Hollis Cline, PhD

Hahn Professor of Neuroscience
Department of Neuroscience


Scripps Research Joint Appointments

Director, Dorris Neuroscience Center
Department of Molecular Medicine
Faculty, Graduate Program

Other Joint Appointments

Adjunct Professor, University of California San Diego
Adjunct Professor, Salk Institute for Biological Studies

Research Focus

Understanding how experience controls brain development.

My laboratory is interested in the role of sensory experience in controlling the development, function and plasticity of the visual circuit and how circuit development and function become disrupted in neurodevelopmental disorders. We conduct state of the art experiments in visual circuit development using molecular genetic manipulations, electrophysiological methods, in vivo time-lapse imaging, electron microscopy and behavior. Over the past 20 years we have demonstrated roles for a variety of activity-dependent mechanisms in controlling structural plasticity of neuronal dendrites and axons, synaptic maturation and topographic map formation. This body of work has helped to generate a comprehensive understanding of the role of experience in shaping brain development. Two key points to emerge from our research is that circuit formation in vivo is a dynamic process throughout development that is continuously guided by experience, and that the basic mechanisms governing brain development, plasticity, information processing and organizational principles of brain circuits are highly conserved across vertebrates. More recently we have begun to address the role of activity-dependent mechanisms in the development of the functional visual circuit, assessed by in vivo recordings of visual responses in intact animals and behavioral assays. This series of studies has revealed critical molecular/genetic players required for the integration of neurons into functional circuits in vivo.

Research Projects

The Dynamic Connectome

A thorough understanding of circuit development and brain function requires knowledge of the connectivity of brain networks. In vivo time-lapse imaging of dendritic and axonal structures have shown that they are dynamic over the timecourse of hours and days. Importantly the structural dynamics are the physical substrate of synaptic dynamics and therefore dynamics in the connectivity map. We have begun to assess the dynamics in the connectivity map of the optic tectum by combining in vivo time lapse imaging with serial section electron microscopy and three-dimensional reconstruction of optic tectal neuronal dendrites and axons. We use 2 photon time lapse imaging of GFP expressing neurons in living animals to identify dynamic branches within neurons and serial section electron microscopy (EM) to generate 3 dimensional reconstructions of labeled neurons and their synaptic partners. By comparing the live imaging data and the serial section EM data, we determine the synaptic connectivity and ultrastructural synaptic features of dynamics and stable dendritic and axonal branches. This type of analysis will allow us to identify stable and dynamic components of the connectome and to determine how connectivity changes with experience and under conditions that model human neurodevelopemental diseases.

Regulation of Neurogenesis

The development of brain networks depends of the spatial and temporal control of cell proliferation and differentiation. We have recently begun several projects to investigate the control of neurogenesis in the tadpole brain. A significant advantage of studying neurogenesis in tadpoles is that the animals develop externally so the entire process from progenitor cell proliferation to neuronal differentiation and integration into brain circuits can be easily visualized and manipulated in the intact animal. We have recently found that visual experience controls neurogenesis and we have conducted microarray analysis to identify candidate molecular genetic pathways through which sensory experience controls neurogenesis.

Balanced inhibition in Visual circuit function and behavior

The retinotectal system processes and integrates visual and mechanosensory information and controls behavioral responses to sensory inputs. The interaction between excitatory and inhibitory synaptic inputs is essential for these brain functions. Excitatory synaptic activity is balanced by inhibitory synaptic input throughout the CNS. Despite the widespread expectation that balanced inhibition to excitation is essential for circuit function and information processing, the consequences of manipulating the ratio of inhibition to excitation on information processing and behavior have not been directly tested. We are using in vivo imaging, electrophysiological methods and behavior combined with molecular genetic manipulations to determine the function of inhibition in visual system function. These projects will the mechanisms controlling the development of inhibitory and excitatory neurons and explore the consequences of disrupting the balance of inhibition to excitation in the intact brain, akin to deficits in information processing seen in neurodevelopmental disorders such as autism spectrum disorders.


B.A., Biology, Bryn Mawr College
Ph.D., Neurobiology, University of California, Berkeley

Professional Experience

Post-Graduate Education

1985-1989 Postdoctoral Fellow, (Advisor: M. Constantine-Paton), Department of Biology, Yale University, New Haven, CT. The role of NMDA receptors in development of the topographic retinotectal projection.

1989-1990 Postdoctoral Fellow, (Advisor: R. Tsien), Department of Molecular and Cellular Physiology, Beckman Center, Stanford University Medical Center, Stanford, CA. Calcium imaging in optic tectal cell cultures.

1995 Student, Cloning of Neural Genes Summer Course, Cold Spring Harbor Laboratory.


1976 Student Research Assistant, (C. DeDuve), Lab of Biochemical Cytology, The Rockefeller University

1977-1979 Research Assistant, (A. S. Schneider) Department of Endocrinology, Sloan Kettering Memorial Cancer Institute

1990-1993 Assistant Professor, Department of Physiology and Biophysics, The University of Iowa, Iowa City, Iowa

1994-1996 Assistant Professor, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York

1997-1998 Associate Professor, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York

1998-2008 Professor, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York

2000-2008 Charles and Marie Robertson Professor of Neuroscience, Cold Spring Harbor Laboratory

2002-2006 Director of Research, Cold Spring Harbor Laboratory

2008- Professor, Depts of Neuroscience & Chemical Physiology, The Scripps Research Institute, CA

2016-present, Co-Chair, Dept. of Neuroscience, Scripps Reseach, CA

Awards & Professional Activities


AAAS: Member, Neuroscience Nominating Committee
AAAS: Electorate Nomination Committee (2004-2006)
Society for Neuroscience: Councilor (2002-2006)
Society for Neuroscience: Program Committee (2001-2004)
NINDS Board of Scientific Counselors (2004-2007)
Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Exec Committee (1998-2006), Founding member
Society for Neuroscience: Secretary (2010-2013)
National Eye Institute, Advisory Council Member (2011-2015)
NICHD Division of Intramural Research, Blue Ribbon Panel Member (2012-2014)
Society for Neuroscience: President (2015-2016)
National Institute of Neurological Disorders and Stroke, Advisory Council  (2018-2021)

Awards and Honors

NIH Director's Pioneer Award
AAAS Fellow (2012)
TSRI Outstanding Mentor Award (2013)
Director, Neurobiology Course, Marine Biological Laboratory, Woods Hole, MA (2008-2009)
Mika Salpeter Lifetime Achievement Award (2019)

Professional Memberships

Society for Neuroscience
American Academy for the Advancement of Science
American Society for Cell Biology
American Physiological Society

Editorial Boards

Frontiers in Neural Circuits
Journal of Developmental Neurobiology
Neural Development

Selected References

Schiapparelli, L. M., Sharma, P., He, H. Y., Li, J., Shah, S. H., McClatchy, D. B., Ma, Y., Liu, H. H., Goldberg, J. L., Yates, J. R., 3rd, Cline, H. T. (2022). Proteomic screen reveals diverse protein transport between connected neurons in the visual system. Cell reports38(4), 110287.

Ta, A. C., Huang, L. C., McKeown, C. R., Bestman, J. E., Van Keuren-Jensen, K., Cline, H. T. (2022). Temporal and spatial transcriptomic dynamics across brain development in Xenopus laevis tadpoles. G3 (Bethesda, Md.)12(1), jkab387. 

Cline H. T. (2022). Imaging Structural and Functional Dynamics in Xenopus Neurons. Cold Spring Harbor protocols2022(2), pdb.top106773. https://doi.org/10.1101/pdb.top106773

He, H. Y., Lin, C. Y., & Cline, H. T. (2022). In Vivo Time-Lapse Imaging and Analysis of Dendritic Structural Plasticity in Xenopus laevis Tadpoles. Cold Spring Harbor protocols2022(1), pdb.prot106781. https://doi.org/10.1101/pdb.prot106781

Gore, S. V., James, E. J., Huang, L. C., Park, J. J., Berghella, A., Thompson, A. C., Cline, H. T., Aizenman, C. D. (2021). Role of matrix metalloproteinase-9 in neurodevelopmental deficits and experience-dependent plasticity in Xenopus laeviseLife10, e62147. https://doi.org/10.7554/eLife.62147

Faulkner, R. L., Wall, N. R., Callaway, E. M., Cline, H. T. (2021). Application of Recombinant Rabies Virus to Xenopus Tadpole Brain. eNeuro8(4), ENEURO.0477-20.2021. Advance online publication. https://doi.org/10.1523/ENEURO.0477-20.2021

Luo, Y., Shen, W., & Cline, H. T. (2021). Electrophysiological Recording for Study of Xenopus Retinotectal Circuitry. Cold Spring Harbor protocols2021(6), 10.1101/pdb.prot106880. https://doi.org/10.1101/pdb.prot106880

Hiramoto, M., & Cline, H. T. (2021). Tetrode Recording in the Xenopus laevis Visual System Using Multichannel Glass Electrodes. Cold Spring Harbor protocols2021(11), pdb.prot107086. https://doi.org/10.1101/pdb.prot107086

Hiramoto, M., & Cline, H. T. (2021). Precisely controlled visual stimulation to study experience-dependent neural plasticity in Xenopus tadpoles. STAR protocols2(1), 100252. https://doi.org/10.1016/j.xpro.2020.100252

Cline, H. T., & Schwarz, T. L. (2020). Editorial overview: Cellular Nneuroscience. Current opinion in neurobiology63, iii–vi. https://doi.org/10.1016/j.conb.2020.07.003

Hiramoto, M., and Cline, H.T. (2020). NMDARs Translate Sequential Temporal Information into Spatial Maps. IScience 23, 101130.

Bestman, J.E., and Cline, H.T. (2020). Morpholino Studies in Xenopus Brain Development. Methods Mol. Biol. 2047, 377–395. PMID: 31552666

McKeown, C.R., and Cline, H.T. (2019). Nutrient restriction causes reversible G2 arrest in Xenopus neural progenitors. Development 146. PMID: 31649012.

Schiapparelli, L.M., Shah, S.H., Ma, Y., McClatchy, D.B., Sharma, P., Li, J., Yates, J.R., Goldberg, J.L., Cline, H.T. (2019). The Retinal Ganglion Cell Transportome Identifies Proteins Transported to Axons and Presynaptic Compartments in the Visual System In Vivo. Cell Rep 28, 1935-1947.e5. PMID: 31412257

Sharma, P., Mesci, P., Carromeu, C., McClatchy, D.R., Schiapparelli, L., Yates, J.R., Muotri, A.R., and Cline, H.T. (2019). Exosomes regulate neurogenesis and circuit assembly. Proc. Natl. Acad. Sci. U.S.A. 116, 16086–16094. PMID: 31320591

He, H.-Y., and Cline, H.T. (2019). What Is Excitation/Inhibition and How Is It Regulated? A Case of the Elephant and the Wisemen. J Exp Neurosci. PMID: 31258334

Gambrill, A.C., Faulkner, R.L., McKeown, C.R., and Cline, H.T. (2018). Enhanced visual experience rehabilitates the injured brain in Xenopus tadpoles in an NMDAR-dependent manner. J Neurophysiol. 

He, H., Shen, W., Zheng, L., Guo, X., and Cline, H.T. (2018). Excitatory synaptic dysfunction cell-autonomously decreases inhibitory inputs and disrupts structural and functional plasticity. Nature Communications 9, 2893.

Liu, H. H., McClatchy, D. B., Schiapparelli, L., Shen, W., Yates III, J. R., & Cline, H. T. (2018). Role of the visual experience-dependent nascent proteome in neuronal plasticity. eLife, 7, e33420.

Gambrill, A. C., Faulkner, R. L., & Cline, H. T. (2018). Direct intertectal inputs are an integral component of the bilateral sensorimotor circuit for behavior in Xenopus tadpoles. Journal of neurophysiology, 119(5), 1947-1961

Lau M, Li J, Cline HT. (2017) In Vivo Analysis of the Neurovascular Niche in the Developing Xenopus Brain. Eneuro Jul-Aug;ecollection. 

McKeown, C. R., Thompson, C. K., & Cline, H. T. (2017). Reversible developmental stasis in response to nutrient availability in the Xenopus laevis central nervous system. Journal of Experimental Biology, 220(3), 358-368.

Pratt, K. G., Hiramoto, M., & Cline, H. T. (2016). An evolutionarily conserved mechanism for activity-dependent visual circuit development. Frontiers in Neural Circuits, 10.

Thompson CK, Cline HT. (2016) Thyroid Hormone Acts Locally to Increase Neurogenesis, Neuronal Differentiation, and Dendritic Arbor Elaboration in the Tadpole Visual System. J Neurosci. Oct 5;36(40):10356-10375. PMID: 27707971.

Gambrill AC, Faulkner R, Cline HT. (2016) Experience-dependent plasticity of excitatory and inhibitory intertectal inputs in Xenopus tadpoles. J Neurophysiol. Aug 31:jn.00611.2016. doi: 10.1152/jn.00611.2016. [Epub ahead of print] PMID:27582296.

Truszkowski TL, James EJ, Hasan M, Wishard TJ, Liu Z, Pratt KG, Cline HT, Aizenman CD. (2016) Fragile X mental retardation protein knockdown in the developing Xenopus tadpole optic tectum results in enhanced feedforward inhibition and behavioral deficits. Neural Dev. Aug 8;11(1):14. doi: 10.1186/s13064-016-0069-7. PMID: 27503008.

Liu HH, Cline HT. (2016) Fragile X Mental Retardation Protein Is Required to Maintain Visual Conditioning-Induced Behavioral Plasticity by Limiting Local Protein Synthesis J Neurosci. Jul 6;36(27):7325-7339

He HY, Shen W, Hiramoto M, Cline HT. (2016) Experience-Dependent Bimodal Plasticity of Inhibitory Neurons in Early Development. Neuron. 2016 Jun 15;90(6):1203-14. doi: 10.1016/j.neuron.2016.04.044. Epub May 26.

Muñoz R, Edwards-Faret G, Moreno M, Zuñiga N, Cline H, Larraín J. (2015) Regeneration of Xenopus laevis spinal cord requires Sox2/3 expressing cells. Dev Biol. 408(2), 229-243.

Bestman JE, Huang LC, Lee-Osbourne J, Cheung P, Cline HT. (2015) An in vivo screen to identify candidate neurogenic genes in the developing Xenopus visual system. Dev Biol Mar 27 doi: 10.1016/j.ydbio.2015.03.010.

Faulkner RL, Wishard TJ, Thompson CK, Liu H-H, Cline HT (2014) Fmrp regulates neurogenesis in vivo in Xenopus laevis tadpoles. eNeuro 2(1) DOI: 10.1523/ENEURO.0055-14.2014.

Hiramoto M, Cline HT. Optic flow instructs retinotopic map formation through a spatial to temporal to spatial transformation of visual information. Proc Natl Acad Sci U S A. 2014 Nov 10. [Epub ahead of print].

Schiapparelli, LM, McClatchy DB, Liu HH, Sharma P, Yates JR 3rd, Cline HT. Direct detection of biotinylated proteins by mass spectrometry. J Proteome Res. 5;13(9);3966-78.

Shen W, Liu HH, Schiapparelli L, McClatchy D, He HY, Yates JR 3rd, Cline HT. (2014) Acute Synthesis of CPEB Is Required for Plasticity of Visual Avoidance Behavior in Xenopus. Cell Rep., Feb 27;6(4):737-47.

Bestman JE, Cline HT. (2014) Morpholino studies in Xenopus brain development. Methods Mol Biol. 2014;1082:155-71. doi: 10.1007/978-1-62703-655-9_11.

Sharma P, Schiapparelli L, Cline HT. (2013) Exosomes function in cell-cell communication during brain circuit development. Curr Opin Neurobiol Dec;23(6):997-1004.

McKeown CR, Sharma P, Sharipov HE, Shen W, Cline HT. (2013), Neurogenesis is required for behavioral recovery after injury in the visual system of Xenopus laevis. J Comp Neurol, Jul 1;521(10):2226-78

Lee PC, He HY, Lin CY, Ching YT, Cline HT. (2013) Computer aided alignment and quantitative 4D structural plasticity analysis of neurons. Neuroinformatics, Apr;11(2):249-57

Cline, H. T. and Kelly, D. (2012), Xenopus as an experimental system for developmental neuroscience: Introduction to a special issue. Dev Neurobiol, 72: 463–4. doi: 10.1002/dneu.22012

Demas JA, Payne H, Cline HT. (2012) Vision drives correlated activity without patterned spontaneous activity in developing Xenopus retina. Dev Neurobiol, Apr;72(4):537-46

Bestman, J. E., Lee-Osbourne, J. and Cline, H. T. (2012), In vivo time-lapse imaging of cell proliferation and differentiation in the optic tectum of Xenopus laevis tadpoles. J. Comp. Neurol, Feb 1;520(2):401–433

Miraucourt LS, Silva JS, Burgos K, Li J, Abe H, Ruthazer ES, Cline HT (2012) GABA expression and regulation by sensory experience in the developing visual system. PLoS One 7(1):e29086

Shen, W., McKeown, C.R., Demas, J.A., and Cline, H.T. (2011). Inhibition to excitation ratio regulates Visual system responses and behavior in vivo. J Neurophysiol Nov;106(5):2285-302

Hiramoto, M., and Cline, H.T. (2011). Mapping dynamic branch displacements: A versatile method to quantify spatiotemporal neurite dynamics. Front Neural Circuits 5:13. Epub Sep 30.

He, H.Y. and Cline, HT (2011) Diadem X: Automated 4 Dimensional Analysis of Morphological Data. Neuroinformatics Sep 9(2-3);107-12

Chiu, SL and Cline, HT (2010) Insulin receptor signaling in the development of neuronal structure and function. Neural Dev 5:7 

Ruthazer, E.S., Schohl, A., Schwartz, N., Tavakoli, A. Tremblay, M and Cline, H.T. (2010) Axons and Dendrites: In Vivo Time-Lapse Imaging of Neuronal Development in Xenopus. in Imaging:  A Laboratory Manual (eds. R. Yuste, F. Lani and A. Konnerth), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

Li, J., Erisir, A. and Cline, H.T. (2010) Rapid synaptic rearrangements during CNS circuit development revealed by combined in vivo time-lapse imaging and serial section electron microscopy. Neuron Jan 27;69(2);273-86

Wurdak, H, Zhu, S., Min, K H, Aimone, L, Lairson, LL, Watson, J, Chopluk, G, Demas, J., Charette, B., Weerapana, E., Cravatt, B.F., Cline, H.T., Peters, E.C., Zhang, J., Walker, J.R., Wu. C., Chang, J., Tuntland, T., Cho, C.Y., Schultz, P.G. (2010) A small molecule accelerates neuronal differentiation in the adult rat. PNAS 107(38):16542-16547.

Sharma, P and Cline, HT (2010) Visual Activity Regulates Neural Progenitor Cells in Developing Xenopus CNS through Musashi1. Neuron 68:442-455

Li, J. and Cline H.T. (2010) Visual deprivation increases accumulation of dense core vesicles in developing optic tectal synapses in Xenopus laevis. J. Comp. Neurol 518: 2365-2381. 

Li, J., Wang, Y., Chiu, SL., and Cline, H.T. (2010) Membrane targeted horseradish peroxidase as a marker for correlative fluorescence and electron microscopy studies. Front. Neural Circuits Feb 26;4:6

Bestman, J.E., and Cline, H.T. (2009) The relationship between dendritic branch dynamics and CPEB-labeled RNP granules captured in vivo. Front Neural Circuits 3:10

Ewald, R.C., and Cline, H.T. (2009) Cloning and Phylogenetic Analysis of NMDA Receptor Subunits NR1, NR2A and NR2B in Xenopus laevis Tadpoles. Frontiers in Molecular Neuroscience 2:4

Chen, C-M., Chiu, S-L., and Cline, H.T. (2009) Co-expression of Argonaute2 enhances short hairpin RNA-induced RNA interference in Xenopus CNS neurons in vivo. Frontiers in Neurosci. 9;3:63

Shen, W., Santos Da Silva, J., He, H.H. and Cline, H.T. (2009) Type A GABAAR-receptor-dependent synaptic transmission sculpts dendritic arbor structure in Xenopus laevis in vivo. J Neuroscience 29: 5032-5043.

Bestman, J.E., and Cline, H.T. (2009) The relationship between dendritic branch dynamics and CPEB labeled RNP granules captured in vivo. Front Neural Circuits 3:10

Hiramoto, M. and Cline, H.T. (2009) Convergence of multisensory inputs into Xenopus tadpole tectum. Developmental Neurobiology 69: 969-971.

Thirumalai V., Cline H.T. (2008) A commanding control of behavior. Nat Neurosci. 11:246-248.

Ewald, R. E. and Cline, H.T. (2008) NMDA Receptors and Brain Development in Biology of the NMDA receptor (ed A. M. Van Dongen) CRC Press.

Haas, K. and Cline, H.T. (2008) The regulation of dendritic arbor development and plasticity by glutamatergic synaptic input:  a review of the synaptotrophic hypothesis. J. Physiol. 586: 1509-17.

Bestman, J.E., and Cline, H.T. (2008) The RNA binding protein CPEB controls dendrite growth and neural circuit assembly in vivo. PNAS: 105: 20494-20499.

Thirumalai, V., and Cline, H.T. (2008). Endogenous dopamine suppresses initiation of swimming in pre-feeding zebrafish larvae. J Neurophysiol. 100:1635-1648.

Chiu, S.L., Chen, C.M., and Cline, H.T. (2008). Insulin receptor signaling regulates synapse number, dendritic plasticity, and circuit function in vivo. Neuron 58, 708-719.

Van Keuren-Jensen, K.R., and Cline, H.T. (2008). Homer proteins shape Xenopus optic tectal cell dendritic arbor development in vivo. Dev Neurobiol. 68:1315-1324.

Bestman, J.E., and Cline, H.T. (2008) The RNA binding protein CPEB controls dendrite growth and neural circuit assembly in vivo. PNAS: 105: 20494-20499.

Akerman, CJ, and Cline, H.T. (2007) Refining the roles of GABAergic transmission during neural circuit formation. TINS 30: 382-389.


The Backwards Brain? Study Shows How Brain Maps Develop to Help Us Perceive the World

The Dynamic Connectome

Kellogg School of Science & Technology @ TSRI

Postdoctoral Training Information

Innovative Approaches to Study Brain Development

UCSD Neuroscience Program

The Dorris Neuroscience Center

The Scripps Research Institute

Activity-dependent Regulation of Neurogenesis

How Brain Circuits Are Built