ZFIN Lab: Scott Fraser Lab

ZFIN ID: ZDB-LAB-000204-2

Scott Fraser Lab

PI/Director:	Fraser, Scott E.
Contact Person:	Fraser, Scott E.
Email:	sefraser@caltech.edu
URL:	http://bioimaging.caltech.edu/
Address:	California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 USA
Country:	United States
Phone:	(626) 395-2863
Fax:	(626) 449-5163
Line Designation:	ct

GENOMIC FEATURES ORIGINATING FROM THIS LAB

Show first 50 of 58 genomic features

STATEMENT OF RESEARCH INTERESTS

LAB MEMBERS

Caneparo, Luca Post-Doc	Dixson, Alana Post-Doc	Hawk, Rasheeda Post-Doc
Koos, David Post-Doc	Ruf-Zamojski, Frederique Post-Doc	Trinh, Le Post-Doc
Dempsey, William Graduate Student	Gong, Ying Graduate Student	Yang, Jennifer Graduate Student
Bak, Magdalena

ZEBRAFISH PUBLICATIONS OF LAB MEMBERS

Chiang, H.J., Koo, D.E.S., Kitano, M., Burkitt, S., Unruh, J.R., Zavaleta, C., Trinh, L.A., Fraser, S.E., Cutrale, F. (2023) HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence. Nature Methods. 20(2):248-258

Djenoune, L., Mahamdeh, M., Truong, T.V., Nguyen, C.T., Fraser, S.E., Brueckner, M., Howard, J., Yuan, S. (2023) Cilia function as calcium-mediated mechanosensors that instruct left-right asymmetry. Science (New York, N.Y.). 379:717871-78

Torres-Pérez, J.V., Anagianni, S., Mech, A.M., Havelange, W., García-González, J., Fraser, S.E., Vallortigara, G., Brennan, C.H. (2022) baz1b loss-of-function in zebrafish produces phenotypic alterations consistent with the domestication syndrome. iScience. 26:105704105704

Sheardown, E., Torres-Perez, J.V., Anagianni, S., Fraser, S.E., Vallortigara, G., Butterworth, B., Miletto-Petrazzini, M.E., Brennan, C.H. (2022) Characterizing ontogeny of quantity discrimination in zebrafish. Proceedings. Biological sciences. 289:20212544

Dempsey, W.P., Du, Z., Nadtochiy, A., Smith, C.D., Czajkowski, K., Andreev, A., Robson, D.N., Li, J.M., Applebaum, S., Truong, T.V., Kesselman, C., Fraser, S.E., Arnold, D.B. (2022) Regional synapse gain and loss accompany memory formation in larval zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 119(3):

Messina, A., Potrich, D., Schiona, I., Sovrano, V.A., Fraser, S.E., Brennan, C.H., Vallortigara, G. (2021) Neurons in the Dorso-Central Division of Zebrafish Pallium Respond to Change in Visual Numerosity. Cerebral cortex (New York, N.Y. : 1991). 32(2):418-428

Keomanee-Dizon, K., Fraser, S.E., Truong, T.V. (2020) A versatile, multi-laser twin-microscope system for light-sheet imaging. The Review of scientific instruments. 91:053703

Messina, A., Potrich, D., Schiona, I., Sovrano, V.A., Fraser, S.E., Brennan, C.H., Vallortigara, G. (2020) Response to change in the number of visual stimuli in zebrafish:A behavioural and molecular study. Scientific Reports. 10:5769

Truong, T.V., Holland, D.B., Madaan, S., Andreev, A., Keomanee-Dizon, K., Troll, J.V., Koo, D.E.S., McFall-Ngai, M.J., Fraser, S.E. (2020) High-contrast, synchronous volumetric imaging with selective volume illumination microscopy. Communications biology. 3:74

Shi, W., Koo, D.E.S., Kitano, M., Chiang, H.J., Trinh, L.A., Turcatel, G., Steventon, B., Arnesano, C., Warburton, D., Fraser, S.E., Cutrale, F. (2020) Pre-processing visualization of hyperspectral fluorescent data with Spectrally Encoded Enhanced Representations. Nature communications. 11:726

Simões, F.C., Cahill, T.J., Kenyon, A., Gavriouchkina, D., Vieira, J.M., Sun, X., Pezzolla, D., Ravaud, C., Masmanian, E., Weinberger, M., Mayes, S., Lemieux, M.E., Barnette, D.N., Gunadasa-Rohling, M., Williams, R.M., Greaves, D.R., Trinh, L.A., Fraser, S.E., Dallas, S.L., Choudhury, R.P., Sauka-Spengler, T., Riley, P.R. (2020) Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair. Nature communications. 11:600

Trinh, L.A., Chong-Morrison, V., Sauka-Spengler, T. (2018) Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish. Methods (San Diego, Calif.). 150:24-31

Trivedi, V., Choi, H.M.T., Fraser, S.E., Pierce, N.A. (2018) Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos. Development (Cambridge, England). 145(1)

Balasanyan, V., Watanabe, K., Dempsey, W.P., Lewis, T.L., Trinh, L.A., Arnold, D.B. (2017) Structure and Function of an Actin-Based Filter in the Proximal Axon. Cell Reports. 21:2696-2705

Lee, D.A., Andreev, A., Truong, T.V., Chen, A., Hill, A.J., Oikonomou, G., Pham, U., Hong, Y.K., Tran, S., Glass, L., Sapin, V., Engle, J., Fraser, S.E., Prober, D.A. (2017) Genetic and neuronal regulation of sleep by neuropeptide VF. eLIFE. 6

Chen, Y., Trinh, L.A., Fingler, J., Fraser, S.E. (2017) 3D in vivo imaging with extended-focus optical coherence microscopy. Journal of biophotonics. 10:1411-1420

Bower, D.V., Lansdale, N., Navarro, S., Truong, T.V., Bower, D.J., Featherstone, N.C., Connell, M.G., Al-Alam, D., Frey, M.R., Trinh, L.A., Fernandez, G.E., Warburton, D., Fraser, S.E., Bennett, D., Jesudason, E.C. (2017) SERCA directs cell migration and branching across species and germ layers. Biology Open. 6(10):1458-1471

Zheng, W., Wu, Y., Winter, P., Fischer, R., Nogare, D.D., Hong, A., McCormick, C., Christensen, R., Dempsey, W.P., Arnold, D.B., Zimmerberg, J., Chitnis, A., Sellers, J., Waterman, C., Shroff, H. (2017) Adaptive optics improves multiphoton super-resolution imaging. Nature Methods. 14(9):869-872

Trinh, L.A., Chong-Morrison, V., Gavriouchkina, D., Hochgreb-Hägele, T., Senanayake, U., Fraser, S.E., Sauka-Spengler, T. (2017) Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome. Cell Reports. 19:425-440

Cutrale, F., Trivedi, V., Trinh, L.A., Chiu, C.L., Choi, J.M., Artiga, M.S., Fraser, S.E. (2017) Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging. Nature Methods. 14(2):149-152

Chen, Y., Trinh, L.A., Fingler, J., Fraser, S.E. (2016) Phase variance optical coherence microscopy for label-free imaging of the developing vasculature in zebrafish embryos. Journal of Biomedical Optics. 21:126022

Cronan, M.R., Beerman, R.W., Rosenberg, A.F., Saelens, J.W., Johnson, M.G., Oehlers, S.H., Sisk, D.M., Jurcic Smith, K.L., Medvitz, N.A., Miller, S.E., Trinh, L.A., Fraser, S.E., Madden, J.F., Turner, J., Stout, J.E., Lee, S., Tobin, D.M. (2016) Macrophage Epithelial Reprogramming Underlies Mycobacterial Granuloma Formation and Promotes Infection. Immunity. 45:861-876

Choi, H.M., Calvert, C.R., Husain, N., Huss, D., Barsi, J.C., Deverman, B.E., Hunter, R.C., Kato, M., Lee, S.M., Abelin, A.C., Rosenthal, A.Z., Akbari, O.S., Li, Y., Hay, B.A., Sternberg, P.W., Patterson, P.H., Davidson, E.H., Mazmanian, S.K., Prober, D.A., van de Rijn, M., Leadbetter, J.R., Newman, D.K., Readhead, C., Bronner, M.E., Wold, B., Lansford, R., Sauka-Spengler, T., Fraser, S.E., Pierce, N.A. (2016) Mapping a multiplexed zoo of mRNA expression. Development (Cambridge, England). 143:3632-3637

Gross, G.G., Straub, C., Perez-Sanchez, J., Dempsey, W.P., Junge, J.A., Roberts, R.W., Trinh, l.e. .A., Fraser, S.E., De Koninck, Y., De Koninck, P., Sabatini, B.L., Arnold, D.B. (2016) An E3-ligase-based method for ablating inhibitory synapses. Nature Methods. 13:673-8

Dempsey, W.P., Hodas, N.O., Ponti, A., Pantazis, P. (2015) Determination of the source of SHG verniers in zebrafish skeletal muscle. Scientific Reports. 5:18119

Ju Shin, Y., Kyun Park, S., Jung Jung, Y., Na Kim, Y., Sung Kim, K., Kyu Park, O., Kwon, S.H., Ho Jeon, S., Trinh, l.e. .A., Fraser, S.E., Kee, Y., Joon Hwang, B. (2015) Nanobody-targeted E3-ubiquitin ligase complex degrades nuclear proteins. Scientific Reports. 5:14269

Dempsey, W.P., Georgieva, L., Helbling, P.M., Sonay, A.Y., Truong, T.V., Haffner, M., Pantazis, P. (2015) In vivo single-cell labeling by confined primed conversion. Nature Methods. 12(7):645-8

Ruf-Zamojski, F., Trivedi, V., Fraser, S.E., Trinh, L.A. (2015) Spatio-Temporal Differences in Dystrophin Dynamics at mRNA and Protein Levels Revealed by a Novel FlipTrap Line. PLoS One. 10:e0128944

Ramspacher, C., Steed, E., Boselli, F., Ferreira, R., Faggianelli, N., Roth, S., Spiegelhalter, C., Messaddeq, N., Trinh, L., Liebling, M., Chacko, N., Tessadori, F., Bakkers, J., Laporte, J., Hnia, K., Vermot, J. (2015) Developmental Alterations in Heart Biomechanics and Skeletal Muscle Function in Desmin Mutants Suggest an Early Pathological Root for Desminopathies. Cell Reports. 11:1564-76

Trivedi, V., Truong, T.V., Trinh, l.e. .A., Holland, D.B., Liebling, M., Fraser, S.E. (2015) Dynamic structure and protein expression of the live embryonic heart captured by 2-photon light sheet microscopy and retrospective registration. Biomedical Optics Express. 6:2056-66

Dempsey, W.P., Qin, H., Pantazis, P. (2014) In Vivo Cell Tracking Using PhOTO Zebrafish. Methods in molecular biology (Clifton, N.J.). 1148:217-28

Trinh, L.A., and Fraser, S.E. (2013) Enhancer and gene traps for molecular imaging and genetic analysis in zebrafish. Development, growth & differentiation. 55(4):434-45

Choe, C.P., Collazo, A., Trinh, L.A., Pan, L., Moens, C.B., and Crump, J.G. (2013) Wnt-Dependent Epithelial Transitions Drive Pharyngeal Pouch Formation. Developmental Cell. 24(3):296-309

Palanca, A.M., Lee, S.L., Yee, L.E., Joe-Wong, C., Trinh, L.A., Hiroyasu, E., Husain, M., Fraser, S.E., Pellegrini, M., and Sagasti, A. (2013) New transgenic reporters identify somatosensory neuron subtypes in larval zebrafish. Developmental Neurobiology. 73(2):152-167

Culi-Viskota, J., Dempsey, W.P., Fraser, S.E., and Pantazis, P. (2012) Surface functionalization of barium titanate SHG nanoprobes for in vivo imaging in zebrafish. Nature Protocols. 7(9):1618-1633

Dempsey, W.P., Fraser, S.E., and Pantazis, P. (2012) PhOTO Zebrafish: A Transgenic Resource for In Vivo Lineage Tracing during Development and Regeneration. PLoS One. 7(3):e32888

Jayasena, C.S., Trinh, L.A., and Bronner, M. (2011) Live imaging of endogenous periodic tryptophan protein 2 gene homologue during zebrafish development. Developmental Dynamics : an official publication of the American Association of Anatomists. 240(11):2578-83

Trinh, A., Hochgreb, T., Graham, M., Wu, D., Ruf-Zamojski, F., Jayasena, C.S., Saxena, A., Hawk, R., Gonzalez-Serricchio, A., Dixson, A., Chow, E., Gonzales, C., Leung, H.Y., Solomon, I., Bronner-Fraser, M., Megason, S.G., and Fraser, S.E. (2011) A versatile gene trap to visualize and interrogate the function of the vertebrate proteome. Genes & Development. 25(21):2306-20

Truong, T.V., Supatto, W., Koos, D.S., Choi, J.M., and Fraser, S.E. (2011) Deep and fast live imaging with two-photon scanned light-sheet microscopy. Nature Methods. 8(9):757-60

Hochheiser, H., Aronow, B.J., Artinger, K., Beaty, T.H., Brinkley, J.F., Chai, Y., Clouthier, D., Cunningham, M.L., Dixon, M., Donahue, L.R., Fraser, S.E., Hallgrimsson, B., Iwata, J., Klein, O., Marazita, M.L., Murray, J.C., Murray, S., de Villena, F.P., Postlethwait, J., Potter, S., Shapiro, L., Spritz, R., Visel, A., Weinberg, S.M., and Trainor, P.A. (2011) The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. Developmental Biology. 355(2):175-182

Zigman, M., Trinh, L.A., Fraser, S.E., and Moens, C.B. (2011) Zebrafish Neural Tube Morphogenesis Requires Scribble-Dependent Oriented Cell Divisions. Current biology : CB. 21(1):79-86

Caneparo, L., Pantazis, P., Dempsey, W., and Fraser, S.E. (2011) Intercellular bridges in vertebrate gastrulation. PLoS One. 6(5):e20230

Quesada-Hernández, E., Caneparo, L., Schneider, S., Winkler, S., Liebling, M., Fraser, S.E., and Heisenberg, C.P. (2010) Stereotypical Cell Division Orientation Controls Neural Rod Midline Formation in Zebrafish. Current biology : CB. 20(21):1966-1972

Choi, H.M., Chang, J.Y., Trinh, L.A., Padilla, J.E., Fraser, S.E., and Pierce, N.A. (2010) Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat. Biotechnol.. 28(11):1208-1212

Pantazis, P., Maloney, J., Wu, D., and Fraser, S.E. (2010) Second harmonic generating (SHG) nanoprobes for in vivo imaging. Proceedings of the National Academy of Sciences of the United States of America. 107(33):14535-14540

Vermot, J., Forouhar, A.S., Liebling, M., Wu, D., Plummer, D., Gharib, M., and Fraser, S.E. (2009) Reversing blood flows act through klf2a to ensure normal valvulogenesis in the developing heart. PLoS Biology. 7(11):e1000246

Aanstad, P., Santos, N., Corbit, K.C., Scherz, P.J., Trinh, L.A., Salvenmoser, W., Huisken, J., Reiter, J.F., and Stainier, D.Y. (2009) The Extracellular Domain of Smoothened Regulates Ciliary Localization and Is Required for High-Level Hh Signaling. Current biology : CB. 19(12):1034-1039

Colantonio, J.R., Vermot, J., Wu, D., Langenbacher, A.D., Fraser, S., Chen, J.N., and Hill, K.L. (2009) The dynein regulatory complex is required for ciliary motility and otolith biogenesis in the inner ear. Nature. 457(7226):205-209

Supatto, W., Fraser, S.E., and Vermot, J. (2008) An All-Optical Approach for Probing Microscopic Flows in Living Embryos. Biophysical journal. 95(4):L29-L31

Lu, J., Pereira, F., Fraser, S.E., and Gharib, M. (2008) Three-dimensional real-time imaging of cardiac cell motions in living embryos. Journal of Biomedical Optics. 13(1):014006

Caneparo, L., Huang, Y.L., Staudt, N., Tada, M., Ahrendt, R., Kazanskaya, O., Niehrs, C., and Houart, C. (2007) Dickkopf-1 regulates gastrulation movements by coordinated modulation of Wnt/betacatenin and Wnt/PCP activities, through interaction with the Dally-like homolog Knypek. Genes & Development. 21(4):465-480

Liebling, M., Forouhar, A.S., Wolleschensky, R., Zimmermann, B., Ankerhold, R., Fraser, S.E., Gharib, M., and Dickinson, M.E. (2006) Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development. Developmental Dynamics : an official publication of the American Association of Anatomists. 235(11):2940-2948

Koster, R.W., and Fraser, S.E. (2006) FGF signaling mediates regeneration of the differentiating cerebellum through repatterning of the anterior hindbrain and reinitiation of neuronal migration. The Journal of neuroscience : the official journal of the Society for Neuroscience. 26(27):7293-7304

Forouhar, A.S., Liebling, M., Hickerson, A., Nasiraei-Moghaddam, A., Tsai, H.J., Hove, J.R., Fraser, S.E., Dickinson, M.E., and Gharib, M. (2006) The embryonic vertebrate heart tube is a dynamic suction pump. Science (New York, N.Y.). 312(5774):751-753

Wang, J., Hamblet, N.S., Mark, S., Dickinson, M.E., Brinkman, B.C., Segil, N., Fraser, S.E., Chen, P., Wallingford, J.B., and Wynshaw-Boris, A. (2006) Dishevelled genes mediate a conserved mammalian PCP pathway to regulate convergent extension during neurulation. Development (Cambridge, England). 133(9):1767-1778

Rieger, S., Kulkarni, R.P., Darcy, D., Fraser, S.E., and Köster, R.W. (2005) Quantum dots are powerful multipurpose vital labeling agents in zebrafish embryos. Developmental Dynamics : an official publication of the American Association of Anatomists. 234(3):670-681

Liebling, M., Forouhar, A.S., Gharib, M., Fraser, S.E., and Dickinson, M.E. (2005) Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences. Journal of Biomedical Optics. 10(5):54001

Trinh, L.A., Yelon, D., and Stainier, D.Y. (2005) Hand2 regulates epithelial formation during myocardial diferentiation. Current biology : CB. 15(5):441-446

Kapsimali, M., Caneparo, L., Houart, C., and Wilson, S.W. (2004) Inhibition of Wnt/Axin/{beta}-catenin pathway activity promotes ventral CNS midline tissue to adopt hypothalamic rather than floorplate identity. Development (Cambridge, England). 131(23):5923-5933

Gong, Y., Mo, C., and Fraser, S.E. (2004) Planar cell polarity signalling controls cell division orientation during zebrafish gastrulation. Nature. 430(7000):689-693

Trinh, L.A., and Stainier, D.Y. (2004) Fibronectin Regulates Epithelial Organization during Myocardial Migration in Zebrafish. Developmental Cell. 6(3):371-382

Caneparo, L. (2004) Antero-posterior patterning of the neural plate in zebrafish. Ph.D. Thesis. :171p

Köster, R.W., and Fraser, S.E. (2004) Time-lapse microscopy of brain development. The Zebrafish: Cellular and Developmental Biology,2nd Ed. Methods Cell Biol.. 76:207-235

Trinh, L.A. (2004) Heart tube morphogenesis : Genetic and cellular analyses in zebrafish. Ph.D. Thesis. :223p

Trinh, L.A., and Stainier, D.Y. (2004) Cardiac development. The Zebrafish: Cellular and Developmental Biology,2nd Ed. Methods Cell Biol.. 76:455-473

Megason, S.G. and Fraser, S.E. (2003) Digitizing life at the level of the cell: high-performance laser-scanning microscopy and image analysis for in toto imaging of development. Mechanisms of Development. 120(11):1407-1420

Bak, M. and Fraser, S.E. (2003) Axon fasciculation and differences in midline kinetics between pioneer and follower axons within commissural fascicles. Development (Cambridge, England). 130(20):4999-5008

Trinh, L.A., Meyer, D., and Stainier, D.Y. (2003) The Mix family homeodomain gene bonnie and clyde functions with other components of the Nodal signaling pathway to regulate neural patterning in zebrafish. Development (Cambridge, England). 130(20):4989-4998

Hove, J.R., Köster, R.W., Forouhar, A.S., Acevedo-Bolton, G., Fraser, S.E., and Gharib, M. (2003) Intracardiac fluid forces are an essential epigenetic factor for embryonic cardiogenesis. Nature. 421(6919):172-177

Houart, C., Caneparo, L., Heisenberg, C.P., Barth, K.A., Take-uchi, M., and Wilson, S.W. (2002) Establishment of the telencephalon during gastrulation by local antagonism of Wnt signaling. Neuron. 35(2):255-265

Keegan, B.R., Feldman, J.L., Lee, D.H., Koos, D.S., Ho, R.K., Stainier, D.Y., and Yelon, D. (2002) The elongation factors Pandora/Spt6 and Foggy/Spt5 promote transcription in the zebrafish embryo. Development (Cambridge, England). 129(7):1623-1632

Köster, R.W. and Fraser, S.E. (2001) Direct imaging of in vivo neuronal migration in the developing cerebellum. Current biology : CB. 11(23):1858-1863

Heisenberg, C.P., Houart, C., Take-uchi, M., Rauch, G.J., Young, N., Coutinho, P., Masai, I., Caneparo, L., Concha, M.L., Geisler, R., Dale, T.C., Wilson, S.W., and Stemple, D.L. (2001) A mutation in the Gsk3-binding domain of zebrafish Masterblind/Axin1 leads to a fate transformation of telencephalon and eyes to diencephalon. Genes & Development. 15(11):1427-1434

Köster, R.W. and Fraser, S.E. (2001) Tracing transgene expression in living zebrafish embryos. Developmental Biology. 233(2):329-346

Kikuchi, Y., Trinh, L.A., Reiter, J.F., Alexander, J., Yelon, D., and Stainier, D.Y.R. (2000) The zebrafish bonnie and clyde gene encodes a Mix family homeodomain protein that regulates the generation of endodermal precursors. Genes & Development. 14(10):1279-1289

Koos, D.S. (2000) Organizing pattern formation in the embryo of the zebrafish, Danio rerio. Ph.D. Thesis.

Koos, D.S. and Ho, R.K. (1999) The nieuwkoid/dharma homeobox gene is essential for bmp2b repression in the zebrafish pregastrula. Developmental Biology. 215(2):190-207

Koos, D.S. and Ho, R.K. (1998) The nieuwkoid gene characterizes and mediates a Nieuwkoop-center-like activity in the zebrafish. Current biology : CB. 8:1199-1206

Woo, K. and Fraser, S.E. (1998) Specification of the hindbrain fate in the zebrafish. Developmental Biology. 197:283-296

Woo, K., and Fraser, S.E. (1997) Specification of the zebrafish nervous system by nonaxial signals. Science (New York, N.Y.). 277(5323):254-257

Shih, J. and Fraser, S.E. (1996) Characterizing the zebrafish organizer: microsurgical analysis at the early-shield stage. Development (Cambridge, England). 122:1313-1322

Shih, J. and Fraser, S.E. (1995) Distribution of tissue progenitors within the shield region of the zebrafish gastrula. Development (Cambridge, England). 121:2755-2765

Woo, K. and Fraser, S.E. (1995) Order and coherence in the fate map of the zebrafish nervous system. Development (Cambridge, England). 121:2595-2609

Woo, K., Shih, J., and Fraser, S.E. (1995) Fate maps of the zebrafish embryo. Current opinion in genetics & development. 5:439-443

Collazo, A., Fraser, S.E., and Mabee, P.M. (1994) A dual embryonic origin for vertebrate mechanoreceptors. Science (New York, N.Y.). 264:426-430