Preprints Out!

Cassidy RM, Bavencoffe AG, Lopez ER, Cheruvu SS, Walters ET, Uribe RA, Krachler AM and Odem MA. (2020). An open-source frequency-independent biological signal identification program (FIBSI) to simplify the analysis of non-stationary time series data. https://doi.org/10.1101/2020.05.29.123042

Howard IV AGA, Baker PA, Ibarra-García-Padilla R, Moore JA, Rivas LJ, Tallman JJ, Singleton EW, Westheimer JL, Corteguera JA  and Uribe RA. (2020) An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution. https://www.biorxiv.org/content/10.1101/2020.06.14.150938v2

Peer-Reviewed Papers

Baker, P.A., Meyer, M.D., Tsang, A. and Uribe, R.A. (2019). Immunohistochemical and ultrastructural analysis of the maturing larval zebrafish enteric nervous system reveals the formation of a neuropil pattern. Scientific Reports, Volume 9, Article number: 6941 www.nature.com/articles/s41598-019-43497-9
  • In this paper, we describe that the zebrafish intestinal wall contains a meshwork of neural tissue, called the myenteric plexus, which matures between 7 and 18 days post fertilization. 

Hutchins, E.J., Kunttas, E., Piacentino, M.L., Howard IV, A.G.A., Bronner, M.E. and Uribe, R.A. (2018). Migration and diversification of the vagal neural crest. Developmental Biology,  Invited Review article in the Special Edition celebrating the 150th Anniversary of the discovery of Neural Crest  doi.org/10.1016/j.ydbio.2018.07.004  PMID: 29981692 
  • In this paper, we summarize current knowledge of vagal neural crest development across vertebrates.

Rajan SG, Gallik KL, Monaghan JR, Uribe RA, Bronner ME, Saxena A. (2018). Tracking neural crest cell cycle progression in vivo. Genesis. e23214. In the Special Anniversary Edition celebrating 150 years of Neural Crest Research doi.org/ 10.1002/dvg.23214 PMID: 29956448
  • In this paper, we collaborated with the Saxena lab to create a novel cell cycle occupancy reporter, in neural crest cells.
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​Uribe, R.A.*, Hong, S.S. and Bronner, M.E. (2018). Retinoic Acid temporally orchestrates colonization of the gut by vagal neural crest cells. Developmental Biology, Jan 1;433(1):17-32. PMID: 29108781 10.1016/j.ydbio.2017.10.021*corresponding author
  • In this study, it was discovered that a very fine window of time is critical for Retinoic Acid to affect vagal neural crest invasion into gut tissue. We also discovered that the transcription factor Meis3 is functionally important downstream of Retinoic Acid, expanding our knowledge of this critical Gene-Environment interaction during development.
Uribe, R.A., Gu, T. and Bronner, M.E.  (2016). A novel subset of enteric neurons revealed by ptf1a:GFP during zebrafish enteric nervous system development. Genesis, Mar; 54(3):123-8. doi: 10.1002/dvg.22927. PMID: 26865080
  • In this study, Dr. Uribe and undergraduate researcher Tiffany Gu characterized the localization of ptf1a:GFP+ cells in the developing enteric plexus in zebrafish fishes.

Uribe R.A.*, Buzzi A.L.*, Bronner M.E. and Strobl-Mazzulla, P.H.  (2015).  Histone demethylase KDM4B regulates otic vesicle invagination via epigenetic control of Dlx3 expression.  The Journal of Cell Biology Nov 23; 211(4): 815-27. doi: 10.1083/jcb.201503071. *equal authorship. (Featured in “News: in this Issue”) PMID: 26598618
  • In this collaborative work, Dr. Uribe worked with graduate student Ailin Buzzi and Dr. Pablo Strobl-Mazzulla while in the Bronner lab to discover that the epigenetic factor KDM4B functions to regulate otic vesicle invagination and epithelial polarization in chick.

Uribe, R.A. and Bronner, M.E. (2015).  Meis3 is required for neural crest invasion of the gut during zebrafish enteric nervous system development. Molecular Biology of the Cell Nov 1; 26(21): 3728-40 doi:10.1091/mbc.E15-02-0112.  PMID: 26354419
  • In this investigative work, Dr. Uribe discovered that the transcription factor Meis3 functions to promote vagal neural crest migration into the primitive gut tube in zebrafish embryos.
   
Lee J., Cox B.D., Daly C., Lee C., Nuckels R.J., Tittle R.K., Uribe R.A. and Gross J.M. (2012). An ENU mutagenesis screen in zebrafish for visual system mutants identifies a novel splice-acceptor site mutation in patched2 that results in colobomas. Investigative Ophthalmology and Visual Science 53(13): 8214-21. PMID: 23150614
  • In this team project while a graduate student in the Gross lab, Dr. Uribe helped to screen through a family of zebrafish mutants for defects in eye formation during development. Of 18 recessive mutants discovered, this paper focuses description of the mutant phenotype called coloboma caused by a mutation in the patched2 gene.

Uribe, R. A., Kwon, T., Marcotte, E.M and Gross, J.M. (2012). Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis. Developmental Biology 371, 280-292. PMID: 22981606
  • This study found that the protein Id2a functions upstream of the Notch pathway to regulate cell cycle exit of retinal progenitors and their ability to undergo neuronal differentiation. This study was one of the first in the zebrafish eye community to leverage RNA-sequencing and bioinformatic analysis of isolated retinal tissue.

Luo, J., Uribe, R.A., Hayton, S., Calinescu, A.A., Gross, J.M. and Hitchcock, P.F.  (2012). Midkine-A functions upstream of Id2a to regulate cell cycle kinetics in the developing vertebrate retina.  Neural Development 7(1): 33. PMID: 23111152​
  • This collaborative work with the Hitchcock lab found that the secreted factor Midkine-A influences the expression of Id2a in order to impact the cell cycle state of retinal progenitor cells.
     
Uribe, R.A. and Gross, J.M.  (2010).  Id2a influences neuron and glia formation in the zebrafish retina by modulating retinoblast cell cycle kinetics. Development 137: 3763-3774. PMID: 20943708
  • In this comprehensive work while a graduate student in the Gross lab, Dr. Uribe discovered that Id2a levels influence the cell cycle state of retinal progenitor cells and their ability to undergo neurogenesis during retinal development in zebrafish. This was the first study to implicate Id genes in retinal growth control to affect neural development.

Ng, A., Uribe, R.A., Yieh, L., Nuckels, R. and Gross, J.M.  (2009).  Zebrafish mutations in gart and paics identify crucial roles for de novo purine synthesis in vertebrate pigmentation and ocular development.  Development 136(15): 2601-11. PMID: 19570845
  • In this Gross lab paper, mutations in the genes gart and paics were discovered to affect pigmentation and eye growth during zebrafish development.
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Uribe, R.A. and Gross, J.M. (2007).  Immunohistochemistry on Cryosections from Embryonic and Adult Zebrafish Eyes.  Cold Spring Harbor Protocols 2007: pdb.prot4779.  (Cover photo) PMID: 21357120​
  • In this protocol paper, a method to prepare, section and perform immunohistochemistry on tissues from eyes is described in zebrafish.

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