Josh Bonkowsky

Associate Professor of Pediatrics and
Adjunct Associate Professor of Neurobiology & Anatomy and of Neurology


B.A. Harvard University

M.D./Ph.D. University of California, San Diego



Josh Bonkowsky's Lab Page

Josh Bonkowsky's PubMed Literature Search

Molecular Biology Program

Function of human disease genes in CNS development


Axon pathfinding and development of CNS connectivity; function of human disease genes in CNS development 

Our research is centered on studying the development of CNS connectivity and neurodevelopmental disorders. Neurodevelopmental disorders are very common, but poorly understood in terms of their pathophysiology and effects on CNS development. 

1. Developmental functions of human disease genes. 

  • We are studying the role of several human disease genes on CNS development. In particular, we are studying genes involved in human leukodystrophies, and developing a zebrafish model for developing novel therapies.    Inherited leukodystrophies are diseases of the myelin, including abnormal myelin development, hypomyelination, or degeneration of myelin.  The incidence of leukodystrophies is almost 1 in 7500 live births.  Typical disease presentation occurs in the first three years of life with a 34% risk of death by age 8 years (Bonkowsky et al., 2010). 
  • Vanishing white matter disease (VWMD) is a frequent cause of leukodystrophies with no known cure.  VWMD is an autosomal recessive leukodystrophy caused by mutations in the eukaryotic initiation factor 2B (eif2B) gene family.  
  • We are developing a zebrafish model for VWMD to use for drug screening and to characterize the fundamental disease mechanisms of VWMD.

2. Effects of hypoxia on CNS Development. 

  • Hypoxic injury to the developing human brain causes life-long intellectual and behavioral deficits. These serious outcomes include autism spectrum disorders, cerebral palsy, depression, epilepsy, and intellectual disabilities. Currently there are no treatments to protect against the effects of prematurity and chronic hypoxic injury to the central nervous system (CNS). The ultimate goal of our research is to understand the fundamental molecular and neurobiological mechanisms by which hypoxia disrupts connectivity.
  • Recently, our lab developed a novel zebrafish system to examine the effects of hypoxia.  Zebrafish’s unique advantage is that it combines vertebrate CNS structures and genes with rapidity and efficiency for testing basic mechanisms. 
  • We use a combination of novel transgenic lines and innovative chemical and imaging approaches. Elucidation of these mechanisms offers the potential for designing effective and targeted therapeutic approaches.

3. Novel techniques for analysis of CNS connectivity. 

  • Understanding how the CNS is wired is extremely complex. We have developed novel technologies to analyze how genetically distinct neurons recognize and target specific connections, and what the functional relevance of these connections are. The first technique describes the use of Gal80 in vertebrates (Fujimoto et al., 2011). The second technique uses an innovative method to permit trans-synaptic labeling in live animals (TCAT).  

Specific visualization and manipulation of neural circuitry has remained a vexing problem in neurobiology.  Classical methods rely upon analysis in fixed tissue, preventing characterization of function or behavior.  Newer methods allow genetic targeting to specific neuron types and even identify single neurons, but synaptic partners and functional circuits are not accessible by these current methods.  A more general related issue is how to induce expression of a transgene in a vertebrate system when two cells make contact.  A solution to these issues could have wide applicability, both for experimental studies, as well as for potentially a variety of therapeutic options.
This project, Trans-Cellular Activation of Transcription to Analyze Dopaminergic Axon Reorganization, funded by the NIH Director's Innovator Award, uses a novel strategy to analyze vertebrate circuit construction and function. It is the first genetic method for visualizing and driving expression in two cells that make contact, and offers the potential to identify and manipulate neuronal circuits in a vertebrate organism.


Selected Publications:

  1. Gao J, Stevenson TJ, Douglass AD, Barrios JP, Bonkowsky JL. The Midline Axon Crossing Decision Is Regulated through an Activity-Dependent Mechanism by the NMDA Receptor. ENeuro. 2018. 17;5(2).
  2. Lambert CJ, Freshner BC, Chung A, Stevenson TJ, Bowles DM, Samuel R, Gale BK, Bonkowsky JL. An automated system for rapid cellular extraction from live zebrafish embryos and larvae: Development and application to genotyping. PLoS One. 2018. 15;13(3):e0193180.
  3. Strachan LR, Stevenson TJ, Freshner B, Keefe MD, Miranda Bowles D, Bonkowsky JL. A zebrafish model of X-linked adrenoleukodystrophy recapitulates key disease features and demonstrates a developmental requirement fro abcdl in oligodenrocyte patterning and myelination. Hum Mol Genet. 2017. 15;26(18):3600-3614.
  4. Keefe MD, Bonkowsky JL. Transvection Arising from Transgene Interactions in Zebrafish. Zebrafish. 2017. 14(1):8-9.
  5. Chen YC, Semenova S, Rozov S, Sundvik M, Bonkowsky JL, Panula P. A Novel Developmental Role for Dopminergic Signaling to Secify Hypothalamic Neurotransmitter Identity. J Biol Chem. 2016. 14;291(42):21880-21892.
  6. Milash B, Gao J, Stevenson TJ, Son JH, Dahl T, Bonkowsky JL. Temporal Dysynchrony in brain connectivity gene expression following hypoxia. BMC Genomics. 2016. 17(1):334.
  7. Son JH, Keefe MD, Stevenson TJ, Barrios JP, Anjewierden S, Newton JB, Douglass AD, Bonkowsky JL. Transgenic FingRs for Live Mapping of Synaptic Dynamics in Genetically-Defined Neurons. Scientific Reports (Nature). 2016. 6:18734.
  8. Xing L, Son JH, Stevenson TJ, Lillesaar C, Bally-Cuif L, Dahl T, Bonkowsky JL. A Serotonin Circuit Acts as an Environmental Sensor to Mediate Midline Axon Crossing through EphrinB2. Journal of Neuroscience. 2015. 35(44):14794-808.
  9. Samuel R, Stephenson R, Roy P, Pryor R, Zhou L, Bonkowsky JL*, Gale BK*. Microfluidic-aided genotyping of zebrafish in the first 48 h with 100% viability. Biomedical Microdevices. 2015. 17(2):43.
  10. Anderson HM, Wilkes J, Korgenski EK, Pulsipher MA, Blaschke AJ, Hersh AL, Srivastava R, Bonkowsky JL. Preventable Infections in Children with Leukodystrophy. Annals of Clinical and Translational Neurology. 2014. 1(5):370-374.
  11. Purnell SM, Bleyl SB, Bonkowsky JL. Clinical exome sequencing identifies a novel TUBB4A mutation in a child with static hypomyelinating leukodystrophy. Pediatric Neurology. 2014. 50(6):608-11.
  12. Xing, L., Quist, T., Stevenson, T., Dahlem, T., Bonkowsky JL. Rapid and Efficient Zebrafish Genotyping Using PCR with High-resolution Melt Analysis. Journal of Visualized Experiments. 2014 Feb 5;(84):e51138.
  13. Schweitzer J, Löhr H, Bonkowsky JL, Hübscher K, Driever W. Sim1a and Arnt2 contribute to hypothalamo-spinal axon guidance by regulating Robo2 activity via a Robo3-dependent mechanism. Development. 2013. 140(1):93-106.
  14. Xing L, Hoshijima K, Grunwald DJ, Fujimoto E, Quist TS, Sneddon J, Chien CB, Stevenson TJ, Bonkowsky JL. Zebrafish foxP2 zinc finger nuclease mutant has normal axon pathfinding. PLoS One. 2012. 7(8):e43968.
  15. Lambert AM, Bonkowsky JL, Masino MA. The dopaminergic diencephalospinal tract mediates a developmental switch in the locomotor pattern of larval zebrafish. Journal of Neuroscience. 2012. 32:13488-13500
  16. Stevenson TJ, Trinh T, Kogelschatz C, Fujimoto E, Lush ME, Piotrowski T, Brimley CJ, Bonkowsky JL. Hypoxia disruption of vertebrate CNS pathfinding through EphrinB2 is rescued by magnesium. PLoS Genetics. 2012. 8(4):e1002638.
  17. Lakhina V, Maraccio C, Shao X, Lush M, Jain R, Fujimoto E, Bonkowsky JL, Granato M, Raper J. Netrin/DCC signaling guides olfactory sensory axons to their correct location in the olfactory bulb. Journal of Neuroscience. 2012. 32(13):4440-56.
  18. Gutnick A, Blechman J, Kaslin J, Affolter M, Bonkowky JL, Levkowitz G. The hypothalamic neuropeptide oxytocin is required for formation of the neuro-vascular interface of the pituitary. Developmental Cell. 2011. 18:642-54.
  19. Fujimoto E, Gaynes B, Brimley CJ, Chien CB, Bonkowsky JL. Gal80 Intersectional Regulation of Cell-Type Specific Expression in Vertebrates. Developmental Dynamics. 2011. 240(10):2324-34.
  20. Fujimoto E, Stevenson TJ, Chien CB, Bonkowsky JL. Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. Developmental Biology. 2011. 352(2):393-404.
  21. Kastenhuber E, Kern U, Bonkowsky JL, Chien CB, Driever W, Schweitzer J. Netrin-DCC, Robo-Slit and HSPGs coordinate lateral positioning of longitudinal dopaminergic diencephalospinal axons. Journal of Neuroscience. 2009. 29:8914-26.
  22. Bonkowsky JL, Wang X, Fujimoto E, Lee EJ, Chien CB, Dorsky RI. Domain-specific regulation of foxP2 CNS expression by lef1. BMC Developmental Biology. 2008. 8:103.
  23. Bonkowsky JL, Chien CB. Isolation and cloning of zebrafish foxP2. Developmental Dynamics. 2005. 234:740-6.
  24. Bonkowsky JL, Bohnsack, JF, Pennington MJ, Viskochil D, Thompson JA. Leukoencephalopathy, arthritis, colitis, and hypogammaglobulinemia (LACH) in two brothers: a novel syndrome? American Journal of Medical Genetics. 2004. 128:52-56.
  25. Bonkowsky JL, Johnson J, Carey J, Smith AD, Swoboda K. An infant with primary tooth loss and palmar hyperkeratosis: a novel mutation in the NTRK1 gene causing congenital insensitivity to pain with anhidrosis. Pediatrics. 2003. 112:e237-241. 
  26. Bonkowsky JL*, Yoshikawa S*, O’Keefe DD, Scully AL, Thomas JB. Axon routing across the midline controlled by the Drosophila Derailed receptor. Nature. 1999. 402: 540-4.
  27. Yoshikawa S*, Bonkowsky JL*, Kokel M, Shyn S, Thomas, JB. The Derailed guidance receptor does not require kinase activity in vivo. Journal of Neuroscience. 2001. 21: RC119.

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Last Updated: 3/13/19