ZFIN Lab: Jochen Wittbrodt Lab<br>SFB 271 Junior Group

ZFIN ID: ZDB-LAB-970512-13

Jochen Wittbrodt Lab
SFB 271 Junior Group

PI/Director:	Wittbrodt, Jochen
Contact Person:	Wittbrodt, Jochen
Email:	Jochen.Wittbrodt@zoo.uni-Heidelberg.de
URL:
Address:	University of Heidelberg and Karlsruhe Institute of Technology, KIT Heidelberg Institute for Zoology Im Neuenheimer Feld 230 D-69120 Heidelberg, GERMANY
Country:	Germany
Phone:	49 6221 546497
Fax:
Line Designation:	uh

GENOMIC FEATURES ORIGINATING FROM THIS LAB

Show all 5 genomic features

STATEMENT OF RESEARCH INTERESTS

Inductive events during eye development of Medaka/Zebrafish.

LAB MEMBERS

Arendt, Detlev Post-Doc	Burgtorf, Carola Post-Doc	Loosli, Felix Post-Doc
Rembold, Martina Graduate Student	Grzebisz, Erika Research Staff	Krone, Annette Research Staff

ZEBRAFISH PUBLICATIONS OF LAB MEMBERS

Agostini, C., Bühler, A., Antico Calderone, A., Aadepu, N., Herder, C., Loosli, F., Carl, M. (2022) Conserved and diverged asymmetric gene expression in the brain of teleosts. Frontiers in cell and developmental biology. 10:1005776

Lucon-Xiccato, T., Loosli, F., Conti, F., Foulkes, N.S., Bertolucci, C. (2022) Comparison of anxiety-like and social behaviour in medaka and zebrafish. Scientific Reports. 12:10926

Cornean, A., Gierten, J., Welz, B., Mateo, J.L., Thumberger, T., Wittbrodt, J. (2022) Precise in vivo functional analysis of DNA variants with base editing using ACEofBASEs target prediction. eLIFE. 11:

Thumberger, T., Tavhelidse-Suck, T., Gutierrez-Triana, J.A., Cornean, A., Medert, R., Welz, B., Freichel, M., Wittbrodt, J. (2022) Boosting targeted genome editing using the hei-tag. eLIFE. 11:

Beedgen, L., Hüllen, A., Gücüm, S., Thumberger, T., Wittbrodt, J., Thiel, C. (2021) A rapid and simple procedure for the isolation and cultivation of fibroblast-like cells from medaka and zebrafish embryos and fin clip biopsies. Laboratory animals. 56(3):270-278

Zilova, L., Weinhardt, V., Tavhelidse, T., Schlagheck, C., Thumberger, T., Wittbrodt, J. (2021) Fish primary embryonic pluripotent cells assemble into retinal tissue mirroring in vivo early eye development. eLIFE. 10:

Tarashansky, A.J., Musser, J.M., Khariton, M., Li, P., Arendt, D., Quake, S.R., Wang, B. (2021) Mapping single-cell atlases throughout Metazoa unravels cell type evolution. eLIFE. 10:

Wagner, N., Beuttenmueller, F., Norlin, N., Gierten, J., Boffi, J.C., Wittbrodt, J., Weigert, M., Hufnagel, L., Prevedel, R., Kreshuk, A. (2021) Deep learning-enhanced light-field imaging with continuous validation. Nature Methods. 18:557-563

Bruch, R., Scheikl, P.M., Mikut, R., Loosli, F., Reischl, M. (2020) epiTracker: A Framework for Highly Reliable Particle Tracking for the Quantitative Analysis of Fish Movements in Tanks. SLAS technology. 26(4):367-376

Bosze, B., Ono, Y., Mattes, B., Sinner, C., Gourain, V., Thumberger, T., Tlili, S., Wittbrodt, J., Saunders, T.E., Strähle, U., Schug, A., Scholpp, S. (2020) Pcdh18a regulates endocytosis of E-cadherin during axial mesoderm development in zebrafish. Histochemistry and cell biology. 154(5):463-480

Gierten, J., Pylatiuk, C., Hammouda, O.T., Schock, C., Stegmaier, J., Wittbrodt, J., Gehrig, J., Loosli, F. (2020) Automated high-throughput heartbeat quantification in medaka and zebrafish embryos under physiological conditions. Scientific Reports. 10:2046

Pylatiuk, C., Zhao, H., Gursky, E., Reischl, M., Peravali, R., Foulkes, N., Loosli, F. (2019) DIY Automated Feeding and Motion Recording System for the Analysis of Fish Behavior. SLAS technology. 24(4):394-398

Lischik, C.Q., Adelmann, L., Wittbrodt, J. (2019) Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation. PLoS One. 14:e0212956

Hammouda, O.T., Böttger, F., Wittbrodt, J., Thumberger, T. (2019) Swift Large-scale Examination of Directed Genome Editing. PLoS One. 14:e0213317

Knickmeyer, M.D., Mateo, J.L., Eckert, P., Roussa, E., Rahhal, B., Zuniga, A., Krieglstein, K., Wittbrodt, J., Heermann, S. (2018) TGFβ-facilitated optic fissure fusion and the role of bone morphogenetic protein antagonism. Open Biology. 8(3)

Lust, K., Wittbrodt, J. (2018) Activating the regenerative potential of Müller glia cells in a regeneration-deficient retina. eLIFE. 7

Lindsey, B.W., Douek, A.M., Loosli, F., Kaslin, J. (2018) A Whole Brain Staining, Embedding, and Clearing Pipeline for Adult Zebrafish to Visualize Cell Proliferation and Morphology in 3-Dimensions. Frontiers in neuroscience. 11:750

Kuri, P., Schieber, N.L., Thumberger, T., Wittbrodt, J., Schwab, Y., Leptin, M. (2017) Dynamics of in vivo ASC speck formation. The Journal of cell biology. 216(9):2891-2909

Nicolás-Pérez, M., Kuchling, F., Letelier, J., Polvillo, R., Wittbrodt, J.,Martínez-Morales, J.R. (2016) Analysis of cellular behavior and cytoskeletal dynamics reveal a constriction mechanism driving optic cup morphogenesis. eLIFE. 5

Levin, M., Anavy, L., Cole, A.G., Winter, E., Mostov, N., Khair, S., Senderovich, N., Kovalev, E., Silver, D.H., Feder, M., Fernandez-Valverde, S.L., Nakanishi, N., Simmons, D., Simakov, O., Larsson, T., Liu, S.Y., Jerafi-Vider, A., Yaniv, K., Ryan, J.F., Martindale, M.Q., Rink, J.C., Arendt, D., Degnan, S.M., Degnan, B.M., Hashimshony, T., Yanai, I. (2016) The mid-developmental transition and the evolution of animal body plans. Nature. 531:637-641

Kromm, D., Thumberger, T., Wittbrodt, J. (2016) An eye on light-sheet microscopy. Methods in cell biology. 133:105-123

Auer, T.O., Xiao, T., Bercier, V., Gebhardt, C., Duroure, K., Concordet, J.P., Wyart, C., Suster, M., Kawakami, K., Wittbrodt, J., Baier, H., Del Bene, F. (2015) Deletion of a kinesin I motor unmasks a mechanism of homeostatic branching control by neurotrophin-3. eLIFE. 4

Heermann, S., Schütz, L., Lemke, S., Krieglstein, K., Wittbrodt, J. (2015) Eye morphogenesis driven by epithelial flow into the optic cup facilitated by modulation of bone morphogenetic protein. eLIFE. 4

Zaucker, A., Bodur, T., Roest Crollius, H., Hadzhiev, Y., Gehrig, J., Loosli, F., Watson, C., Müller, F. (2014) Description of Embryonic Development of Spotted Green Pufferfish (Tetraodon nigroviridis). Zebrafish. 11(6):509-17

Mazaheri, F., Breus, O., Durdu, S., Haas, P., Wittbrodt, J., Gilmour, D., Peri, F. (2014) Distinct roles for BAI1 and TIM-4 in the engulfment of dying neurons by microglia. Nature communications. 5:4046

Ravi, V., Bhatia, S., Gautier, P., Loosli, F., Tay, B.H., Tay, A., Murdoch, E., Coutinho, P., van Heyningen, V., Brenner, S., Venkatesh, B., and Kleinjan, D.A. (2013) Sequencing of pax6 Loci from the elephant shark reveals a family of pax6 genes in vertebrate genomes, forged by ancient duplications and divergences. PLoS Genetics. 9(1):e1003177

Schulz, S., Chachami, G., Kozaczkiewicz, L., Winter, U., Stankovic-Valentin, N., Haas, P., Hofmann, K., Urlaub, H., Ovaa, H., Wittbrodt, J., Meulmeester, E., and Melchior, F. (2012) Ubiquitin-specific protease-like 1 (USPL1) is a SUMO isopeptidase with essential, non-catalytic functions. EMBO reports. 13(10):930-938

Harden, M.V., Pereiro, L., Ramialison, M., Wittbrodt, J., Prasad, M.K., McCallion, A.S., and Whitlock, K.E. (2012) Close association of olfactory placode precursors and cranial neural crest cells does not predestine cell mixing. Developmental Dynamics : an official publication of the American Association of Anatomists. 241(7):1143-1154

Centanin, L., Hoeckendorf, B., Wittbrodt, J. (2011) Fate restriction and multipotency in retinal stem cells. Cell Stem Cell. 9:553-62

Keller, P.J., Schmidt, A.D., Wittbrodt, J., and Stelzer, E.H. (2011) Digital Scanned Laser Light-Sheet Fluorescence Microscopy (DSLM) of Zebrafish and Drosophila Embryonic Development. Cold Spring Harbor protocols. 2011(10):1235-43

Maurya, A.K., Tan, H., Souren, M., Wang, X., Wittbrodt, J., and Ingham, P.W. (2011) Integration of Hedgehog and BMP signalling by the engrailed2a gene in the zebrafish myotome. Development (Cambridge, England). 138(4):755-765

d'Alencon, C.A., Pena, O.A., Wittmann, C., Gallardo, V.E., Jones, R.A., Loosli, F., Liebel, U., Grabher, C., and Allende, M.L. (2010) A high-throughput chemically induced inflammation assay in zebrafish. BMC Biology. 8:151

Brown, K.E., Keller, P.J., Ramialison, M., Rembold, M., Stelzer, E.H., Loosli, F., and Wittbrodt, J. (2010) Nlcam modulates midline convergence during anterior neural plate morphogenesis. Developmental Biology. 339(1):14-25

Signore, I.A., Guerrero, N., Loosli, F., Colombo, A., Villalón, A., Wittbrodt, J., and Concha, M.L. (2009) Zebrafish and medaka: model organisms for a comparative developmental approach of brain asymmetry. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 364(1519):991-1003

Keller, P.J., Schmidt, A.D., Wittbrodt, J., and Stelzer, E.H. (2008) Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy. Science (New York, N.Y.). 322(5904):1065-1069

Grabher, C., and Wittbrodt, J. (2008) Recent advances in meganuclease-and transposon-mediated transgenesis of medaka and zebrafish. Methods in molecular biology (Clifton, N.J.). 461:521-539

Tessmar-Raible, K., Raible, F., Christodoulou, F., Guy, K., Rembold, M., Hausen, H., and Arendt, D. (2007) Conserved sensory-neurosecretory cell types in annelid and fish forebrain: insights into hypothalamus evolution. Cell. 129(7):1389-1400

Jékely, G., and Arendt, D. (2007) Cellular resolution expression profiling using confocal detection of NBT/BCIP precipitate by reflection microscopy. Biotechniques. 42(6):751-755

Yokoi, H., Shimada, A., Carl, M., Takashima, S., Kobayashi, D., Narita, T., Jindo, T., Kimura, T., Kitagawa, T., Kage, T., Sawada, A., Naruse, K., Asakawa, S., Shimizu, N., Mitani, H., Shima, A., Tsutsumi, M., Hori, H., Wittbrodt, J., Saga, Y., Ishikawa, Y., Araki, K., and Takeda, H. (2007) Mutant analyses reveal different functions of fgfr1 in medaka and zebrafish despite conserved ligand-receptor relationships. Developmental Biology. 304(1):326-337

Grabher, C., and Wittbrodt, J. (2007) Meganuclease and transposon mediated transgenesis in medaka. Genome biology. 8(1):S10

Ason, B., Darnell, D.K., Wittbrodt, B., Berezikov, E., Kloosterman, W.P., Wittbrodt, J., Antin, P.B., and Plasterk, R.H. (2006) Differences in vertebrate microRNA expression. Proceedings of the National Academy of Sciences of the United States of America. 103(39):14385-14389

Rembold, M., Loosli, F., Adams, R. J., Wittbrodt, J. (2006) Individual Cell Migration Serves as the Driving Force for Optic Vesicle Evagination. Science (New York, N.Y.). 313:1130-1134

Rembold, M., Lahiri, K., Foulkes, N.S., and Wittbrodt, J. (2006) Transgenesis in fish: efficient selection of transgenic fish by co-injection with a fluorescent reporter construct. Nature Protocols. 1(3):1133-1139

Schäfer, M., Rembold, M., Wittbrodt, J., Schartl, M., and Winkler, C. (2005) Medial floor plate formation in zebrafish consists of two phases and requires trunk-derived Midkine-a. Genes & Development. 19(8):897-902

Furutani-Seiki, M., and Wittbrodt, J. (2004) Medaka and zebrafish, an evolutionary twin study. Mechanisms of Development. 121(7-8):629-637

Henrich, T., Ramialison, M., Segerdell, E., Westerfield, M., Furutani-Seiki, M., Wittbrodt, J., Kondoh, H. (2004) GSD: a genetic screen database. Mechanisms of Development. 121(7-8):959-963

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

Loosli, F., Staub, W., Finger-Baier, K.C., Ober, E.A., Verkade, H., Wittbrodt, J., and Baier, H. (2003) Loss of eyes in zebrafish caused by mutation of chokh/rx3. EMBO reports. 4(9):894-899

Hammerschmidt, M., Kramer, C., Nowak, M., Herzog, W., and Wittbrodt, J. (2003) Loss of maternal Smad5 in zebrafish embryos affects patterning and morphogenesis of optic primordia. Developmental Dynamics : an official publication of the American Association of Anatomists. 227(1):128-133

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

Adamska, M., Wolff, A., Kreusler, M., Wittbrodt, J., Braun, T., and Bober, E. (2001) Five Nkx5 genes show differential expression patterns in anlagen of sensory organs in medaka: insight into the evolution of the gene family. Development genes and evolution. 211(7):338-349

Delot, E., Kataoka, H., Goutel, C., Yan, Y.L., Postlethwait, J., Wittbrodt, J., and Rosa, F.M. (1999) The BMP-related protein Radar: a maintenance factor for dorsal neuroectoderm cells?. Mechanisms of Development. 85(1-2):15-25

Boeddrich, A., Burgtorf, C., Crollius, H.R., Hennig, S., Bernot, A., Clark, M., Reinhardt, R., Lehrach, H., and Francis, F. (1999) Analysis of the spermine synthase gene region in Fugu rubripes, Tetraodon fluviatilis, and Danio rerio. Genomics. 57(1):164-168

Burgtorf, C., Welzel, K., Hasenbank, R., Zehetner, G., Weis, S., and Lehrach, H. (1998) Gridded genomic libraries of different chordate species: a reference library system for basic and comparative genetic studies of chordate genomes. Genomics. 52:230-232

Rissi, M., Wittbrodt, J., Delot, E., Naegeli, M., and Rosa, F.M. (1995) Zebrafish Radar: a new member of the TGF-ß superfamily defines dorsal regions of the neural plate and the embryonic retina. Mechanisms of Development. 49(3):223-34

Wittbrodt, J. and Rosa, F.M. (1994) Disruption of mesoderm and axis formation in fish by ectopic expression of activin variants: the role of maternal activin. Genes & Development. 8:1448-1462