ZFIN ID: ZDB-PERS-960805-277
Joly, Jean-Stephane
Email: joly@inaf.cnrs-gif.fr
URL: https://tps.tefor.net/
Affiliation: Team Neuro-Infection and Immunity
and also: TEFOR Paris-Saclay
Address: UMS TEFOR Paris-Saclay – CNRS UMS2010 / INRA UMS1451 Paris-Saclay University Bat 32, 1 Avenue de la Terrasse 91190 Gif-sur-Yvette France
Country: France
Phone: (+33) 1 69 82 41 28

As part of the TEFOR infrastructure, UMS TEFOR Paris-Saclay CNRS UMS2010 / INRA UMS1451 (UMS TPS) conducts genome editing and phenotyping programs in zebrafish, particularly at larval stages and in the adult brain.

UMS TPS is dedicated to Research and Development of new techniques in the field of genome editing and fluorescence microscopy :
- Genome editing : UMS TPS works with the TACGENE platform on base editing, a targeted and fine edition of the genome.
- Phenotyping : UMS TPS conducts programs to optimize microscopy tools and methodologies, and develops collections of optimal 3D images and navigation tools in these databases.

In order to offer a complete and innovative range of services, UMS TPS coordinates a network of expert centres: a consortium of laboratories and partner platforms experts in fish models whose complementary activities best meet the needs of the scientific community. This way, UMS TPS wishes to help the users in defining the scientific project and relieve them of administrative processes that can be heavy, acting as the main point of contact and support.

Through the creation of the EFOR network (network of functional studies in model organisms), UMS TPS also aims to support and increase the visibility of research projects using model organisms. By developing the accumulated knowledge of the different model organisms and creating spaces for discussion on bioethical issues, EFOR aims to be in line with the 3Rs principles : Reduce, Refine, Replace.

Lempereur, S., Machado, E., Licata, F., Simion, M., Buzer, L., Robineau, I., Hémon, J., Banerjee, P., De Crozé, N., Léonard, M., Affaticati, P., Talbot, H., Joly, J.S. (2022) ZeBraInspector, a platform for the automated segmentation and analysis of body and brain volumes in whole 5 days post-fertilization zebrafish following simultaneous visualization with identical orientations. Developmental Biology. 490:86-99
Banerjee, P., Joly, P., Jouneau, L., Jaszczyszyn, Y., Bourge, M., Affaticati, P., Levraud, J.P., Boudinot, P., Joly, J.S. (2022) Molecular and Cellular Analysis of the Repair of Zebrafish Optic Tectum Meninges Following Laser Injury. Cells. 11(13)
Lindsey, B.W., Hall, Z.J., Heuzé, A., Joly, J.S., Tropepe, V., Kaslin, J. (2018) The role of neuro-epithelial-like and radial-glial stem and progenitor cells in development, plasticity, and repair. Prog. Neurobiol.. 170:99-114
Bouffard, S., Dambroise, E., Brombin, A., Lempereur, S., Hatin, I., Simion, M., Corre, R., Bourrat, F., Joly, J.S., Jamen, F. (2018) Fibrillarin is essential for S-phase progression and neuronal differentiation in zebrafish dorsal midbrain and retina. Developmental Biology. 437(1):1-16
Affaticati, P., Simion, M., De Job, E., Rivière, L., Hermel, J.M., Machado, E., Joly, J.S., Jenett, A. (2017) zPACT: Tissue Clearing and Immunohistochemistry on Juvenile Zebrafish Brain. Bio-protocol. 7:e2636
Passoni, G., Langevin, C., Palha, N., Mounce, B.C., Briolat, V., Affaticati, P., De Job, E., Joly, J.S., Vignuzzi, M., Saleh, M.C., Herbomel, P., Boudinot, P., Levraud, J.P. (2017) Imaging of viral neuroinvasion in the zebrafish reveals that Sindbis and chikungunya viruses favour different entry routes. Disease models & mechanisms. 10(7):847-857
Frétaud, M., Rivière, L., Job, É., Gay, S., Lareyre, J.J., Joly, J.S., Affaticati, P., Thermes, V. (2017) High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis. Scientific Reports. 7:43012
Benítez-Santana, T., Simion, M., Orraze, G., Médale, F., Joly, J.S. (2017) Effect of nutrient availability on progenitor cells in zebrafish (Danio rerio). Developmental Neurobiology. 77(1):26-38
Mayrhofer, M., Gourain, V., Reischl, M., Affaticati, P., Jenett, A., Joly, J.S., Benelli, M., Demichelis, F., Poliani, P.L., Sieger, D., Mione, M. (2017) A novel brain tumour model in zebrafish reveals the role of YAP activation in MAPK/PI3K induced malignant growth. Disease models & mechanisms. 10(1):15-28
Haeussler, M., Schönig, K., Eckert, H., Eschstruth, A., Mianné, J., Renaud, J.B., Schneider-Maunoury, S., Shkumatava, A., Teboul, L., Kent, J., Joly, J.S., Concordet, J.P. (2016) Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome biology. 17:148
Dambroise, E., Monnier, L., Ruisheng, L., Aguilaniu, H., Joly, J.S., Tricoire, H., Rera, M. (2016) Two phases of aging separated by the Smurf transition as a public path to death. Scientific Reports. 6:23523
Radev, Z., Hermel, J.M., Elipot, Y., Bretaud, S., Arnould, S., Duchateau, P., Ruggiero, F., Joly, J.S., Sohm, F. (2015) A TALEN-Exon Skipping Design for a Bethlem Myopathy Model in Zebrafish. PLoS One. 10:e0133986
Recher, G., Jouralet, J., Brombin, A., Heuzé, A., Mugniery, E., Hermel, J.M., Desnoulez, S., Savy, T., Herbomel, P., Bourrat, F., Peyriéras, N., Jamen, F., and Joly, J.S. (2013) Zebrafish midbrain slow-amplifying progenitors exhibit high levels of transcripts for nucleotide and ribosome biogenesis. Development (Cambridge, England). 140(24):4860-9
Gautier, A., Sohm, F., Joly, J.S., Le Gac, F., and Lareyre, J.J. (2011) The Proximal Promoter Region of the Zebrafish gsdf Gene Is Sufficient to Mimic the Spatio-Temporal Expression Pattern of the Endogenous Gene in Sertoli and Granulosa Cells. Biology of reproduction. 85(6):1240-51
Gibert, Y., Bernard, L., Debiais-Thibaud, M., Bourrat, F., Joly, J.S., Pottin, K., Meyer, A., Retaux, S., Stock, D.W., Jackman, W.R., Seritrakul, P., Begemann, G., and Laudet, V. (2010) Formation of oral and pharyngeal dentition in teleosts depends on differential recruitment of retinoic acid signaling. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 24(9):3298-3309
Grabher, C., Joly, J.S., and Wittbrodt, J. (2004) Highly efficient zebrafish transgenesis mediated by the meganuclease I-SceI. The Zebrafish: Genetics, Genomics and Informatics, 2nd ed., Methods Cell Biol.. 77:381-401
Thermes, V., Grabher, C., Ristoratore, F., Bourrat, F., Choulika, A., Wittbrodt, J., and Joly, J.S. (2002) I-SceI meganuclease mediates highly efficient transgenesis in fish. Mechanisms of Development. 118(1-2):91-98
Deschet, K., Thermes, V., and Joly, J.S. (2001) The transgenesis among the fishes. Bull. Soc. Zool. France. 126(3):255-268
Deschet, K., Bourrat, F., Ristoratore, F., Chourrout, D., and Joly, J.S. (1999) Expression of the medaka (Oryzias latipes) Ol-Rx3 paired-like gene in two diencephalic derivatives, the eye and the hypothalamus. Mechanisms of Development. 83(1-2):179-182
Postlethwait, J.H, Yan, Y.-L., Gates, M.A., Horne, S., Amores, A., Brownlie, A., Donovan, A., Egan, E.S., Force, A., Gong, Z., Goutel, C., Fritz, A., Kelsh, R., Knapik, E., Liao, E., Paw, B., Ransom, D., Singer, A., Thomson, M., Abduljabbar, T.S., Yelick, P., Beier, D., Joly, J.-S., Larhammar, D., Rosa, F., Westerfield, M., Zon, L.I., Johnson, S.L., and Talbot, W.S. (1998) Vertebrate genome evolution and the zebrafish gene map. Nature Genetics. 18:345-349
Barro, O., Vriz, S., Joly, J.S., Joly, C., Condamine, H., and Boulekbache, H. (1995) Widespread expression of the eve1 gene in zebrafish embryos affects the anterior-posterior axis pattern. Developmental genetics. 17:117-128
Joly, J.S., Joly, C., Schulte-Merker, S., Boulekbache, H., and Condamine, H. (1993) The ventral and posterior expression of the zebrafish homeobox gene eve1 is perturbed in dorsalized and mutant embryos. Development (Cambridge, England). 119:1261-1275
Joly, J.S., Maury, M., Joly, C., and Boulekbache, H. (1993) Ventral and posterior expression of the homeobox gene eve1 in zebrafish (Brachydanio rerio) is repressed in dorsalized embryos. Comptes rendus des seances de la Societe de biologie et de ses filiales. 187:356-363
Joly, J.S., Maury, M., Joly, C., Duprey, P., Boulekbache, H., and Condamine, H. (1992) Expression of a zebrafish caudal homeobox gene correlates with the establishment of posterior cell lineages at gastrulation. Differentiation; research in biological diversity. 50:75-87
Joly, J.S., Maury, M., Joly, C., Boulekbache, H., and Condamine, H. (1991) Towards vertebrate developmental genetics structural and functional conservation of an even-skipped gene in fish, amphibian, and mammal. Bull. Soc. Zool. Fr. Evol. Zool.. 116:123-128

Brombin A, Grossier JP, Heuzé A, Radev Z, Bourrat F, Joly JS, Jamen F.
Genome-wide analysis of the POU genes in medaka, focusing on expression in the optic tectum. Dev Dyn. 2011 Oct;240(10):2354-63. doi: 10.1002/dvdy.22727. Epub 2011 Aug 26. PubMed PMID: 21932313.

Haeussler M, Joly JS. When needles look like hay: how to find tissue-specific enhancers in model organism genomes. Dev Biol. 2011 Feb 15;350(2):239-54.

Tassy O, Dauga D, Daian F, Sobral D, Robin F, Khoueiry P, Salgado D, Fox V, Caillol D, Schiappa R, Laporte B, Rios A, Luxardi G, Kusakabe T, Joly JS, Darras S, Christiaen L, Contensin M, Auger H, Lamy C, Hudson C, Rothbächer U, Gilchrist MJ, Makabe KW, Hotta K, Fujiwara S, Satoh N, Satou Y, Lemaire P. The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program. Genome Res. 2010 Oct;20(10):1459-68.

Alunni A, Hermel JM, Heuzé A, Bourrat F, Jamen F, Joly JS. Evidence for neural stem cells in the medaka optic tectum proliferation zones. Dev Neurobiol. 2010 Sep;70(10):693-713.

Haeussler M, Jaszczyszyn Y, Christiaen L, Joly JS. A cis-regulatory signature for chordate anterior neuroectodermal genes. PLoS Genet. 2010 Apr15;6(4):e1000912.

Auger H, Sasakura Y, Joly JS, Jeffery WR. Regeneration of oral siphon pigment organs in the ascidian Ciona intestinalis. Dev Biol. 2010 Mar 15;339(2):374-89.

Auger H, Lamy C, Haeussler M, Khoueiry P, Lemaire P, Joly JS. Similar regulatory logic in Ciona intestinalis for two Wnt pathway modulators, ROR and SFRP-1/5. Dev Biol. 2009 May 15;329(2):364-73.

Dahlberg C, Auger H, Dupont S, Sasakura Y, Thorndyke M, Joly JS. Refining the Ciona intestinalis model of central nervous system regeneration. PLoS One. 2009;4(2):e4458.