilité a pris en compte sous forme de covariables les caractéristiques du milieu définies au cours de la description précédente et a permis ainsi de constater que le comportement des génotypes se différencie uniquement pendant le remplissage. Par ailleurs, les 2 modèles d’analyse de l’interaction, régression conjointe et régression factorielle, ont permis de préciser que le comportement des lignées INRA est bien différent de celui des témoins. En effet, les génotypes sélectionnés à Rennes sont, à l’inverse des témoins, les plus résistants aux conditions défavorables de milieu. Deux autres lignées sélectionnées à Clermont-Ferrand et à Estrées-Mons sont à la fois productives et stables, présentant une bonne adaptabilité générale et un assez bon niveau de résistance aux conditions défavorables de milieu, ce qui laisse présager qu’il est possible d’associer rusticité et productivité en sélection., The yield stability of 12 lines of winter wheat bred by INRA (Institut National de Recherche Agronomique) and 3 controls has been studied in the INRA network. The material was evaluated in randomized 2-block designs, elementary plots measuring at least 5.9 m2. Twenty-four various environments have been studied over 3 seasons: 1990-1991, 1991-1992 and 1992-1993. They are combinations of levels of 3 factors: location, condition and year. Each environment has been biologically described during the period of the establishment of the number of grains per square meter and the grain-filling period. The analysis of stability included environmental characteristics as covariates. These were defined in a previous description and showed that the genotypes only behaved in a different way during the grain-filling period. In addition, the 2 models used for the analysis of interaction, joint regression and factorial regression showed that the behaviour of the INRA lines was quite different from that of controls. In contrast to controls, the genotypes selected in Rennes are the most resistant to unfavourable conditions of the environment. Two other entries, selected in Clermont-Ferrand and Estrées-Mons, are simultaneously productive, stable, with good general adaptability and a rather good resistance to unfavourable conditions of environment, which indicates that it is possible to associate hardiness and yield potential in a breeding programme.
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- 1994
26. Selection et stabilite du rendement chez le ble tendre d'hiver
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Brancourt-Humel, M., Lecomte, C., Leleu, M., Bérard, Pierre Antoine, Galic, B., Sausseau, C., Unité de recherche Génétique et amélioration des plantes (GAP), Institut National de la Recherche Agronomique (INRA), UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité d'Amélioration des plantes (CL CLERMONT GENETQ), and Service d'expérimentation de La Minière
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RUSTICITE ,[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,STABILITE - Abstract
National audience; The yield stability of 12 lines of winter wheat bred by INRA (Institut National de Recherche Agronomique) and 3 controls has been studied in the INRA network. The material was evaluated in randomized 2-block designs, elementary plots measuring at least 5.9 m2. Twenty-four various environments have been studied over 3 seasons: 1990-1991, 1991-1992 and 1992-1993. They are combinations of levels of 3 factors: location, condition and year. Each environment has been biologically described during the period of the establishment of the number of grains per square meter and the grain-filling period. The analysis of stability included environmental characteristics as covariates. These were defined in a previous description and showed that the genotypes only behaved in a different way during the grain-filling period. In addition, the 2 models used for the analysis of interaction, joint regression and factorial regression showed that the behaviour of the INRA lines was quite different from that of controls. In contrast to controls, the genotypes selected in Rennes are the most resistant to unfavourable conditions of the environment. Two other entries, selected in Clermont-Ferrand and Estrées-Mons, are simultaneously productive, stable, with good general adaptability and a rather good resistance to unfavourable conditions of environment, which indicates that it is possible to associate hardiness and yield potential in a breeding programme.; Douze lignées de blé tendre en cours de sélection à l’INRA et 3 témoins ont été étudiés pour la stabilité du rendement dans le réseau multilocal INRA. Ce matériel a été évalué dans des dispositifs à 2 blocs randomisés, les parcelles élémentaires totalisant au moins 5,9 m2. Au total, 24 milieux diversifiés ont été étudiés durant les campagnes 1990-1991, 1991-1992 et 1992-1993. Le facteur milieu a été défini par la combinaison des niveaux des facteurs lieu, mode cultural et année. Dans chaque milieu, une description biologique a été réalisée pendant les phases de mise en place du nombre de grains par m2 et de remplissage du grain. L’analyse de la stabilité a pris en compte sous forme de covariables les caractéristiques du milieu définies au cours de la description précédente et a permis ainsi de constater que le comportement des génotypes se différencie uniquement pendant le remplissage. Par ailleurs, les 2 modèles d’analyse de l’interaction, régression conjointe et régression factorielle, ont permis de préciser que le comportement des lignées INRA est bien différent de celui des témoins. En effet, les génotypes sélectionnés à Rennes sont, à l’inverse des témoins, les plus résistants aux conditions défavorables de milieu. Deux autres lignées sélectionnées à Clermont-Ferrand et à Estrées-Mons sont à la fois productives et stables, présentant une bonne adaptabilité générale et un assez bon niveau de résistance aux conditions défavorables de milieu, ce qui laisse présager qu’il est possible d’associer rusticité et productivité en sélection.
- Published
- 1994
27. Processing and analyzing ChIP-seq data: from short reads to regulatory interactions
- Author
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Leleu, M., primary, Lefebvre, G., additional, and Rougemont, J., additional
- Published
- 2010
- Full Text
- View/download PDF
28. Interaction between cultivar and crop management effects on winter wheat diseases, lodging, and yield
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Loyce, C., primary, Meynard, J.M., additional, Bouchard, C., additional, Rolland, B., additional, Lonnet, P., additional, Bataillon, P., additional, Bernicot, M.H., additional, Bonnefoy, M., additional, Charrier, X., additional, Debote, B., additional, Demarquet, T., additional, Duperrier, B., additional, Félix, I., additional, Heddadj, D., additional, Leblanc, O., additional, Leleu, M., additional, Mangin, P., additional, Méausoone, M., additional, and Doussinault, G., additional
- Published
- 2008
- Full Text
- View/download PDF
29. USE OF MICROARRAYS AND IMMUNOHISTOCHEMISTRY TO INVESTIGATE ACCELERATED ATHEROSCLEROSIS IN HUMAN GRAFT CORONARY ARTERY DISEASE
- Author
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Rousoulieres, A., primary, Collot-Teixeira, S., additional, Chalabreysse, L., additional, Morser, K., additional, McDermott-Roe, C., additional, Yilmaz, S., additional, Leleu, M., additional, De Lorenzo, F., additional, Guzman, A., additional, Michel, J.B., additional, Sebbag, L., additional, Boissonnat, P., additional, Thivolet-Bejui, F., additional, and McGregor, J.L., additional
- Published
- 2008
- Full Text
- View/download PDF
30. Secrétaires assistantes en santé travail : parties prenantes dans l’actionpluridisciplinaire
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André, C., primary, Hoffmann, C., additional, Devouge, I., additional, Leleu, M., additional, and Renaud, L., additional
- Published
- 2006
- Full Text
- View/download PDF
31. S?lection et stabilit? du rendement chez le bl? tendre d'hiver
- Author
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Brancourt-Hulmel, M., Lecomte, C., Leleu, M., B?rard, P., Galic, N., Trouv?, B., and Sausseau, C.
- Abstract
Douze lign?es de bl? tendre en cours de s?lection ? l'INRA et 3 t?moins ont ?t? ?tudi?s pour la stabilit? du rendement dans le r?seau multilocal INRA. Ce mat?riel a ?t? ?valu? dans des dispositifs ? 2 blocs randomis?s, les parcelles ?l?mentaires totalisant au moins 5,9 m2. Au total, 24 milieux diversifi?s ont ?t? ?tudi?s durant les campagnes 1990-1991, 1991-1992 et 1992-1993. Le facteur milieu a ?t? d?fini par la combinaison des niveaux des facteurs lieu, mode cultural et ann?e. Dans chaque milieu, une description biologique a ?t? r?alis?e pendant les phases de mise en place du nombre de grains par m2et de remplissage du grain. L'analyse de la stabilit? a pris en compte sous forme de covariables les caract?ristiques du milieu d?finies au cours de la description pr?c?dente et a permis ainsi de constater que le comportement des g?notypes se diff?rencie uniquement pendant le remplissage. Par ailleurs, les 2 mod?les d'analyse de l'interaction, r?gression conjointe et r?gression factorielle, ont permis de pr?ciser que le comportement des lign?es INRA est bien diff?rent de celui des t?moins. En effet, les g?notypes s?lectionn?s ? Rennes sont, ? l'inverse des t?moins, les plus r?sistants aux conditions d?favorables de milieu. Deux autres lign?es s?lectionn?es ? Clermont-Ferrand et ? Estr?es-Mons sont ? la fois productives et stables, pr?sentant une bonne adaptabilit? g?n?rale et un assez bon niveau de r?sistance aux conditions d?favorables de milieu, ce qui laisse pr?sager qu'il est possible d'associer rusticit? et productivit? en s?lection. Breeding and yield stability of winter wheat. The yield stability of 12 lines of winter wheat bred by INRA (Institut National de Recherche Agronomique) and 3 controls has been studied in the INRA network. The material was evaluated in randomized 2-block designs, elementary plots measuring at least 5.9 m2. Twenty-four various environments have been studied over 3 seasons: 1990-1991, 1991-1992 and 1992-1993. They are combinations of levels of 3 factors: location, condition and year. Each environment has been biologically described during the period of the establishment of the number of grains per square meter and the grain-filling period. The analysis of stability included environmental characteristics as covariates. These were defined in a previous description and showed that the genotypes only behaved in a different way during the grain-filling period. In addition, the 2 models used for the analysis of interaction, joint regression and factorial regression showed that the behaviour of the INRA lines was quite different from that of controls. In contrast to controls, the genotypes selected in Rennes are the most resistant to unfavourable conditions of the environment. Two other entries, selected in Clermont-Ferrand and Estr?es-Mons, are simultaneously productive, stable, with good general adaptability and a rather good resistance to unfavourable conditions of environment, which indicates that it is possible to associate hardiness and yield potential in a breeding programme.
- Published
- 1994
- Full Text
- View/download PDF
32. T cell receptor signaling controls Foxp3 expression via PI3K, Akt, and mTOR
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Sauer, S, Bruno, L, Hertweck, A, Finlay, D, Leleu, M, Spivakov, M, Knight, Z A, Cobb, B S, Cantrell, D, O'Connor, E, Shokat, K M, Fisher, A G, Merkenschlager, M, California, Dundee, and Imperial College London
33. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes
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Loviglio, M N, Leleu, M, Männik, K, Passeggeri, M, Giannuzzi, G, Van Der Werf, I, Waszak, S M, Zazhytska, M, Roberts-Caldeira, I, Gheldof, N, Migliavacca, E, Alfaiz, A A, Hippolyte, L, Maillard, A M, Loviglio, Maria Nicla, Männik, Katrin, Van Der Werf, Ilse, Giannuzzi, Giuliana, Zazhytska, Marianna, Gheldof, Nele, Migliavacca, Eugenia, Alfaiz, Ali A, Roberts-Caldeira, Inês, Hippolyte, Loyse, Maillard, Anne M, Ferrarini, Alessandra, Butschi, Florence Niel, Conrad, Bernard, Addor, Marie-Claude, Belfiore, Marco, Roetzer, Katharina, Dijck, Anke Van, Blaumeiser, Bettina, Kooy, Frank, Roelens, Filip, Dheedene, Annelies, Chiaie, Barbara Delle, Menten, Björn, Oostra, Ann, Caberg, Jean-Hubert, Carter, Melissa, Kellam, Barbara, Stavropoulos, Dimitri J, Marshall, Christian, Scherer, Stephen W, Weksberg, Rosanna, Cytrynbaum, Cheryl, Bassett, Anne, Lowther, Chelsea, Gillis, Jane, Mackay, Sara, Bache, Iben, Ousager, Lilian B, Smerdel, Maja Patricia, Graakjaer, Jesper, Kjaergaard, Susanne, Metspalu, Andres, Mathieu, Michele, Bonneau, Dominique, Guichet, Agnes, Parent, Philippe, Férec, Claude, Gerard, Marion, Plessis, Ghislaine, Lespinasse, James, Masurel, Alice, Marle, Nathalie, Faivre, Laurence, Callier, Patrick, Layet, Valerie, Meur, Nathalie Le, Le Goff, Céline, Duban-Bedu, Bénédicte, Sukno, Sylvie, Boute, Odile, Andrieux, Joris, Blanchet, Patricia, Geneviève, David, Puechberty, Jacques, Schneider, Anouck, Leheup, Bruno, Jonveaux, Philippe, Mercier, Sandra, David, Albert, Le Caignec, Cédric, De Pontual, Loic, Pipiras, Eva, Jacquette, Aurelia, Keren, Boris, Gilbert-Dussardier, Brigitte, Bilan, Frederic, Goldenberg, Alice, Chambon, Pascal, Toutain, Annick, Till, Marianne, Sanlaville, Damien, Leube, Barbara, Royer-Pokora, Brigitte, Grabe, Hans Jörgen, Schmidt, Carsten Oliver, Schurmann, Claudia, Homuth, Georg, Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Bernardini, Laura, Novelli, Antonio, Micale, Lucia, Merla, Giuseppe, Zollino, Marcella, Mari, Francesca, Rizzo, Caterina Lo, Renieri, Alessandra, Silengo, Margherita, Vulto-Van Silfhout, Anneke T, Schouten, Meyke, Pfundt, Rolph, De Leeuw, Nicole, Vansenne, Fleur, Maas, Saskia M, Barge-Schaapveld, Daniela Qcm, Knegt, Alida C, Stadheim, Barbro, Rodningen, Olaug, Houge, Gunnar, Price, Sue, Hawkes, Lara, Campbell, Carolyn, Kini, Usha, Vogt, Julie, Walters, Robin, Blakemore, Alexandra, Gusella, James F, Shen, Yiping, Scott, Daryl, Bacino, Carlos A, Tsuchiya, Karen, Ladda, Roger, Sell, Susan, Asamoah, Alexander, Hamati, Aline I, Rosenfeld, Jill A, Shaffer, Lisa G, Mitchell, Elyse, Hodge, Jennelle C, Beckmann, Jacques S, Jacquemont, Sébastien, Reymond, Alexandre, Ewans, Lisa J, Mowat, David, Walker, Jan, Amor, David J, Esch, Hilde Van, Leroy, Patricia, Bamforth, John-Steven, Babu, Deepti, Isidor, Bertrand, Didonato, Nataliya, Hackmann, Karl, Passeggeri, Marzia, Haeringen, Arie Van, Smith, Rosemarie, Ellingwood, Sara, Farber, Darren M, Puri, Vinay, Zadeh, Neda, Weaver, David D, Miller, Mandy, Wilks, Timothy, Jorgez, Carolina J, Lafayette, Deedee, Van Dijck, A, Kooy, R F, Sanlaville, D, Rosenfeld, J A, Shaffer, L G, Andrieux, J, Marshall, C, Scherer, S W, Shen, Y, Gusella, J F, Thorsteinsdottir, U, Thorleifsson, G, Dermitzakis, E T, Deplancke, B, Beckmann, J S, Rougemont, J, Jacquemont, S, Reymond, A, 2p15 Consortium, and 16p11 2 Consortium
- Abstract
Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts’ maps could uncover functionally and clinically related genes.
34. AMPK promotes survival of c-Myc-positive melanoma cells by suppressing oxidative stress
- Author
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Kfoury, A, Armaro, M, Collodet, C, Sordet-Dessimoz, J, Giner, MP, Christen, S, Moco, S, Leleu, M, de Leval, L, Koch, U, Trumpp, A, Sakamoto, K, Beermann, F, and Radtke, F
35. REST selectively represses a subset of RE1-containing neuronal genes in mouse embryonic stem cells
- Author
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Jorgensen, H. F., Terry, A., Beretta, C., Pereira, C. F., Leleu, M., Chen, Z.-F., Kelly, C., Merkenschlager, M., and Fisher, A. G.
36. Runx proteins regulate Foxp3 expression
- Author
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Bruno, L, Mazzarella, L, Hoogenkamp, M, Hertweck, A, Cobb, B S, Sauer, S, Hadjur, S, Leleu, M, Naoe, Y, Telfer, J C, Bonifer, C, Taniuchi, L, Fisher, A G, Merkenschlager, M, Imperial College London, Inst of Physical & Chemical Research...., Japan, Japan Science And Technology Agency, Leeds, and Massachusetts
37. Atmogeochemistry applied to mineral prospecting.
- Author
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Degranges P., Baubron J.C., Leleu M., Degranges P., Baubron J.C., and Leleu M.
- Abstract
Considerable progress has been made over the last few years in the field of atmogeochemistry applied to prospecting for deep or concealed deposits, altered or in the process of alteration. Volatile or gaseous elements associated with deposits are generally of the following groups: gases directly associated with primary ore genesis (halogens, CO2); gases formed by supergene alteration (sulphur gases) or secondary reactions with the host rock (CO2 in carbonate environments); and solid or liquid components of the deposit which are volatile under certain thermodynamic conditions (Hg, I, As). Methods of soil analysis for these pathfinder elements and techniques used by BRGM including mercurometry and in situ analysis of soil gases are described., Considerable progress has been made over the last few years in the field of atmogeochemistry applied to prospecting for deep or concealed deposits, altered or in the process of alteration. Volatile or gaseous elements associated with deposits are generally of the following groups: gases directly associated with primary ore genesis (halogens, CO2); gases formed by supergene alteration (sulphur gases) or secondary reactions with the host rock (CO2 in carbonate environments); and solid or liquid components of the deposit which are volatile under certain thermodynamic conditions (Hg, I, As). Methods of soil analysis for these pathfinder elements and techniques used by BRGM including mercurometry and in situ analysis of soil gases are described.
38. Hydrogeochemistry in the zinc—lead mining district of “Les Malines” (Gard, France)
- Author
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Bosch, B., primary, Leleu, M., additional, Oustrière, P., additional, Sarcia, C., additional, Sureau, J-F., additional, Blommaert, W., additional, Gijbels, R., additional, Sadurski, A., additional, Vandelannoote, R., additional, Van Grieken, R., additional, and Van 'T Dack, L., additional
- Published
- 1986
- Full Text
- View/download PDF
39. Essais de visualisation in situ de certains types d'écoulements dphasiques en milieux poreux
- Author
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Martin, J. -M., primary, Crouzil, G., additional, Leleu, M., additional, and Combarnous, M., additional
- Published
- 1975
- Full Text
- View/download PDF
40. Trace-elemental anomalies in surface water near a small lead-zinc mineralization at Menez-Albot (Brittany, France)
- Author
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Vandelannoote, R., primary, Blommaert, W., additional, Sadurski, A., additional, Van 'T Dack, L., additional, Gijbels, R., additional, Van Grieken, R., additional, Bosch, B., additional, Leleu, M., additional, Rochon, J., additional, Sarcia, C., additional, and Sureau, J.F., additional
- Published
- 1984
- Full Text
- View/download PDF
41. Geological applications of the laser probe mass spectrometer (L.P.M.S.II)
- Author
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Eloy, J.F., primary, Leleu, M., additional, and Unsöld, E., additional
- Published
- 1983
- Full Text
- View/download PDF
42. The geothermal zone of lake Assal (F.T.A.I.), geochemical and experimental studies
- Author
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Bosch, B., primary, Deschamps, J., additional, Leleu, M., additional, Lopoukhine, M., additional, Marce, A., additional, and Vilbert, C., additional
- Published
- 1977
- Full Text
- View/download PDF
43. Note preliminaire sur le comportement des elements Cu, Pb, Zn, Ag, Mn, As, Bi, lors de l'alteration supergene d'une mineralisation sulfuree
- Author
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Laville-Timsit, L., primary, Leleu, M., primary, and Wilhelm, E., primary
- Published
- 1976
- Full Text
- View/download PDF
44. Pseudo-iron deficiency in a French population living near high-voltage transmission lines: a dilemma for clinicians
- Author
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Hachulla, E., Caulier-Leleu, M. T., Fontaine, O., Mehianoui, L., and Pelerin, P.
- Published
- 2000
- Full Text
- View/download PDF
45. Corrigendum to `Pseudo-iron deficiency in a French population living near high-voltage transmission lines: a dilemma for clinicians`
- Author
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Hachulla, E., Caulier-Leleu, M. T., Fontaine, O., Mehianoui, L., and Pelerin, P.
- Published
- 2001
- Full Text
- View/download PDF
46. Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock
- Author
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Bart Deplancke, Frédéric Schütz, Nouria Hernandez, Federica Gilardi, Nicolas GUEX, Leonor Rib, Ian Willis, Beatrice Desvergne, CycliX Consortium, Hernandez, N., Delorenzi, M., Deplancke, B., Desvergne, B., Guex, N., Herr, W., Naef, F., Rougemont, J., Schibler, U., Andersin, T., Cousin, P., Gilardi, F., Lammers, F., Mange, F., Villeneuve, D., David, F., Fabbretti, R., Jacquet, P., Krier, I., Kuznetsov, D., Leleu, M., Liechti, R., Martin, O., Migliavacca, E., Naldi, A., Praz, V., Rib, L., Sobel, J., Vlegel, V., and Xenarios, I.
- Subjects
0301 basic medicine ,Transcription, Genetic ,Circadian clock ,ARNTL Transcription Factors/deficiency ,ARNTL Transcription Factors/genetics ,Animals ,Circadian Clocks/genetics ,Circadian Rhythm/genetics ,Eating/genetics ,Fasting/metabolism ,Gene Expression Profiling ,Gene Expression Regulation ,Liver/metabolism ,Mice ,Mice, Knockout ,Oligonucleotide Array Sequence Analysis ,Protein Binding ,RNA Polymerase III/genetics ,RNA Polymerase III/metabolism ,Repressor Proteins/deficiency ,Repressor Proteins/genetics ,Signal Transduction ,Repressor ,Biology ,RNA polymerase III ,Eating ,03 medical and health sciences ,0302 clinical medicine ,Transcription (biology) ,Circadian Clocks ,Gene expression ,Genetics ,Circadian rhythm ,Genetics (clinical) ,Regulation of gene expression ,Research ,ARNTL Transcription Factors ,RNA Polymerase III ,Fasting ,Circadian Rhythm ,Cell biology ,Repressor Proteins ,ARNTL ,030104 developmental biology ,Liver ,030217 neurology & neurosurgery - Abstract
RNA polymerase III (Pol III) synthesizes short noncoding RNAs, many of which are essential for translation. Accordingly, Pol III activity is tightly regulated with cell growth and proliferation by factors such as MYC, RB1, TRP53, and MAF1. MAF1 is a repressor of Pol III transcription whose activity is controlled by phosphorylation; in particular, it is inactivated through phosphorylation by the TORC1 kinase complex, a sensor of nutrient availability. Pol III regulation is thus sensitive to environmental cues, yet a diurnal profile of Pol III transcription activity is so far lacking. Here, we first use gene expression arrays to measure mRNA accumulation during the diurnal cycle in the livers of (1) wild-type mice, (2) arrhythmic Arntl knockout mice, (3) mice fed at regular intervals during both night and day, and (4) mice lacking the Maf1 gene, and so provide a comprehensive view of the changes in cyclic mRNA accumulation occurring in these different systems. We then show that Pol III occupancy of its target genes rises before the onset of the night, stays high during the night, when mice normally ingest food and when translation is known to be increased, and decreases in daytime. Whereas higher Pol III occupancy during the night reflects a MAF1-dependent response to feeding, the rise of Pol III occupancy before the onset of the night reflects a circadian clock-dependent response. Thus, Pol III transcription during the diurnal cycle is regulated both in response to nutrients and by the circadian clock, which allows anticipatory Pol III transcription.
- Published
- 2017
47. Differential regulation of RNA polymerase III genes during liver regeneration
- Author
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Meghdad Yeganeh, Cristian Carmeli, Dominic Villeneuve, Mauro Delorenzi, Winship Herr, Leonor Rib, Nouria Hernandez, Viviane Praz, Nicolas Guex, CycliX consortium, Hernandez, N., Delorenzi, M., Deplancke, B., Desvergne, B., Guex, N., Herr, W., Naef, F., Rougemont, J., Schibler, U., Andersin, T., Cousin, P., Gilardi, F., Gos, P., Lammers, F., Lopes, M., Mange, F., Minocha, S., Raghav, S., Villeneuve, D., Fabbretti, R., Vlegel, V., Xenarios, I., Migliavacca, E., Praz, V., David, F., Jarosz, Y., Kuznetsov, D., Liechti, R., Martin, O., Delafontaine, J., Cajan, J., Carmeli, C., Gustafson, K., Krier, I., Leleu, M., Molina, N., Naldi, A., Rib, L., Sobel, J., Symul, L., Bounova, G., and Jacquet, P.
- Subjects
Chromatin Immunoprecipitation ,Transcription, Genetic ,DNA polymerase ,DNA polymerase II ,viruses ,RNA polymerase II ,RNA polymerase III ,Histones ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Transcription (biology) ,Genetics ,Animals ,Hepatectomy ,Humans ,Gene ,030304 developmental biology ,0303 health sciences ,biology ,Cell Cycle ,Gene regulation, Chromatin and Epigenetics ,Gene Expression Regulation, Developmental ,RNA Polymerase III ,Histone-Lysine N-Methyltransferase ,Liver regeneration ,Liver Regeneration ,Housekeeping gene ,Cell biology ,Liver ,biology.protein ,RNA Polymerase II ,Cell Division ,030217 neurology & neurosurgery ,Protein Binding - Abstract
Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcription. Our results broadly define a class of genes close to H3K4me3 and Pol II peaks, whose Pol III occupancy is high and stable, and another class, distant from Pol II peaks, whose Pol III occupancy strongly increases after partial hepatectomy. Pol III regulation in the liver thus entails both highly expressed housekeeping genes and genes whose expression can adapt to increased demand.
- Published
- 2019
48. A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver
- Author
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Mauro Delorenzi, Irina Krier, Teemu Andersin, Li Long, Nicolas Guex, Arnaud Fortier, David Bernasconi, Marion Leleu, Guillaume Rey, Julia Cajan, Fabrice P. A. David, Winship Herr, Fabienne Lammers, Sunil K. Raghav, Olivier Martin, Jacques Rougemont, Aurélien Naldi, Roberto Fabbretti, Eugenia Migliavacca, Pascal Gos, Viviane Praz, Robin Liechti, Ueli Schibler, Gwendal LeMartelot, Nouria Hernandez, Laura Symul, Pascal Cousin, Frederick J. Ross, Yohan Jarosz, Béatrice Desvergne, Donatella Canella, Nacho Molina, Ioannis Xenarios, Felix Naef, Lucas Sinclair, Volker Vlegel, Federica Gilardi, Gwendal Le Martelot, Bart Deplancke, Dmitry Kuznetsov, University of Zurich, Delorenzi, Mauro, CycliX Consortium, Hernandez, N., Delorenzi, M., Deplancke, B., Desvergne, B., Guex, N., Herr, W., Naef, F., Rougemont, J., Schibler, U., Andersin, T., Cousin, P., Gilardi, F., Gos, P., Le Martelot, G., Lammers, F., Canella, D., Raghav, S., Fabbretti, R., Fortier, A., Long, L., Vlegel, V., Xenarios, I., Migliavacca, E., Praz, V., David, F., Jarosz, Y., Kuznetsov, D., Liechti, R., Martin, O., Ross, F., Sinclair, L., Cajan, J., Krier, I., Leleu, M., Molina, N., Naldi, A., Rey, G., Symul, L., and Bernasconi, D.
- Subjects
Male ,Chromatin Immunoprecipitation ,2716 Genetics (clinical) ,Pseudogene ,genetic processes ,Biology ,RNA polymerase III ,Mice ,chemistry.chemical_compound ,RNA, Transfer ,SX00 SystemsX.ch ,1311 Genetics ,Transcription (biology) ,RNA polymerase ,Gene expression ,Genetics ,Animals ,Humans ,SX04 CycliX ,Gene ,Genetics (clinical) ,Oligonucleotide Array Sequence Analysis ,Models, Genetic ,Gene Expression Profiling ,Research ,RNA Polymerase III ,RNA ,Genomics ,Sequence Analysis, DNA ,Molecular biology ,Mice, Inbred C57BL ,enzymes and coenzymes (carbohydrates) ,Liver ,chemistry ,Transfer RNA ,570 Life sciences ,biology ,bacteria ,Chromatin Immunoprecipitation/methods ,Genomics/methods ,Liver/metabolism ,RNA Polymerase III/genetics ,RNA Polymerase III/metabolism ,RNA, Transfer/genetics ,RNA, Transfer/metabolism ,Sequence Analysis, DNA/methods - Abstract
The genomic loci occupied by RNA polymerase (RNAP) III have been characterized in human culture cells by genome-wide chromatin immunoprecipitations, followed by deep sequencing (ChIP-seq). These studies have shown that only ∼40% of the annotated 622 human tRNA genes and pseudogenes are occupied by RNAP-III, and that these genes are often in open chromatin regions rich in active RNAP-II transcription units. We have used ChIP-seq to characterize RNAP-III-occupied loci in a differentiated tissue, the mouse liver. Our studies define the mouse liver RNAP-III-occupied loci including a conserved mammalian interspersed repeat (MIR) as a potential regulator of an RNAP-III subunit-encoding gene. They reveal that synteny relationships can be established between a number of human and mouse RNAP-III genes, and that the expression levels of these genes are significantly linked. They establish that variations within the A and B promoter boxes, as well as the strength of the terminator sequence, can strongly affect RNAP-III occupancy of tRNA genes. They reveal correlations with various genomic features that explain the observed variation of 81% of tRNA scores. In mouse liver, loci represented in the NCBI37/mm9 genome assembly that are clearly occupied by RNAP-III comprise 50 Rn5s (5S RNA) genes, 14 known non-tRNA RNAP-III genes, nine Rn4.5s (4.5S RNA) genes, and 29 SINEs. Moreover, out of the 433 annotated tRNA genes, half are occupied by RNAP-III. Transfer RNA gene expression levels reflect both an underlying genomic organization conserved in dividing human culture cells and resting mouse liver cells, and the particular promoter and terminator strengths of individual genes.
- Published
- 2012
49. Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
- Author
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Bonhoure, Nicolas, Bounova, Gergana, Bernasconi, David, Praz, Viviane, Lammers, Fabienne, Canella, Donatella, Willis, Ian M., Herr, Winship, Hernandez, Nouria, Delorenzi, Mauro, Deplancke, Bart, Desvergne, Béatrice, Guex, Nicolas, Naef, Felix, Rougemont, Jacques, Schibler, Ueli, Andersin, Teemu, Cousin, Pascal, Gilardi, Federica, Gos, Pascal, Raghav, Sunil, Villeneuve, Dominic, Fabbretti, Roberto, Vlegel, Volker, Xenarios, Ioannis, Migliavacca, Eugenia, David, Fabrice, Jarosz, Yohan, Kuznetsov, Dmitry, Liechti, Robin, Martin, Olivier, Delafontaine, Julien, Cajan, Julia, Gustafson, Kyle, Krier, Irina, Leleu, Marion, Molina, Nacho, Naldi, Aurélien, Rib, Leonor, Symul, Laura, CycliX Consortium, Hernandez, N., Delorenzi, M., Deplancke, B., Desvergne, B., Guex, N., Herr, W., Naef, F., Rougemont, J., Schibler, U., Andersin, T., Cousin, P., Gilardi, F., Gos, P., Lammers, F., Raghav, S., Villeneuve, D., Fabbretti, R., Vlegel, V., Xenarios, I., Migliavacca, E., Praz, V., David, F., Jarosz, Y., Kuznetsov, D., Liechti, R., Martin, O., Delafontaine, J., Cajan, J., Gustafson, K., Krier, I., Leleu, M., Molina, N., Naldi, A., Rib, L., Symul, L., Bounova, G., University of Zurich, and Hernandez, N
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Quality Control ,Normalization (statistics) ,2716 Genetics (clinical) ,Chromatin Immunoprecipitation ,Occupancy ,SX20 Research, Technology and Development Projects ,Immunoprecipitation ,Sample (material) ,Method ,Biology ,Mice ,03 medical and health sciences ,0302 clinical medicine ,SX00 SystemsX.ch ,1311 Genetics ,Genetics ,Animals ,Humans ,Genetics(clinical) ,SX04 CycliX ,Genetics (clinical) ,030304 developmental biology ,Quantile normalization ,0303 health sciences ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,Reference Standards ,Chromatin ,570 Life sciences ,biology ,Spike (software development) ,Biological system ,Chromatin immunoprecipitation ,030217 neurology & neurosurgery - Abstract
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments are widely used to determine, within entire genomes, the occupancy sites of any protein of interest, including, for example, transcription factors, RNA polymerases, or histones with or without various modifications. In addition to allowing the determination of occupancy sites within one cell type and under one condition, this method allows, in principle, the establishment and comparison of occupancy maps in various cell types, tissues, and conditions. Such comparisons require, however, that samples be normalized. Widely used normalization methods that include a quantile normalization step perform well when factor occupancy varies at a subset of sites, but may miss uniform genome-wide increases or decreases in site occupancy. We describe a spike adjustment procedure (SAP) that, unlike commonly used normalization methods intervening at the analysis stage, entails an experimental step prior to immunoprecipitation. A constant, low amount from a single batch of chromatin of a foreign genome is added to the experimental chromatin. This “spike” chromatin then serves as an internal control to which the experimental signals can be adjusted. We show that the method improves similarity between replicates and reveals biological differences including global and largely uniform changes.
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- 2014
50. Rhythmic Changes in Gene Activation Power the Circadian Clock
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Gwendal Le Martelot, Donatella Canella, Laura Symul, Eugenia Migliavacca, Federica Gilardi, Robin Liechti, Olivier Martin, Keith Harshman, Mauro Delorenzi, Béatrice Desvergne, Winship Herr, Bart Deplancke, Ueli Schibler, Jacques Rougemont, Nicolas Guex, Nouria Hernandez, Felix Naef, CycliX Consortium, University of Zurich, Hernandez, Nouria, CycliX Consortium, Hernandez, N., Delorenzi, M., Deplancke, B., Desvergne, B., Guex, N., Herr, W., Naef, F., Rougemont, J., Schibler, U., Andersin, T., Cousin, P., Gilardi, F., Gos, P., Le Martelot, G., Lammers, F., Canella, D., Raghav, S., Fabbretti, R., Fortier, A., Long, L., Vlegel, V., Xenarios, I., Migliavacca, E., Praz, V., David, F., Jarosz, Y., Kuznetsov, D., Liechti, R., Martin, O., Delafontaine, J., Sinclair, L., Cajan, J., Krier, I., Leleu, M., Molina, N., Naldi, A., Rey, G., Symul, L., and Bernasconi, D.
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Male ,Time Factors ,Transcription, Genetic ,Circadian clock ,RNA polymerase II ,Biochemistry ,Epigenesis, Genetic ,Histones ,Mice ,0302 clinical medicine ,SX00 SystemsX.ch ,Transcription (biology) ,2400 General Immunology and Microbiology ,Gene expression ,Molecular Cell Biology ,Transcriptional regulation ,RNA Processing, Post-Transcriptional ,Biology (General) ,Promoter Regions, Genetic ,Regulation of gene expression ,Genetics ,0303 health sciences ,Reverse Transcriptase Polymerase Chain Reaction ,General Neuroscience ,Systems Biology ,2800 General Neuroscience ,Genomics ,Chromatin ,Circadian Rhythm ,Liver ,DNA methylation ,Synopsis ,RNA Polymerase II ,Transcription Initiation Site ,General Agricultural and Biological Sciences ,Half-Life ,Research Article ,Chromatin Immunoprecipitation ,SX20 Research, Technology and Development Projects ,QH301-705.5 ,E-box ,1100 General Agricultural and Biological Sciences ,Biology ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Rhythm ,1300 General Biochemistry, Genetics and Molecular Biology ,Animals ,Circadian rhythm ,RNA, Messenger ,SX04 CycliX ,Gene ,Post-transcriptional regulation ,030304 developmental biology ,Chromatin Assembly and Disassembly ,DNA Methylation ,Histones/genetics ,Histones/metabolism ,Kinetics ,Liver/cytology ,Liver/metabolism ,Mice, Inbred C57BL ,Models, Genetic ,RNA Polymerase II/genetics ,RNA Polymerase II/metabolism ,RNA, Messenger/analysis ,RNA, Messenger/metabolism ,Transcriptome ,General Immunology and Microbiology ,Computational Biology ,Promoter ,biology.protein ,570 Life sciences ,biology ,Chromatin immunoprecipitation ,Neuroscience ,030217 neurology & neurosurgery - Abstract
Genome-wide rhythms in RNA polymerase II loading and dynamic chromatin remodeling underlie periodic gene expression during diurnal cycles in the mouse liver., Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization of cell physiology in mammals. To understand the transcriptional and epigenetic basis of diurnal rhythms in mouse liver genome-wide, we generated temporal DNA occupancy profiles by RNA polymerase II (Pol II) as well as profiles of the histone modifications H3K4me3 and H3K36me3. We used these data to quantify the relationships of phases and amplitudes between different marks. We found that rhythmic Pol II recruitment at promoters rather than rhythmic transition from paused to productive elongation underlies diurnal gene transcription, a conclusion further supported by modeling. Moreover, Pol II occupancy preceded mRNA accumulation by 3 hours, consistent with mRNA half-lives. Both methylation marks showed that the epigenetic landscape is highly dynamic and globally remodeled during the 24-hour cycle. While promoters of transcribed genes had tri-methylated H3K4 even at their trough activity times, tri-methylation levels reached their peak, on average, 1 hour after Pol II. Meanwhile, rhythms in tri-methylation of H3K36 lagged transcription by 3 hours. Finally, modeling profiles of Pol II occupancy and mRNA accumulation identified three classes of genes: one showing rhythmicity both in transcriptional and mRNA accumulation, a second class with rhythmic transcription but flat mRNA levels, and a third with constant transcription but rhythmic mRNAs. The latter class emphasizes widespread temporally gated posttranscriptional regulation in the mouse liver., Author Summary In mammalian organs such as the liver, many metabolic and physiological processes occur preferentially at specific times during the 24-hour daily cycle. The timing of these rhythmic functions depends on a complex interplay between the endogenous circadian clock and environmental timing cues relayed through the master circadian clock in the suprachiasmatic nucleus, or via feeding rhythms. These rhythms can be implemented on several regulatory levels, and here we aimed at a better understanding of the transcriptional and epigenetic changes that regulate diurnal rhythms. We performed genome-wide analysis of the locations of RNA polymerase II (Pol II) and the epigenetic histone modifications H3K4me3 and H3K36me3 at specific times of day, relating these data to mRNA expression levels. Our analyses show that Pol II transcriptional rhythms are biphasic in mouse liver, having predominant peak activities in the morning and evening. Moreover, dynamic changes in histone marks lag transcription rhythms genome-wide, indicating that the epigenetic landscape can be remodeled during the 24-hour cycle. Finally, a quantitative analysis of temporal Pol II and mRNA accumulation profiles indicates that posttranscriptional regulation significantly contributes to the amplitude and phase of mRNA accumulation profiles. While many studies have analyzed how transcription and chromatin states are modified during irreversible cell differentiation processes, our work highlights how these states can evolve reversibly in a system exhibiting periodicity in time.
- Published
- 2012
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