Xenbase

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Xenbase is a model organism database, providing informatics resources, genomic and biological data on the frogs, Xenopus laevis and Xenopus tropicalis.[1]

Xenopus as a model organism

Main article: Xenopus

The Xenopus model organism is responsible for large amounts of new knowledge on embryonic development and cell biology. Xenopus has a number of unique experimental advantages as a vertebrate model. Paramount among these is the robustness of early embryos and their amenability to microinjection and microsurgery. This makes them a particularly attractive system for testing the ectopic activity of gene products and loss-of-function experiments using antagonizing reagents such as morpholinos, dominant-negatives and neomorphic proteins. Morpholinos are synthetic oligonucleotides that can be used to inhibit nuclear RNA splicing or mRNA translation and are the common gene inhibition reagent in Xenopus as neither siRNA or miRNA have yet been shown to reproducibly function in frog embryos.[2] Xenopus embryos develop very quickly and form a full set of differentiated tissues within days of fertilization, allowing rapid analysis of the effects of manipulating embryonic gene expression.[3]The large size of embryos and amenability to microinjection also makes them extremely well suited to microarray approaches. Furthermore, these same characteristics make Xenopus, one of the few vertebrate model organisms suited for chemical screens.[4] Xenbase provides a large database of images illustrating the full genome, movies detailing embryogenesis, and multiple online tools useful for designing and conducting experiments using Xenopus.

Xenbase Contents and Tools

Xenbase provides many tools useful for both both professional research as well as academic learning. Highlighted below are a few of the tools, along with a brief description. For full details on provides tools, users are referred to the following articles published in Nucleic Acids Research Database issue:

  • "Xenbase: gene expression and improved integration."[5]
  • "Xenbase: expansion and updates of the Xenopus model organism.[6]
  • Genome browser
  • Expression Search and Clone Search (search by gene symbol, gene name, or Affymetrix id)
  • Gene nomenclature guidelines
  • Literature search: Textpresso- uses an algorithm to match your search to specific criteria or section of a paper. For example, you could identify papers describing HOX genes and limit your results to only papers which used morpholinos.
  • Anatomy and Development:  images, fate maps, and videos
  • Community Link --- jobs, labs which study Xenopus
  • Protocol List- identify clones, antibodies, procedures
  • Stock Centre- The National Xenopus Resource (maintains frog stocks, offers advanced research training)

Xenopus Background Information

The Nobel Prize for Medicine or Physiology was awarded to John B. Gurdon and Shinya Yamanaka on October 8, 2012 [7] for nuclear reprogramming in Xenopus[8][9]

Importance: Gurdon's experiments challenged the dogma of the time which suggested that differentiated cells are committed to their fate (Example:a liver cell remains a liver cell and cannot return to an undifferentiated state).

Specifically, John Gurdon's experiments showed that a mature or differentiated cell can be returned to its immature undifferentiated form; this is the 1st instance of cloning of a vertebrate animal.

Experiment: Gurdon used a technique known as nuclear transplantation to replace the nucleus of a frog (Xenopus) egg with a nucleus from a mature cell (intestinal epithelial). The tadpoles resulting from these eggs did not survive long (past the gastrulation stage), however, further transformation of the nuclei from these Xenopus eggs to a second set of Xenopus eggs resulted in fully developed tadpoles. This process (transfer of nuclei from cloned cells) is referred to as serial transplantation.

Xenopus Research Utilizing Xenbase Tools

To provide examples of how Xenbase could be used to facilitate academic research, two research articles are briefly described below.

  • Genetic Screens for Mutations Affecting Development of X. tropicalis[10]

This paper uses Xenbase resources to create and characterize mutations in Xenopus tropicalis. Goda et al., performed a large scale forward genetics screen on X. tropicalis embryos to identify novel mutations (2006). Defects were noted and put into 10 different categories as follows: eye, ear, neural crest/pigment, dwarf, axial, gut, cardiovascular, head, cardiovascular plus motility, and circulation. Further studies were performed on the whitehart mutant "wha" which does not have normal circulating blood. The Xenopus Molecular Marker Resource page was used to design a microarray experiment which compared wild type (normal circulation) and "wha" mutant X. tropicalis. Analysis of microarray data revealed that 216 genes had significant changes in expression, with genes involved in hemoglobin and heme biosynthesis being the most affected, consistent with the observation that "wha" may have a role in hematopoiesis.

  • High efficiency TALENs enable F0 functional analysis by targeted gene disruption in Xenopus laevis embryos[11]

The 2013 paper by Suzuki et al. describes the use of a relatively new gene knockdown technique in X. laevis. Traditionally, antisense morpholino oligonucleotides have been the method of choice to study the effects of transient gene knockdown in Xenopus.

In comparison to morpholinos which disrupt gene expression by inhibiting translational machinery TALENs disrupt gene expression by binding to DNA and introducing double stranded breaks [12][13] Xenbase was utilized to obtain publicly available sequences for tyrosinase (tyr) and pax6, needed for TALEN design. Knockdown of both pax6 and tyr was highly efficient using TALENs,suggesting that gene disruption using TALENs may be an alternative or better method to use in comparison to antisense morpholino's.

References

  1. ↑ Peter Vize, Jeff B. Bowes, Kevin A. Snyder, Erik Segerdell, Ross Gibb, Chris Jarabek, Etienne Noumen1, Nicolas Pollet (2008). "Xenbase: a Xenopus biology and genomics resource". Nucleic Acids Res. 36 (Database issue): D761–D767. doi:10.1093/nar/gkm826. PMC 2238855. PMID 17984085. 
  2. ↑ Eisen, J.a.S., J. . (2008). Controlling morpholino experiments: don't stop making antisense. Development, 135(10): p. 1735-1743.
  3. ↑ Xenbase Gene Expression
  4. ↑ Wheeler, G. N. and A. W. Brändli (2009). "Simple vertebrate models for chemical genetics and drug discovery screens: Lessons from zebrafish and Xenopus." Developmental dynamics 238(6): 1287-1308.
  5. ↑ Bowes, J. B., K. A. Snyder, et al. (2010). "Xenbase: gene expression and improved integration." Nucleic Acids Research 38(suppl 1): D607-D612
  6. ↑ James-Zorn, C., V. G. Ponferrada, et al. (2013). "Xenbase: expansion and updates of the Xenopus model organism database." Nucleic Acids Research 41(D1): D865-D870.
  7. ↑ http://www.nobelprize.org/nobel_prizes/medicine/laureates/2012/press.html
  8. ↑ http://xenbase.org/community/static/GurdonWinsNobel.jsp
  9. ↑ Gurdon, J.B. (1962). The Developmental Capacity of Nuclei taken from Intestinal Epithelium Cells of Feeding Tadpoles. Journal of Embryology and Experimental Morphology, 10(4): p. 622-640.
  10. ↑ Goda, T., Abu-Daya, Anita, Carruthers, Samantha, Clark, Matthew D., Stemple, Derek L., Zimmerman, Lyle B. (2006). "Genetic Screens for Mutations Affecting Development of Xenopus tropicalis." PLoS Genet 2(6): e91.
  11. ↑ Suzuki, K.-i. T., Y. Isoyama, et al. (2013). "High efficiency TALENs enable F0 functional analysis by targeted gene disruption in Xenopus laevis embryos." Biology Open.
  12. ↑ Boch, J. (2011). "TALEs of genome targeting." Nat Biotech 29(2): 135-136.
  13. ↑ Huang, P., A. Xiao, et al. (2011). "Heritable gene targeting in zebrafish using customized TALENs." Nat Biotech 29(8): 699-700.

External links

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