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Interneuron Development in the Zebrafish Spinal Cord

Department of Biology

Applications accepted all year round Competition Funded PhD Project (Students Worldwide)

About the Project

The Lewis Lab moved to Syracuse University from Cambridge University in the UK in 2010. We use Genetics, Cell Biology and Developmental Biology to investigate how the correct number and pattern of interneurons forms in the vertebrate spinal cord, and how these interneurons acquire their specific characteristics and functions.

The vertebrate nervous system contains many different specialized neurons that form at characteristic positions and develop specific axonal connections and functions. Most of these neurons are interneurons, but we currently know very little about how different types of interneurons are specified.

We primarily use zebrafish embryos as a model system, as the embryos develop outside the mother and are transparent and their relatively simple nervous system facilitates studies of neuronal circuitry and function. We use transgenic lines of zebrafish in which neurons express Green Fluorescent protein to study these cells in live and fixed embryos. As most of the genes involved in spinal cord development are conserved between vertebrates, the insights that we gain about the functions of specific genes should be widely applicable.

A PhD project is available to investigate the roles of specific regulatory genes in determining different neuronal characteristics in the zebrafish spinal cord.

Experiments included in this project may include:

1. Investigating the functions of particular regulatory genes in interneuron specification by ectopically expressing mRNAs and/or knocking out gene function using mutants and examining the effects on molecular markers and interneuron characteristics such as morphology and neurotransmitter expression.

2. Observing the development and morphology of specific interneurons using confocal microscopy.

3. Determining which regulatory genes are expressed by particular interneurons using in situ hybridisation and antibody stainings and/or fluorescent activated cell sorting (FACS) and microarray analysis.

4. Constructing lines of zebrafish in which Green Fluorescent Protein (GFP) is expressed in cells that normally express a particular gene

5. Using calcium indicators such as the genetically encoded calcium indicator GCAMP to monitor the electrical activity of specific neurons in wild-type and experimental embryos during particular behaviours.

See for more information about our research.

Application Deadline: December 1st 2018 for a start date of end of August 2019. If it is after Dec 1st - please apply ASAP or contact us. In 2019 we will start to accept applications for August 2020.

Application information can be found at

Syracuse has its own airport (15 minute drive from downtown) and is close to Toronto, New York City, Philadelphia, Montreal as well as the natural beauty of Upstate New York (Niagara Falls, The Finger Lakes, Adirondack lakes and mountains).

Syracuse University shares a campus with SUNY Upstate Medical University that has active research programs in Cell and Developmental Biology and Neuroscience

Funding Notes

Funding is guaranteed for 5 years. Deadline is December 1st but late applications may be considered.
Funding is a mixture of teaching and research assistantships. Students rotate in 3 labs in first year and then choose one for PhD. Other Developmental Biology and Neuroscience labs at Syracuse University include:

Sarah Hall View Website
Melissa E. Pepling View Website
Eleanor Maine View Website.
Sandra Hewitt View Website
James Hewitt View Website
Jessica McDonald View Website

For a full list of faculty see View Website

For more details on graduate program see View Website


Some recent papers.

L. Andrzejczuk, S. Banerjee, S. England, C. Voufo, K. Kamara and K. E. Lewis (2018). Tal1, Gata2a and Gata3 have distinct functions in the development of V2b and cerebrospinal fluid-contacting KA neurons. Frontiers in Neuroscience. 12:170 doi: 10.3389/fnins.2018.00170

R. Wilk, N. Ali, S. J. England, K. E. Lewis (2018) Using Zebrafish to Bring Hands-On Laboratory Experiences to Urban Classrooms. Zebrafish 15: 2

S. J. England, P. C. Campbell, S. Banerjee, A. Swanson, and K. E. Lewis (2017) Identification and expression analysis of the complete family of zebrafish pkd genes. Frontiers in Cell and Developmental Biology 5:5.

J. L. Juárez-Morales, R. I. Martinez-De Luna, M. E. Zuber, A. Roberts and K. E. Lewis (2017) Zebrafish transgenic constructs label specific neurons in Xenopus laevis spinal cord and identify frog V0v spinal neurons. Developmental Neurobiology: 77 (8), 1007-1020. DOI: 10.1002/dneu.22490.

William C Hilinski; Johnathan R Bostrom; Samantha J England; José L Juárez-Morales; Sarah de Jager; Olivier Armant; Jessica Legradi; Uwe Strähle; Brian A Link; Katharine E Lewis (2016) Lmx1b is required for the glutamatergic fates of a subset of spinal cord neurons. Neural Development 11:16 DOI: 10.1186/s13064-016-0070-1

J. L. Juarez-Morales, C. Schulte, S. A. Pezoa, G. K. Vallejo, W. Hilinski, S. England, S. de Jager and K. E. Lewis (2016) Evx1 and Evx2 specify excitatory neurotransmitter fates and suppress inhibitory fates through a Pax2 independent mechanism. Neural Development. 11: 5 DOI:  10.1186/s13064-016-0059-9

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